Abstract:
We have determined the complete 1,694,969 nucleotide sequence of the GC-rich genome of  Methanopyrus kandleri  using a novel approach. It is based on unlinking genomic DNA with the ThermoFidelase version of  M. kandleri  topoisomerase V and cycle sequencing directed by 2′-modified oligonucleotides (Fimers). 3.3× sequencing redundancy was sufficient to assemble the genome with &lt;1 error per 40 kb. Using a combination of sequence database searches and coding potential prediction, 1692 protein-coding genes and 39 genes for structural RNAs were identified.  M. kandleri  proteins show an unusually high content of negatively charged amino acids, which might be an adaptation to its high intracellular salinity. Previous phylogenetic analysis of 16S RNA suggested that  M. kandleri  belonged to a very deep branch, close to the root of the archaeal tree. However, genome comparisons, using both trees constructed from concatenated alignments of ribosomal proteins and trees based on gene content, indicate that  M. kandleri  consistently groups with other archaeal methanogens.  M. kandleri  shares the set of genes implicated in methanogenesis and, in part, its operon organization with  Methanococcus jannaschii  and  Methanothermobacter thermoautotrophicus . These findings indicate that archaeal methanogens are monophyletic. A distinctive feature of  M. kandleri  is the paucity of proteins involved in signaling and regulation of gene expression: Also,  M. kandleri  appears to have fewer genes acquired via lateral transfer than other archaea. These features might reflect the extreme habitat of this organism.

Description:
CROSS-REFERENCE TO OTHER APPLICATIONS  
       [0001]     This patent claims priority to U.S. Provisional Patent application 60/361,742 filed Mar. 4, 2002 and 60/410,974 entitled “Helix-hairpin-helix motifs to manipulate properties of DNA processing enzymes,” filed Sep. 16, 2002, both of which are hereby incorporated by reference. 
     
    
     CONTRACTUAL ORIGIN OF INVENTION  
       [0002]     This work was supported in part by DOE and NIH grants (DE-FG02-98ER82577, 00ER83009, R44GM55485, R43HG02186) to S.A.K and A.I.S. 
     
    
     BACKGROUND OF THE INVENTION  
       [0003]     1. Field of the Invention  
         [0004]     This invention relates to novel methods of sequencing directly from genomic DNA. In particular, the genomic DNA of the bacterial species  Methanopyrus kandleri  AV19 was unlinked with ThermoFidelase version of  M. kandleri  topoisomerase V and its entire nucleotide sequence was determined by directed cycle sequencing using 2′-modified oligonucleotides (Fimers). The resulting genomic sequences, protein sequences from  M. kandleri  and there uses in research and diagnostics fields are herein disclosed.  
         [0005]     2. Description of the State of Art  
         [0006]      Methanopyrus kandleri  was isolated from the sea floor at the base of a 2,000 meter-deep “black smoker” chimney in the Gulf of California (Huber, R., et al.,  Nature,  342:833-6 (1989)). The organism is a rod-shaped, Gram-positive methanogen that grows chemolithoautotrophically at 80 to 110° C. in the H 2 —CO 2  atmosphere (Kurr, M., et al.,  Arch Microbiol,  156:239-47 (1991)). The discovery of  Methanopyrus  showed that biogenic methanogenesis was possible above 100° C. and could account for isotope discrimination at such temperatures (Huber, R., et al.,.  Nature,  342:833-6 (1989)).  
         [0007]     Certain aspects of  M. kandleri  biochemistry place this organism aside from other archaea. First, the membrane of  M. kandleri  consists of a terpenoid lipid (Hafenbradl, D., et al.,  System Appl Microbiol,  16:165-9 (1993)), which is considered to be the most primitive membrane lipid and is the direct precursor of phytanyl diethers found in the membranes of all other archaea (Wachtershauser, G., et al.,  Microbiol Rev,  52:452-84 (1988)). Second,  M. kandleri  contains a high intracellular concentration (1.1 M) of a trivalent anion, cyclic 2,3-diphosphoglycerate, which has been reported to confer activity and stability at high temperatures to  M. kandleri  enzymes (Shima, S., et al.,  Arch Microbiol,  170:469-72 (1998)). Finally,  M. kandleri  has several unique enzymes, the most notable ones being the novel type 1B DNA topoisomerase V and the two-subunit reverse gyrase (Slesarev, A. I., et al.,  Nature,  364:735-7 (1993); Belova, G. I., et al.,  Proc Natl Acad Sci, USA  98:6015-20 (2001); Slesarev, A. I., et al.,  Methods Enzymol,  334:17992 (2001); Kozyavkin, S. A., et al.,  J Biol Chem,  269:11081-9 (1994); and Krah, R., et al.,  Proc Natl Acad Sci USA,  93:106-10 (1996)).  
         [0008]     Perhaps the most distinctive feature of  M. kandleri  is its apparent position in the archaeal phylogeny. Several analyses, based on phylogenetic trees for 16S rRNA and the presence/absence of an 11-amino-acid insertion in EF-1α placed  M. kandleri  close to the root of the Euryarchaeota and did not suggest any specific affinity with other archaeal methanogens (Burggraf, S., et al.,  System Appl Microbiol,  14:346-51 (1991); Rivera, M. C., et al.,  Int J Syst Bacteriol,  46:348-51 (1996); and Nolling, J., et al.,  Int J Syst Bacteriol,  46:1170-3 (1996)). Furthermore, some signatures shared with Crenarchaeota were noticed in the 16S RNA sequence of  M. kandleri . (Burggraf, S., et al.,  System Appl Microbiol,  14:346-51 (1991)). In contrast, the methyl coenzyme M reductase operon of  M. kandleri  consists of genes that are unique to archaeal methanogens (Polushin, N., et al.,  Nucleosides Nucleotides Nucleic Acids,  20:973-6 (2001)). The genome comparison reported here reveals clustering of  M. kandleri  with the other methanogens in phylogenetic trees based on concatenated alignments of ribosomal proteins, which, together with the congruence of the sets of predicted genes, suggests that this group is monophyletic. However,  M. kandleri  appears to be a “minimalist” organism whose regulatory and signaling systems are generally scaled down compared to those of other archaea. The comparative genome analysis of  M. kandleri, M. jannaschii  and  M. thermoautotrophicus  resulted in the delineation of a distinct set of genes characteristic of archaeal methanogens.  
       SUMMARY OF THE INVENTION  
       [0009]     This invention provides the genomic sequences of  M. kandleri . The sequence information is useful for a variety of diagnostic and analytical methods. The genomic sequence may be embodied in a variety of media, including computer readable forms, or as a nucleic acid comprising a selected fragment of the sequence. Such fragments generally consist of an open reading frame, transcriptional or translational control elements, or fragments derived therefrom.  M. kandleri  proteins encoded by the open reading frames are useful for diagnostic purposes, as specific and non-specific stabilizing additives for other proteins, as well as for their enzymatic or structural activity.  
         [0010]     Additional objects, advantages, and novel features of this invention shall be set forth in part in the description and examples that follow, and in part will become apparent to those skilled in the art upon examination of the following or may be learned by the practice of the invention. The objects and the advantages of the invention may be realized and attained by means of the instrumentalities and in combinations particularly pointed out in the appended claims.  
         [0011]     Nucleotide or nucleic acid sequences defined herein are represented by one-letter symbols for the bases as follows: 
        A (adenine)     C (cytosine)     G (guanine)     T (thymine)     U (uracil)     M (A or C)     R (A or G)     W (A or T/U)     S (C or G)     Y (C or T/U)     K (G or T/U)     V (A or C or G; not T/JU)     H (A or C or T/U; not G)     D (A or G or T/U; not C)     B (C or G or T/U; not A)     N (A or C or G or T/U) or (unknown)        
 
         [0028]     Peptide and polypeptide sequences defined herein are represented by one-letter or three symbols for amino acid residues as follows:  
         [0029]     A/Ala (alanine); R/Arg (arginine); N/Asn (asparagine); D/Asp (aspartic acid); C/Cys (cysteine); Q/Gln (glutamine); E Glu (glutamic acid); G Gly (glycine); H/His (histidine); I/Ile (isoleucine); L/Leu (leucine); K/Lys (lysine); M/Met (methionine); F/Phe (phenylalanine); P/Pro (proline); S/Ser (serine); T/Thr (threonine); W/Trp (tryptophan); Y/Tyr (tyrosine); V/Val (valine); X/Xaa (frame shift); and U/Sec (selenocysteine).  
         [0030]     The present invention may be more fully understood by reference to the following detailed description of the invention, non-limiting examples of specific embodiments of the invention and the appended figures. 
     
    
     BRIEF DESCRIPTION OF THE DRAWINGS  
       [0031]     The accompanying drawings, which are incorporated in and form a part of the specifications, illustrate the preferred embodiments of the present invention, and together with the description serve to explain the principles of the invention.  
         [0032]     In the Drawings:  
         [0033]      FIG. 1  illustrates the expression and purification of RPA from  E. coli  cells.  
         [0034]      FIG. 2  illustrates DNA-binding activity of RPA analyzed by 8% native PAGE, stained with fluorescein. Lane 1, RPA, 1.7 mM (I); lane 2, PDYE, 0.87 mM; lane 3, (I)+ PDYE; lane 4, (II)+ PDYE; lane 5, RPA, 2.4 mM (II); lane 6, (III)+ PDYE; lane 7, RPA, 6 mM (III).  
         [0035]      FIG. 3  illustrates Coomassie Blue G-250-stained RPA. Lane 1, RPA, 1.7 mM (I); lane 2, PDYE, 0.87 mM; lane 3, (I)+ PDYE; lane 4, (II)+ PDYE; lane 5, RPA, 2.4 mM (II); lane 6, (III)+ PDYE; lane 7, RPA, 6 mM (III).  
         [0036]      FIG. 4  illustrates the expression and purification of Ligase-1 from  E. coli  cells.  
         [0037]      FIG. 5  illustrates the expression and purification of Ligase-2 from  E. coli  cells.  
         [0038]      FIG. 6  illustrates the expression and purification of MCM2 — 1 from  E. coli  cells.  
         [0039]      FIG. 7  illustrates the expression and purification of Fen1 from  E. coli  cells.  
         [0040]      FIG. 8  illustrates the activity of Fen1 from MK Av19.  
         [0041]      FIG. 9  illustrates the expression and purification of Ppa from  E. coli  cells.  
         [0042]      FIG. 10  illustrates the expression and purification of RFC-S from  E. coli  cells.  
         [0043]      FIG. 11  illustrates the expression and purification of RFC-L from  E. coli  cells.  
         [0044]      FIG. 12  illustrates the expression and purification of Pol B from  E. coli  cells.  
         [0045]      FIG. 13  illustrates DNA polymerase activity of DNA polymerase polB in various media.  
         [0046]      FIG. 14  illustrates the effect of betaine on thermostability of DNA polymerase polB in 1 M potassium glutamate at 100° C.  
         [0047]      FIG. 15  illustrates effect of potassium glutamate on the activity and processivity of DNA polymerase PolB.  
         [0048]      FIG. 16  illustrates a duplex.  
         [0049]      FIG. 17  illustrates a duplex.  
         [0050]      FIG. 18  illustrates the amplification of 110 nt region of ssDNA M13mp18(+) with ALF M13 Universal fluorescent primer (Amersham Pharmacia Biotech) and primer caggaaacagctatgacc (M13 reverse) in the presence of 1 M potassium glutamate with polB DNA polymerase.  
         [0051]      FIG. 19  illustrates the expression and purification of PCNA from  E. coli  cells.  
         [0052]      FIG. 20  illustrates the effect of PCNA on formation of fluorescent products in primer extension reaction catalyzed by polB DNA polymerase.  
         [0053]      FIG. 21  illustrates the expreesion and purification of Topo I from  E. coli  cells.  
         [0054]      FIG. 22  illustrates the relaxation of closed circular pBR322 DNA by Mka Topo I in 100 mM NaCl (lane 2) and 1 M KGlu (lane 5) at 80° C.  
         [0055]      FIG. 23  illustrates the expression and purification of MCM2 — 2 from  E. coli  cells.  
         [0056]      FIG. 24  illustrates the purification of P41P46complex from  E. coli  cells.  
         [0057]      FIG. 25  demonstrates primase activity assay for complex p41p46. 
     
    
     DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENT  
       [0058]     In a first aspect, the invention provides nucleic acid including the  M. kandleri  nucleotide sequence shown in SEQ ID NO. 1693 in Attachment A hereto. It also provides nucleic acid comprising sequences having sequence identity to the nucleotide sequence disclosed herein. Depending on the particular sequence, the 35 degree of sequence identity is preferably greater than 70% (e.g., 80%, 90%, 92%, 96%, 99% or more). Sequence identity is determined as above disclosed. These homologous DNA sequences include mutants and allelic variants, encoded within the  M. kandleri  nucleotide sequence set out herein, as well as homologous DNA sequences from other  Methanopyrus  strains.  
         [0059]     The invention also provides nucleic acid including sequences complementary to those described above (e.g., for antisense, for probes, or for amplification primers).  
         [0060]     Nucleic acid according to the invention can, of course, be prepared in many ways (e.g., by chemical synthesis, from DNA libraries, from the organism itself, etc.) and can take various forms (e.g., single-stranded, double-stranded, vectors, probes, primers, etc.). The term “nucleic acid” includes DNA and RNA, and also their analogs, such as those containing modified backbones, and also peptide nucleic acid (PNA) etc.  
         [0061]     The invention also provides vectors including nucleotide sequences of the invention (e.g., expression vectors, sequencing vectors, cloning vectors, etc.) and host cells transformed with such vectors.  
         [0062]     According to a further aspect, the invention provides a protein including an amino acid sequence encoded within a  M. kandleri  nucleotide sequence set out herein. It also provides proteins comprising sequences having sequence identity to those proteins. Depending on the particular sequence, the degree of sequence identity is preferably greater than 50% (e.g., 60%, 70%, 80%, 90%, 95%, 99% or more). Sequence identity is determined as above disclosed. These homologous proteins include mutants and allelic variants, encoded within the  M. kandleri  nucleotide sequence set out herein.  
         [0063]     According to a further aspect, the invention provides highly thermostable polypeptides that work in high temperature and high salt conditions where previously disclosed proteins do not.  
         [0064]     The proteins of the invention can, of course, be prepared by various means (e.g., recombinant expression, purification from cell culture, chemical synthesis, etc.) and in various forms (e.g., native, fusions, etc.). They are preferably prepared in substantially isolated form (i.e., substantially free from other  M. kandleri  host cell proteins).  
         [0065]     Various tests can assess the in vivo immunogenicity of the proteins of the invention. For example, the proteins can be expressed recombinantly or chemically synthesized and used to screen patient sera by immunoblot. A positive reaction between the protein and patient serum indicates that the patient has previously mounted an immune response to the protein in question; i.e., the protein is an immunogen. This method can also be used to identify immunodominant proteins.  
         [0066]     The invention also provides nucleic acid encoding a protein of the invention.  
         [0067]     In a further aspect, the invention provides a computer, a computer memory, a computer storage medium (e.g., floppy disk, fixed disk, CD-ROM, etc.), and/or a computer database containing the nucleotide sequence of nucleic acid according to the invention. Preferably, it contains one or more of the  M. kandleri  nucleotide sequences set out herein.  
         [0068]     This may be used in the analysis of the  M. kandleri  nucleotide sequences set out herein. For instance, it may be used in a search to identify open reading frames (ORFs) or coding sequences within the sequences.  
         [0069]     In a further aspect, the invention provides a method for identifying an amino acid sequence, comprising the step of searching for putative open reading frames or protein-coding sequences within a  M. kandleri  nucleotide sequence set out herein. Similarly, the invention provides the use of a  M. kandleri  nucleotide sequence set out herein in a search for putative open reading frames or protein-coding sequences.  
         [0070]     A search for an open reading frame or protein-coding sequence may comprise the steps of searching a  M. kandleri  nucleotide sequence set out herein for an initiation codon and searching the upstream sequence for an in-frame termination codon. The intervening codons represent a putative protein-coding sequence. Typically, all six possible reading frames of a sequence will be searched.  
         [0071]     An amino acid sequence identified in this way can be expressed using any suitable system to give a protein. This protein can be used to raise antibodies which recognize epitopes within the identified amino acid sequence. These antibodies can be used to screen  M. kandleri  to detect the presence of a protein comprising the identified amino acid sequence.  
         [0072]     Furthermore, once an ORF or protein-coding sequence is identified, the sequence can be compared with sequence databases. Sequence analysis tools can be found at NCBI (http://www.ncbi.nlm.nih.gov) e.g., the algorithms BLAST, BLAST2, BLASTn, BLASTp, tBLASTn, BLASTx, &amp; tBLASTx. See also Altschul, et al., “Gapped BLAST and PSI-BLAST: new generation of protein database search programs,”  Nucleic Acids Research,  25:2289-3402 (1997). Suitable databases for comparison include the nonredundant GenBank, EMBL, DDBJ and PDB sequences, and the nonredundant GenBank CDS translations, PDB, SwissPot, Spupdate and PIR sequences. This comparison may give an indication of the function of a protein.  
         [0073]     Hydrophobic domains in an amino acid sequence can be predicted using algorithms such as those based on the statistical studies of Esposti et al. Critical evaluation of the hydropathy of membrane proteins  Eur J Biochem,  190:207-219 (1990). Hydrophobic domains represent potential transmembrane regions or hydrophobic leader sequences, which suggest that the proteins may be secreted or be surface-located. These properties are typically representative of good immunogens.  
         [0074]     Similarly, transmembrane domains or leader sequences can be predicted using the PSORT algorithm (http://psort/nibb/ac/ip), and functional domains can be predicted using the MOTIFS program (GCG Wisconsin &amp; PROSITE).  
         [0075]     The invention also provides nucleic acid including an open reading frame or protein-coding sequence present in a  M. kandleri  nucleotide sequence set out herein. Furthermore, the invention provides a protein including the amino acid sequence encoded by this open reading frame or protein-coding sequence.  
         [0076]     According to a further aspect, the invention provides antibodies, which bind to these proteins. These may be polyclonal or monoclonal and may be produced by any suitable means known to those skilled in the art.  
         [0077]     The antibodies of the invention can be used in a variety of ways, e.g., for confirmation that a protein is expressed, or to confirm where a protein is expressed. Labeled antibody (e.g., fluorescent labeling for FACS) can be incubated with intact bacteria and the presence of label on the bacterial surface confirms the location of the protein, for instance.  
         [0078]     According to a further aspect, the invention provides compositions including protein, antibody, and/or nucleic acid according to the invention. These compositions may be suitable as vaccines, as immunogenic compositions, or as diagnostic reagents.  
         [0079]     The invention also provides nucleic acid, protein, or antibody according to the invention for use as medicaments (e.g., as vaccines) or as diagnostic reagents.  
         [0080]     According to a further aspect, the invention provides compositions including  M. kandleri  protein(s) and other proteins. These compositions, both covalent and non-covalent, may be more stable and may work in broader salt and pH conditions than individual proteins.  
         [0081]     According to further aspects, the invention provides various processes.  
         [0082]     A process for producing proteins of the invention is provided, comprising the step of culturing a host cell according to the invention under conditions, which induce protein expression. A process which may further include chemical synthesis of proteins and/or chemical synthesis (at least in part) of nucleotides.  
         [0083]     A process for detecting polynucleotides of the invention is provided, comprising the steps of: (a) contacting a nucleic probe according to the invention with a biological sample under hybridizing conditions to form duplexes; and (b) detecting said duplexes.  
         [0084]     A process for detecting proteins of the invention is provided, comprising the steps of: (a) contacting the antibody according to the invention with a biological sample under conditions suitable for the formation of an antibody-antigen complexes; and (b) detecting said complexes.  
         [0085]     Another aspect of the present invention provides for a process for detecting antibodies that selectably bind to antigens or polypeptides or proteins specific to any species or strain of  M. kandleri  where the process comprises the steps of: (a) contacting antigen or polypeptide or protein according to the invention with a biological sample under conditions suitable for the formation of an antibody-antigen complexes; and detecting said complexes.  
         [0086]     Having now generally described the invention, the same will be more readily understood through reference to the following examples which are provided by way of illustration, and are not intended to be limiting of the present invention, unless specified.  
         [0000]     Directed Genomic Sequencing  
         [0087]     A novel genome sequencing strategy was adopted to sequence  M. kandleri  strain AV19 (DSM 6324). The Sequence is listed in Attachment A as Seq ID No.: 1693.  
         [0088]     Skimming shotgun Phase. A small insert (2-4 kb) shotgun library in pUC18 cloning vector (SeqWright) was prepared from 150 μg genomic DNA of  M. kandleri  strain AV19 (DSM 6324) isolated as described (Slesarev, A. I., et al.,  Nucleic Acids Res,  26:427-30 (1998)). Approximately 1,000 purified plasmid clones and 3,000 unpurified clones (i.e., aliquots of overnight cultures) were sequenced from both ends using dye-terminator chemistry (Applied Biosystems), ThermoFidelase I (Slesarev, A. I., et al.,  Methods Enzymol,  334:179-92 (2001)) and standard end Fimers (Polushin, N. et al.,  Nucleosides Nucleotides Nucleic Acids,  20:973-6 (2001); and (Polushin, N., et al.,  Nucleosides Nucleotides Nucleic Acids,  20:507-14 (2001)); (Fidelity Systems) on an ABI377. A total of 3,986 sequences, corresponding to ˜0.5× coverage, were assembled into 901 contigs using the Phred/Phrap/Consed software (P. Green, unpubl., Ewing, B., et al.,  Genome Res,  8:186-94 (1998); Ewing, B., et al.,  Genome Res,  8:175-85 (1998); and Gordon, D., et at.,  Genome Res,  8:195-202 (1998)). http://qenome.washington.edu).  
         [0089]     Directed sequencing phase. The assembled contigs from the previous phase were used as islands to select Fimers for directed sequencing off the genomic DNA. Eleven rounds of Fimer selection-sequencing-assembly were performed, which allowed the genome to be assembled into 29 contigs with a 2.5× sequencing redundancy. A total of 5,499 Fimers were synthesized during this phase, from which 6,470 chromatograms were obtained. The program PrimoU (http://www.genome.ou.edu/informatics/primou.html) was used to select priming sites at the ends of contigs.  
         [0090]     Gap closure and assembly verification. DNA was isolated from 293 clones of the  M. kandleri  EMBL3 lambda library (Krah, R., et al.,  Proc Natl Acad Sci USA,  93:106-10 (1996); and Slesarev, A. I., et al.,  Nucleic Acids Res,  26:427-30 (1998)). Remaining gaps in the genome, as well as low-quality and single-stranded regions, were closed by directed reads from genomic and lambda DNA. Fimers sequences for whole genome reads and lambda clone custom reads were selected using the Autofinish program (Gordon, D., et al.,  Genome Res,  8: 195-202 (1998); and Gordon, D., et al., Genome Res, 11: 614-25 (2001)). After generating 1,585 chromatograms, the genome was assembled into a unique contig with an estimated error rate of 0.4/10 kb. This was done with 12,046 reads (˜3.0× coverage). With an additional 2,147 genomic and lambda walking reads, an accuracy of less than one error per 40,000 bases was achieved (total 14,139 reads, 3.3× coverage). Lambda clones covered 85% of the genome, with an average insert size of 14,500 bp (min 12,230; max 19,324). There were no discrepancies between the expected insert lengths in lambda clones and the corresponding regions in the final genome sequence.  
         [0091]     Detailed sequencing protocols are provided for below in the Examples section.  
         [0000]     Computational Genome Analysis  
         [0092]     The tRNA genes were identified using the tRNA-SCAN program (Fichant, G. A., et al.,  J Mol Biol,  220:659-71 (1991)) and the rRNA genes were identified using the BLASTN program (Altschul, S. F., et al.,  Nucleic Acids Res,  25:3389402 (1997)) with archaeal rRNA as search queries. For the identification of the protein-coding genes, the genome sequence was conceptually translated in 6 frames to generate potential protein products of open reading frames (ORFS) longer than 100 codons (from stop to stop). These potential protein sequences were compared to the database of Clusters of Orthologous Groups (COGs) of proteins using COGNITOR (Tatusov, R. L., et al.,  Science,  278:631-7 (1997)). After manual verification of the COG assignments and selection of start sites, the validated COG members from  M. kandleri  were considered protein-coding genes. The COG assignment procedure was repeated for ORF products greater than 60 codons obtained from the intergenic regions. Other potential protein sequences were compared to the non-redundant (NR) protein sequence database using the BLASTP program and to a six-frame translation of unfinished microbial genomes using the TBLASTN program. Those that produced hits with E (expectation) values &lt;0.01 were added to the protein set after an examination of the alignments. Finally, protein-coding regions were predicted using the GeneMarkS (Besemer, J., et al.,  Nucleic Acids Res.  29:2607-18 (2001)) and SYNCOD (Rogozin, I. B., et al.,  Gene,  226:129-37 (1999)) programs. The genes predicted with these methods in the regions between evolutionarily conserved genes were added to produce the final protein set. (See Attachment B SEQ ID Nos.; 1-1691) 1-1688 and 1690-1692.  
         [0093]     Protein function prediction was based primarily on the COG assignments. In addition, searches for conserved domains were performed using the CDD-search option of BLAST (http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi), the SMART system (http://smart.embl-heidelberg.de/) (Schultz, J., et al.,  Proc Natl Acad Sci USA,  95:5857-64 (1998)) and customized position-specific score matrices for different classes of DNA-binding proteins. In-depth, iterative database searches were performed using the PSI-BLAST program (Altschul, S. F., et al.,  Nucleic Acids Res,  25:3389-402 (1997)). The KEGG database (http://www.genome.ad.jp/kegg/metabolism.html) (Kanehisa, M. et al.,  Nucleic Acids Res,  28:27-30 (2000)) was used, in addition to the COGs, for the reconstruction of metabolic pathways. Paralogous protein families were identified by single-linkage clustering of  M. kandleri  proteins after comparing the predicted protein set to itself using the BLASTP program (Makarova, K. S., et al.,  Microbiol Mol Biol Rev,  65:44-79 (2001)). Signal peptides in proteins were predicted using the SignalP (Nielsen, H., et al.,  Int J Neural Syst,  8:581-99 (1997)) program and transmembrane helices were predicted using the MEMSAT program (McGuffin, L. J., et al.,  Bioinformatics,  16:404-5 (2000)). See Table 1, Attachment C).  
         [0094]     Gene orders in archaeal and bacterial genomes were compared using the LAMARCK program (Wolf, Y. I., et al.,  Genome Res,  11:356-72 (2001)). For phylogenetic analysis, multiple alignments of ribosomal protein sequences were constructed using the T_Coffee program (Notredame, C., et al.,  J Mol Biol,  302:205-17 (2000)) and concatenated head-to-tail. Maximum likelihood (ML) trees were generated by exhaustive search of all possible topologies using the ProtML program of the MOLPHY package, with the JTT-F model of amino acid substitutions (Adachi, J., et al.,  Computer Science Monographs  27; (Institute of Statistical Mathematics, Tokyo) (1992)). Bootstrap analysis was performed for each ML tree using the Resampling of Estimated Log-Likelihoods (RELL) method (10000 replications) (Hasegawa, M., et al.,  J Mol Evol,  32:443-5 (1991)); and (Kishino, H., et al.,  J. Mol. Evol.,  31:151-160 (1990)). The likelihoods of alternative placements of  M. kandleri  in ML trees were compared using the Kishino-Hasegawa test (Kishino, H., et al.,  J. Mol. Evol.,  31:151-160 (1990)).  
         [0000]     Design, Expression, and Purification of Protein Chimeras  
         [0095]     The 5′ to 3′ exonuclease domain of Taq DNA polymerase is a structurally and functionally separate unit (Kim, Y., et al.,  Nature,  274:612-616 (1995)). Its removal produces active DNA polymerases, the Stoffel fragment and KlenTaq variants with enhanced thermostability and higher fidelity but with low processivity (Gelfand, D. H. and White, T. J.  PCR Protocols A Guide to Methods and Applications , ed. Innis, M. A., et al., (Academic Press, NY) (1990); Barnes, W. M.  Gene,  112:29-35 (1992)).  
         [0096]     DNA Topoisomerase V from  M. kandleri  is an extremely thermophilic enzyme whose ability to bind DNA is preserved at very high ionic strengths (Slesarev, A. I., et al.,  J. Biol. Chem.,  269:3295-3303 (1994)). An explicit domain structure, with multiple C-terminal HhH repeats is responsible for DNA binding properties of the enzyme at high salt concentrations (Belova, G. I., et al.,  Proc Natl. Acad. Sci. USA,  98:6015-6020 (2001); Belova, G. I., et al.,  J. Biol. Chem.,  277:4959-4965 (2002)). Thus, if the inhibition of Taq DNA polymerase, which has only one HhH motif, or its active derivatives (which lack the HhH motif) by salts is due to the inability of these enzymes to bind DNA, the transfer of HhH domain(s) derived from Topo V to Taq polymerase catalytic domain would restore the DNA polymerase at high salt concentrations.  
         [0097]     In one embodiment, the chimeric DNA polymerase has a DNA polymerase domain that is thermophilic, e.g., is the DNA polymerase domain present in a thermophilic DNA polymerase, such as one from the DNA polymerase in  Thermus aquaticus, Thermus thermophilus , Pfu DNA polymerase, Vent DNA polymerase, or  Bacillus sterothermophilus  DNA polymerase. The amino acid sequence comprising one or more HhH domains, when bound to the DNA polymerase, causes an increase in the processivity of the chimeric DNA polymerase. Five protein chimeras (also referred to herein as “hybrid proteins” “hybrid enzymes” or “chimeric constructs”) containing either the Stoffel fragment of Taq DNA polymerase or whole size Pfu polymerase and a different number of HhH motifs derived from Topo V were designed. Specifically, the designed chimeras are TopoTaq, containing HhH repeats H-L of Topo V (10 HhH motifs) linked to the N-terminus of the Stoffel fragment; TaqTopoC1 comprising Topo V&#39;s repeats B-L (21 HhH motifs) linked to the C-terminus of the Stoffel fragment, TaqTopoC2 comprising Topo Vs repeats E-L (16 HhH motifs) linked to the C-terminus of the Stoffel fragment, TaqTopoC3 comprising Topo Vs repeats H-L (10 HhH motifs) linked to the C-terminus of the Stoffel fragment, and PfuC2 comprising repeats E-L at the C-terminus of the Pfu polymerase. Repeats are designated as in (Belova, G. I., et al.,  Proc Natl. Acad. Sci. USA,  98:6015-6020 (2001). Repeats H-L (also known as Topo34) and F-L with a half of the repeat E are dispensable for the topoisomerase activity of Topo V (Belova, G. I., et al.,  J. Bio. Chem.,  277:4959-4965 (2002) The overall structures of HhH domains are likely the same as in native Topo V, since the domains are resistant to proteolysis both in Topo V and when expressed separately (Topo 34; ((Belova, G. I., et al.,  J. Bio. Chem.,  277:4959-4965 (2002). Also, it was thought that all Topo V domains have high internal stability in order to be functional at extremely high temperatures.  
         [0098]     The chimeras were expressed in  E. coli  BL21 pLysS and purified using a simple two-step procedure. The purification procedure takes advantage of the extreme thermal stability of recombinant proteins that allows the lysates to be heated and about 90% of  E. coli  proteins to be removed by centrifugation. The second step involves a heparin-sepharose chromatography. Due to the high affinity of Topo Vs HhH repeats to heparin Slesarev, A. I., et al.,  J. Biol. Chem.,  269:3295-3303 (1994), the chimeras elute from a heparin column around 1.25M NaCl to give nearly homogeneous protein preparations (&gt;95% purity). All expressed constructs possessed high DNA polymerase activity that was comparable to that of commercial Taq DNA polymerase.  
         [0099]     In one embodiment, the chimeric proteins of this invention may comprise a DNA polymerase fragment linked directly end-to-end to the HhH domain. Chemical means of joining the two domains are described, e.g., in  Bioconjugate Techniques , Hermanson, Ed., Academic Press (1996), which is incorporated herein by reference. These include, for example, derivitization for the purpose of linking the moieties to each other by methods well known in the art of protein chemistry, such as the use of coupling reagents. The means of linking the two domains may also comprise a peptidyl bond formed between moieties that are separately synthesized by standard peptide synthesis chemistry or recombinant means. The chimeric protein itself can also be produced using chemical methods to synthesize an amino acid sequence in whole or in part, e.g., using solid phase techniques such as the Merrifield solid phase synthesis method.  
         [0100]     Alternatively, the DNA polymerase fragment can be linked indirectly via an intervening linker such as an amino acid or peptide linker. The linking group can be a chemical crosslinking agent, including, for example, succinimidyl-(N-maleimidomethyl)-cyclohexane-1-carboxylate (SMCC). The linking group can also be an additional amino acid sequence. Other chemical linkers include carbohydrate linkers, lipid linkers, fatty acid linkers, polyether linkers, e.g. PEG, etc. The linker moiety may be designed or selected empirically to permit the independent interaction of each component DNA-binding domain with DNA without steric interference. A linker may also be selected or designed so as to impose specific spacing and orientation on the DNA-binding domains. The linker may be derived from endogenous flanking peptide sequence of the component domains or may comprise one or more heterologous amino acids. Linkers may be designed by modeling or identified by experimental trial.  
         [0101]     As demonstrated in the discussion and examples provided below, this invention also provides methods of amplifying a nucleic acid by thermal cycling such as in a polymerase chain reaction (PCR) or in DNA sequencing. The methods include combining the nucleic acid with a chimeric DNA polymerase having a DNA polymerase linked to an amino acid sequence comprising one or more helix-hairpin-helix (HhH) motifs not naturally associated with said DNA polymerase, wherein said amino acid sequence is derived from Topoisomerase V. The nucleic acid and said chimeric DNA polymerase are combined in an amplification reaction mixture under conditions that allow for amplification of the nucleic acid. Such methods are well known to those skilled in the art and need not be described in further detail.  
         [0000]     HhH Domains Confer DNA Polymerase Activity on Chimeras in High Salts  
         [0102]     The polymerase activities of the four chimeras were tested by measuring initial rates of primer extension reactions. The reactions were carried out at low concentrations of substrate, when the initial rates were proportional both to total protein and PTJ concentrations. When [PTJ] is much less than Km app , the initial rate is determined as in Equation 1: 
 
 v   1   =k   app   /Km   app   *[E   t   ]*[PTJ]   1   Eq. 1 
        where Km app  and k app  are apparent Michaelis and catalytic constants, respectively.        
 
         [0104]     The concentrations of sodium chloride (NaCl), potassium chloride (KCl) and potassium glutamate (K-Glu) were varied to assess inhibition of the Stoffel fragment and KlenTaq, and the four chimeras by salts, and to estimate the effects of the HhH domains.  
         [0105]     Table 2 shows the inhibition constants (K i ) and the cooperativity factors (a) of Taq DNA polymerase, Taq DNA polymerase fragments (Stoffel fragment and KlenTaq), the four Taq-Topo V chimeras, and Pfu and PfuC2 polymerases determined from the analysis of initial rates of primer extension reactions in salts using the DNA duplex of  FIG. 16 . Experimental values of initial polymerization rates were analyzed by nonlinear regression analysis using Equation 2:  
             v   =       v   o       1   +       (       [   Salt   ]       K   i       )     α                 Eq   .           ⁢   2             
 
 where v and v 0  are initial primer extension rates with and without salt, respectively, K i  is the apparent inhibition constant; and α is the cooperativity parameter. The values for K i  and a are listed in Table 2. 
 
         [0106]     In Table 2, to take into account the activation of Pfu polymerase and the PfuC2 hybrid by KGlu (data entries marked with an asterisk (*), the experimental values of initial polymerization rates were analyzed by nonlinear regression using the Equation 3:  
             v   =         v   o     ⁢     •   (     1   +     β   ·       [   Salt   ]     y               1   +       (       [   Salt   ]       K   i       )     α                 Eq   .           ⁢   3             
 
         [0107]     where v and v 0  are initial primer extension rates with and without salt, respectively; K i  is an apparent inhibition constant, α is a parameter of cooperativity, β and γ are parameters of activation. Since γ≅2, it is likely that two ions of Glu −  bind to the Pfu polymerase catalytic domain without inhibiting the polymerase activity.  
                                                               TABLE 2                           Parameters of inhibition of Taq and Pfu DNA polymerases,       and TopoTaq and PfuC2 chimeras by salts                NaCl   KCl   K-Glu            Protein   K i     α   K i     A   K i     α               TopoTaq   241.3 ± 14   7.04 ± 1.4   291.1 ± 10   6.45 ± 0.6   1403.0 ± 20    6.03 ± 0.4       TaqTopoC1   228.4 ± 6    4.27 ± 0.2   231.2 ± 12   5.02 ± 0.6   1730.0 ± 125   2.45 ± 0.6       TaqTopC2   238.4 ± 3    6.77 ± 0.2   251.0 ± 6    8.97 ± 0.6   1164.5 ± 42    4.34 ± 0.5       TaqTopC3    69.0 ± 14   1.86 ± 0.2   187.7 ± 2    3.87 ± 0.1   295.8 ± 92   1.21 ± 0.2       Taq   138.7 ± 6    3.24 ± 0.5   161.0 ± 6    3.50 ± 0.2     610 ± 51   4.45 ± 0.3       Polymerase       Stoffel   38.6 ± 3   3.45 ± 0.2   45.8 ± 4   2.92 ± 0.1    59.6 ± 38   1.47 ± 0.4       Fragment       KlenTaq   40.0 ± 5   1.83 ± 0.1   32.7 ± 7   1.49 ± 0.2    71.0 ± 24   0.89 ± 0.1       Pfu   51.5 ± 1   2.39 ± 0.1   42.6 ± 1   3.65 ± 0.1   42.8* ± 6    3.24 ± 0.2       polymerase       PfuC2   159.6 ± 33   3.62 ± 0.8   176.8 ± 3    4.68 ± 0.1   424.8* ± 9    5.76* ± 0.2                   
 
         [0108]     For Taq polymerase, inhibition constants (K i ) for NaCl and KCl are essentially the same, yet substituting KCl with KGlu increases the K i  4-fold (Table 2). Hence, Taq polymerase is sensitive to anions. The cooperativity parameter α was very similar for all salts tested and suggests that as many as four anions bound simultaneously to the protein are involved.  
         [0109]     The Stoffel and KlenTaq fragments of Taq DNA polymerase have almost equal sensitivities to chloride ions, which is about four times higher that the sensitivity of Taq polymerase to chloride ions. Potassium glutamate inhibited these fragments only about 1.5 to 2 times less efficiently than NaCl or KCl, implying that the HhH domain can be responsible for the resistance of Taq polymerase to glutamate ions. It was observed that KlenTaq had consistently lower values of the cooperativity parameter α than the Stoffel fragment, suggesting that the additional N-terminal amino acids could mask some anion-binging sites on the catalytic domain.  
         [0110]     As shown in Table 2, TopoTaq has higher inhibition constants (K i ) in salts as compared with Taq polymerase, and may require six to seven anions to be bound for inhibition. As a result, TopoTaq is active at much higher salt concentrations than Taq DNA polymerase. For example, a 20% inhibition of primer extension reaction occurs at about 200 mM NaCl for TopoTaq versus about 90 mM NaCl for Taq DNA polymerase. The TopoTaq chimera also displays little distinction between sodium and potassium cations and is less sensitive to glutamate anions versus chloride anions.  
         [0111]     It was observed that the 21 and 16 HhH motifs at the COOH terminus of the Stoffel fragment in TaqTopoC1 and TaqTopoC2, respectively, also increase the polymerase activities of chimeras in the presence of salts. For example, 20% inhibition occurred at about 160 mM NaCl for TaqTopoC1 and at about 195 mM NaCl for TaqTopoC2. Similar to Taq polymerase, the TaqTopoC1 and TaqTopoC2 chimeras show no difference in inhibition by KCl versus NaCl (with the cooperativity parameter α about equal to 5), and glutamate anions were much more preferable than chloride anions. However, the cooperativity parameter for the TaqTopoC1 and TaqTopoC2 chimeras in the case of glutamate is lower compared to that of Taq polymerase or TopoTaq, suggesting that only two glutamate ions are involved in the rate inhibition.  
         [0112]     TaqTopoC3 behaves differently in salts than TaqTopoC1 and TaqTopoC2. Although inhibition of TaqTopoC3 by KCl is similar to that of TaqTopoC1 or TaqTopoC2 (with α≈5, but with a slightly lower K i  similar to that of Taq DNA polymerase), replacement of potassium ions by sodium ions results in a much stronger inhibition of the TaqTopoC3 polymerase activity and, at the same time, decreases the number of inhibiting ions to about 2. Consequently, just 30 mM NaCl inhibits the enzyme by 20%. TaqTopoC3 has about a fivefold relative decrease in sensitivity to K-Glu with respect to NaCl (but not to KCl), which is similar to other hybrids. However, in case of glutamate no cooperativity at all was found, suggesting that only one glutamate ion per molecule is involved in the inhibition of TaqTopoC3.  
         [0113]     Introduction of C-terminal domains of Topo V into the hybrid proteins significantly extends the range of salt concentrations for the polymerase activity. This effect is due to the increase of both K, and cc, allowing chimeras to maintain their full activity at high salt concentrations. Raising the number of HhH motifs from 11 to 23 at the COOH-terminus of the Stoffel fragment made the hybrid enzymes progressively more resistant to salts. TopoTaq had the highest resistance to chloride-containing salts.  
         [0114]     The sensitivity of Pfu DNA polymerase to salts was almost identical to that of Stoffel or KlenTaq fragments of DNA polymerase from  Thermus aquaticus , possibly indicating the close functional similarity of charged amino acid residues in the active sites of these enzymes from different structural families. Attachment of Topo V HhH domains to C-terminus of Pfu polB significantly increased the resistance of polymerase activity to salts (Table 2). Both Pfu DNA polymerase and the chimera PfuC2 demonstrated virtually indistinguishable curves for KCl versus NaCl, suggesting no role for cations in inhibition. However, the Topo V domains greatly increased the resistance of Pfu pol activity to high levels of KGlu.  
         [0115]     The invention is further illustrated by the following non-limited examples. All scientific and technical terms have the meanings as understood by one with ordinary skill in the art. The specific examples which follow illustrate the methods in which the genomic sequence, polypeptides of the present invention may be prepared and used and are not to be construed as limiting the invention in sphere or scope. The methods may be adapted to variation in order to produce compositions embraced by this invention but not specifically disclosed. Further, variations of the methods to produce the same compositions in somewhat different fashion will be evident to one skilled in the art.  
       EXAMPLES  
       [0116]     The examples herein are meant to exemplify the various aspects of carrying out the invention and are not intended to limit the invention in any way.  
         M. kandleri  AV19 Replication Factor A RPA (MK1441)  
       [0000]     Construction of Expression Vector  
         [0117]     pET21d-M.ka-AV19-RPA: 1128 bp RPA cds was PCR-amplified from  M. kandleri  AV19 genomic DNA using following primers:  
                                                                 (SEQ ID No.:1694)                    5′-ATTCCATGGGTGTGAAGCTGATGCGAACGG               and                        ((SEQ ID No.:1695)                    5′-ATAGAATTCACTCAGCTTCCTCTCCTTCACTCTCCTCC.              
 
         [0118]     NcoI+EcoRI-digested PCR fragment (NcoI and EcoRI sites were introduced in the primers) was cloned into NcoI, EcoRI sites of pET21d vector. Sequencing of several inserts revealed clones carrying the correct sequence. The resulting protein sequence lacks first 56 amino acids of MK1441.  
         [0000]     Expression and Purification of Mka RPA  
         [0119]      E. coli  strain BL21 pLysS (Novagen) was transformed with expression plasmid. LB medium (2 L) containing 100 μg/ml ampicillin and 34 μg/ml chloramphenicol was inoculated with transformed cells, and the protein expression was induced by adding 1 mM isopropylthio-β-galactoside (IPTG) and carried out at 37° C. for 3 hours. The cells were harvested and dissolved in 60 ml lysis buffer containing 50 mM Tris-HCl pH 8.0, 0.6 M NaCl, 1 mM EDTA, 5 mM β-mercaptoethanol, and protease inhibitors (Roche). The lysate was centrifuged at 38000 g for 20 minutes, heated at 75° C. for 30 minutes, and centrifuged again at 38,000 g for 30 minutes. The supernatant was filtered through a 0.22 μm Millipore filter, diluted to 0.25M NaCl and applied on a Q-Sepharose column (1.6×17 cm), equilibrated with 50 mM Tris pH 7.5, containing 0.25 M NaCl and 2 mM ME. After washing with the same buffer RPA was eluted with linear gradient of 0.25-0.5 M NaCl. Fractions containing RPA were pooled, concentrated by Centriprep, followed by Centricon YM-30, and passed through a Superdex 200 (1.0×30 cm), equilibrated with 50 mM Tris-HCl pH 7.5, containing 0.15M NaCl and 2 mM ME. 15-20 mg of RPA was purified.  
         [0120]     Shown in  FIG. 1  is the expression and purification of RPA from  E. coli  cells. Cell lysate before induction (lane 2), cell lysate after induction (lane 3) and purified protein (lane 4) were analyzed by SDS-PAGE (10% gel) and visualized by Coomassie Blue G-250. Lane 1 is molecular size marker 10-225 kDa (Novagen).  
         [0000]     DNA Binding Activity of RPA  
         [0121]     DNA-binding activity was checked with a 20-mer oligonucleotide and analyzed by native PAGE. The data is shown in  FIGS. 21 and 22 .  
         [0122]     DNA-binding activity of RPA analyzed by 8% native PAGE, stained with fluorescein ( FIG. 2 ) and Coomassie Blue G-250 ( FIG. 3 ) RPA. Lane 1, RPA, 1.7 μM, (I); lane 2, PDYE, 0.87 μM; lane 3, (I)+ PDYE; lane 4, (II)+ PDYE; lane 5, RPA, 2.4 μM, (II); lane 6, (III)+ PDYE; lane 7, RPA, 6 μM (III).  
         [0123]     From the experiments ontitration of 1.5 μM RPA by oligonucleotide in 1×TAE buffer pH 8.0 in the presence of 10% glycerol dissociation constant K d  was determined as described in Pavlov &amp; Karam, 1994. K d =0.21±0.15 μM.  
         M. kandleri  Strain AV19 ATP-Dependent DNA Ligase (MK0999)  
       [0000]     Construction of an Expression Vector for Mka Ligase (Variant-1)  
         [0124]     pET21d-Mka-AV19-Ligase1: 1896 bp DNA ligase long variant eds was PCR-amplified from  M. kandleri  (av19) genomic DNA using following primers:  
                                                         (SEQ ID No.:1696)                5′-ATTCCATGGTAGGGGTGGTGAACGTGACTCGACCC           and                    (SEQ ID No.:1697)                5′-AATGAATTCTAGTGCTTCTGCAGTACTTCCTCGTAGATCCTCC.              
 
 NcoI+EcoRI-digested PCR fragment (NcoI and EcoRI sites were introduced in the primers) was cloned into NcoI, EcoRI sites of pET21d vector. Sequencing of several inserts revealed clones carrying the correct sequence. The expressed protein contains additional Met at the N-terminus. 
 
 Expression and Purification of Mka DNA Ligase (Variant-1). 
 
         [0125]      E. coli  strain BL21 pLysS (Novagen) was transformed with expression plasmid. LB medium (2 L) containing 100 μg/ml ampicillin and 34 μg/ml chloramphenicol was inoculated with transformed cells, and the protein expression was induced by adding 1 mM isopropylthio-β-galactoside (IPTG) and carried out at 37° C. for 3 hours. The cells were harvested and dissolved in 50 ml lysis buffer containing 50 mM Tris-HCl pH 8.0, 0.6 M NaCl, 1 mM EDTA, 5 mM β-mercaptoethanol, and protease inhibitors (Roche). The lysate was centrifuged at 38000 g for 20 minutes, filtered through a 0.22 μm Millipore filter, diluted to 0.5 M NaCl and applied on a heparin high trap 5 ml column (APB), equilibrated with 50 mM Tris pH 8.0, containing 0.5 M NaCl and 2 mM ME. After washing the column with 50 mM Tris pH 8.0, containing 0.75 M NaCl and 2 mM ME, Ligase-1 was eluted with 1.4 M NaCl in the same buffer.  
         [0126]     Shown in  FIG. 4  is the expression and purification of Ligase-1 from  E. coli  cells. Cell lysate before induction (lane 4), cell lysate after induction (lane 3) and purified protein (lane 2) were analyzed by SDS-PAGE (10% gel) and visualized by Coomassie Blue G-250. Lane 1 is molecular size marker 10-225 kDa (Novagen).  
         [0000]     Construction of an Expression Vector for Mka Ligase (Variant-2)  
         [0000]     pET21d-M.ka-AV19-Lig2:  
         [0127]     1677 bp DNA ligase long variant cds was PCR-amplified from  M. kandleri  (av19) genomic DNA using following primers:  
                                                         (SEQ ID No.:1698)                5′-TATCCATGGTGTACTACTCGTCCCTGGCGGAGGC           and                    (SEQ ID No.:1699)                5′-AATGAATTCTAGTGCTTCTGCAGTACTTCCTCGTAGATCCTCC.              
 
 NcoI+EcoRI-digested PCR fragment (NcoI and EcoRI sites were introduced in the primers) was cloned into NcoI, EcoRI sites of pET21d vector. Sequencing of several inserts revealed clones carrying the correct sequence. The expressed protein contains an additional Met at the N-terminus. 
 
 Expression and Purification of Mka DNA Ligase (variant-2). 
 
         [0128]      E. coli  strain BL21 pLysS (Novagen) was transformed with expression plasmid. LB medium (2 L) containing 100 μg/ml ampicillin and 34 μg/ml chloramphenicol was inoculated with transformed cells, and the protein expression was induced by adding 1 mM isopropylthio-β-galactoside (IPTG) and carried out at 37° C. for 3 hours. The cells were harvested and dissolved in 60 ml lysis buffer containing 50 mM Tris-HCl pH 8.0, 0.6M NaCl, 1 mM EDTA, 5 mM β-mercaptoethanol, and protease inhibitors (Roche). The lysate was centrifuged at 38000 g for 20 minutes, heated at 75° C. for 30 minutes, and centrifuged again at 38000 g for 30 minutes. The supernatant was filtered through a 0.22 μm Millipore filter, diluted to 0.3M NaCl and applied on a heparin high trap 5 ml column (APB), equilibrated with 50 mM Tris pH 7.5, containing 0.3 M NaCl and 2 mM ME. After washing with the same buffer, the column was washed with 1 M NaCl, then Ligase was eluted with 1.4 M NaCl in the same buffer. Fractions containing Ligase were passed through a Superdex 200 (1.0×30 cm), equilibrated with 50 mM Tris-HCl pH 7.5, containing 0.15M NaCl and 2 mM ME.  
         [0129]     Shown in  FIG. 5  is the expression and purification of Ligase-2 from  E. coli  cells. Cell lysate before induction (lane 2), cell lysate after induction (lane 3) and purified protein (lane 4) were analyzed by SDS-PAGE (10% gel) and visualized by Coomassie Blue G-250. Lane 1 is molecular size marker 10-225 kDa (Novagen).  
         M. kandleri  AV19 ATP-Dependent Helicase MCM2 — 1 (MK0965)  
       [0000]     Construction of an Expression Vector for Helicase MCM2 — 1  
         [0000]     pET21d-M.ka-AV19-MCM2 — 1:  
         [0130]     1962 bp MCM-1 cds was PCR-amplified from  M. kandleri  (av19) genomic DNA using following primers:  
                                                                 (SEQ ID No.:1700)                    5′-AATCCATGGAGCGTGAGTTCGAAGAGGCTCTCA               and                        (SEQ ID No.:1701)                    5′-AATGAATTCACATCGGGAGGTACACTCCGGGC.              
 
         [0131]     NcoI-incompletely digested and EcoRI-digested PCR fragment (NcoI and EcoRI sites were introduced in the primers; additional NcoI site is presented in the cds) was cloned into NcoI, EcoRI sites of pET21d vector. Sequencing of several inserts revealed clones carrying the correct sequence.  
         [0000]     Expression and Purification of MCM2 — 1  
         [0132]      E. coli  strain BL21 pLysS (Novagen) was transformed with expression plasmid. LB medium (2 L) containing 100 μg/ml ampicillin and 34 μg/ml chloramphenicol was inoculated with transformed cells, and the protein expression was induced by adding 1 mM isopropylthio-β-galactoside (IPTG) and carried out at 37° C. for 3 hours. The cells were harvested and dissolved in 60 ml lysis buffer containing 50 mM Tris-HCl pH 8.0, 0.6M NaCl, 1 mM EDTA, 5 mM β-mercaptoethanol, and protease inhibitors (Roche). The lysate was centrifuged at 38000 g for 20 minutres, heated at 75° C. for 30 minutes, and centrifuged again at 38000 g for 30 minutes. The supernatant was filtered through a 0.22 μm Millipore filter, diluted to 0.3M NaCl and applied on a Q-Sepharose column (1.6×17 cm), equilibrated with 50 mM Tris pH 7.5, containing 0.3 M NaCl and 2 mM ME. After washing with the same buffer MCM2 — 1 was eluted with linear gradient of 0.3-1.0 M NaCl. Fractions containing MCM2 — 1 were pooled, concentrated by Centriprep, followed by Centricon YM-30, and passed through a Superdex 200 (1.0×30 cm), equilibrated with 50 mM Tris-HCl pH 7.5, containing 0.15M NaCl and 2 mM ME. MCM2 — 1-containing fractions were applied on a heparin high trap 5 ml column (APB), equilibrated with 50 mM Tris pH 7.5, containing 0.15 M NaCl and 2 mM ME. After washing column with the same buffer, MCM2 — 1 was eluted with linear gradient of 0.3-1.0 M NaCl in the same buffer.  
         [0133]     Shown in  FIG. 6  is the expression and purification of MCM2 — 1 from  E. coli  cells. Cell lysate before induction (lane 2), cell lysate after induction (lane 3) and purified protein (lane 4) were analyzed by SDS-PAGE (10% gel) and visualized by Coomassie Blue G-250. Lane 1 is molecular size marker 10-225 kDa (Novagen).  
         M. kandleri  5′-3′ Exonuclease Fen1 (MK0566)  
       [0000]     Construction of an Expression Vector for 5′-3′ Exonuclease Fen1  
         [0000]     pET21d-M.ka-AV19-Fen1:  
         [0134]     1077 bp Fen1 cds was PCR-amplified from  M. kandleri  (av19) genomic DNA using following primers:  
                                                                 (SEQ ID No.:1702)                    5′-ATTCCATGGTTCGATCCACAGGGGTTCCTGGAGG               and                        (SEQ ID No.:1703)                    5′-ATAGAATTCAGAAGAACGCGTCCAGGGTCTCTTG.              
 
 NcoI+EcoRI-digested PCR fragment (NcoI and EcoRI sites were introduced in the primers) was cloned into NcoI, EcoRI sites of pET21d vector. Sequencing of several inserts revealed clones carrying the correct sequence. The expressed protein contains an additional Met at the N-terminus. 
 
 Expression and Purification of 5′-3′ Exonuclease Fen1 
 
         [0135]      E. coli  strain BL21 pLysS (Novagen) was transformed with expression plasmid. LB medium (2 L) containing 100 μg/ml ampicillin and 34 μg/ml chloramphenicol was inoculated with transformed cells, and the protein expression was induced by adding 1 mM isopropylthio-β-galactoside (IPTG) and carried out at 37° C. for 3 hours. The cells were harvested and dissolved in 100 ml lysis buffer containing 50 mM Tris-HCl pH 8.0, 0.6 M NaCl, 1 mM EDTA, 5 mM β-mercaptoethanol, and protease inhibitors (Roche). The lysate was centrifuged at 38000 g for 20 minutes, heated at 75° C. for 30 minutes, and centrifuged again at 38000 g for 30 minutes. The supernatant was filtered through a 0.22 μm Millipore filter, diluted to 0.25 M NaCl and applied on heparin high trap 5 ml column (APB) equilibrated with 0.25 M NaCl in 50 mM Tris-HCl buffer, pH 8.0, containing 2 mM β-mercaptoethanol. Fen1 was washed with the same buffer, and applied on a β-Sepharose column (1.6×17 cm), equilibrated with 50 mM Tris pH 8.0, containing 0.25 M NaCl and 2 mM ME. After washing with the same buffer Fen1 was eluted with linear gradient of 0.25-0.5 M NaCl. Fractions containing Fen1 were pooled, concentrated by Centricon YM-30, and passed through a Superdex 200 (1.0×30 cm), equilibrated with 50 mM Tris-HCl pH 7.5, containing 0.15M NaCl and 2 mM ME.  
         [0136]     Shown in  FIG. 7  is the expression and purification of Fen1 from  E. coli  cells. Cell lysate before induction (lane 2), cell lysate after induction (lane 3) and purified protein (lane 4) were analyzed by SDS-PAGE (10% gel) and visualized by Coomassie Blue G-250. Lane 1 is molecular size marker 10-225 kDa (Novagen).  
         [0137]     Activity assay for Fen1. For activity measurements of Fen1 a fluorescein—labeled oligonucleotide has been synthesized: 
    *FL-CTATAGGGAGACCGGAATTCGAGCTCGCCCGGGCGAGCTCGAATTCCGTG TATTTATA (SEQ ID No.:1704) which could form various secondary structures shown below that could be cleaved by flap endonucleases: 
 
 Hairpins: 
 
 Most Stable Hairpin: 
   
 
         [0139]     ΔG=−38.11 kcal/mol  
                                       CCCGCTCGAGCTTAAGGCCAGAGGGATATC-FI* 5′                ∥∥∥∥∥∥           GGGCGAGCTCGAATTCCGTGTATTTATA 3′          
 
 Dimers: 
 
 Most Stable Dimer: 
 
         [0140]     ΔG=−85.97 kcal/mol  
                           5′ FI*- CTATAGGGAGACCGGAATTCGAGCTCGCCCGGGCGAGCTCGAATTCCGTGTATTTATA 3′                  ∥∥∥∥∥∥∥∥∥∥∥∥∥∥       3′ ATATTTATGTGCCTTAAGCTCGAGCGGGCCCGCTCGAGCTTAAGGCCAGAGGGATATC-FI* 5′          
 
         [0141]      FIG. 8  demonstrates the activity of Fen1 from MK Av19. Lane 1—Primer APAV0062 without enzymes; Lane 2—APAV0062 after 10 minutes incubation with 1 u AmpliTaq in the presence of 2 mM Mg 2+  at 55° C. (positive control); Lane 3—APAV0062 after 10 minutes incubation with Fen I in the presence of 1 mM Mn 2+  at 55° C.  
         M. kandleri  AV19 Inorganic Pyrophosphatase Ppa (MK1450)  
       [0000]     Construction of an Expression Vector for Inorganic Pyrophosphatase Ppa  
         [0000]     pET21d-M.ka-AV19-Ppa:  
         [0142]     525 bp Pyrophosphatase cds was PCR-amplified from  M. kandleri  (av19) genomic DNA using following primers:  
                                                                 (SEQ ID No.:1705)                    5′-TAACCATGGACCTCTGGAAAGACCTGGAACCGG               and                        ((SEQ ID No.:1706)                    5′-ATAGAATTCACCCGTGCTCCTCCTCGTACAGCT.              
 
         [0143]     NcoI+EcoRI-digested PCR fragment (NcoI and EcoRI sites were introduced in the primers) was cloned into NcoI, EcoRI sites of pET21d vector. Sequencing of several inserts revealed clones carrying the correct sequence. Expression protein starts with Met-Asp instead of Met-Asn, as it is in MK1450.  
         [0000]     Expression and Purification of Inorganic Pyrophosphatase Ppa  
         [0144]      E. coli  strain BL21 pLysS (Novagen) was transformed with expression plasmid. LB medium (2 L) containing 100 μg/ml ampicillin and 34 μg/ml chloramphenicol was inoculated with transformed cells, and the protein expression was induced by adding 1 mM isopropylthio-β-galactoside (IPTG) and carried out at 37° C. for 3 hours. The cells were harvested and dissolved in 60 ml lysis buffer containing 50 mM Tris-HCl pH 8.0, 0.6 M NaCl, 1 mM EDTA, 5 mM β-mercaptoethanol, and protease inhibitors (Roche). The lysate was centrifuged at 38000 g for 20 minutes, heated at 75° C. for 30 minutes, and centrifuged again at 38000 g for 30 minutes. The supernatant was filtered through a 0.22 μm Millipore filter, diluted to 0.25 M NaCl and applied on a Q-Sepharose column (1.6×17 cm), equilibrated with 50 mM Tris pH 8.0, containing 0.25 M NaCl and 2 mM MgCl 2 . After washing with the same buffer Ppa was eluted with linear gradient of 0.25-1.0 M NaCl. Fractions containing Ppa were pooled, concentrated by Centriprep, followed by Centricon YM-30, and passed through a Superdex 200 (1.0×30 cm), equilibrated with 50 mM Tris-HCl pH 8.0, containing 0.15M NaCl and 2 mM MgCl 2 .  
         [0145]     Shown in  FIG. 9  is the expression and purification of Ppa from  E. coli  cells. Cell lysate before induction (lane 2), cell lysate after induction (lane 3) and purified protein (lane 4) were analyzed by SDS-PAGE (10% gel) and visualized by Coomassie Blue G-250. Lane 1 is molecular size marker 10-225 kDa (Novagen).  
         [0000]     Ppa Activity  
         [0146]     Purified Ppa has high activity at both 20° C. and 75° C. using potassium pyrophosphate as a substrate in the presence of MgCl 2 . The specific activity of the enzyme is about 250 μM min −1  mg −1  at 20° C. and 1440 μM min −1 mg −1  at 75° C.  
         M. kandleri  Replication Factor C Small Subunit RFC-S (MK0006)  
       [0000]     Construction of an Expression Vector for RFC-S  
         [0000]     pET21d-M.ka-AV19-RFC-S:  
         [0147]     1905 bp RFC-S cds (containing an intein) was PCR-amplified from  M. kandleri  (av19) genomic DNA using following primers:  
                                                                 (SEQ ID No.:1707)                    5′-ATACTGCAGCCATGGCCGAGCACGAGCTACGCG               and                        (SEQ ID No.:1708)                    5′-ATAAAGCTTCTACCCGCCGGAGTACTCGTTACCGAGT.              
 
         [0148]     PstI+HindIII-digested PCR fragment (PstI, NcoI and HindIII sites were introduced in the primers) was cloned into PstI, HindIII sites of pUC19 vector. A pool of isolated plasmid DNAs was used for the next round of PCR aimed to remove intein sequence. Primers  
                                                                 (SEQ ID No.:1709)                    5′-GCGTTCAGCTCGAGGAAGTTGTCTCTCCA               and                        (SEQ ID No.:1710)                    5′-CTCCGATGAGAGGGGTATCGACGTAATTCG              
 
 were designed against the intein boundaries in the inverse orientation in order to amplify the cds region without the intein, but still containing the pUC19 sequence. The resulted PCR fragment (ca. 3.7 kb: 989 bp of cds lacking intein+2.7 kb of pUC19 sequence) was circularized, and after transformation of  E. coli  with this vector, several plasmid DNAs were isolated and sequenced. The correct insert carrying RFC-S cds without the intein was cut out from pUC19 vector DNA by double NcoI+HindIII digestion and cloned into the NcoI+HindIII-digested pET21d vector. 
 
 Expression and Purification of RFC-S. 
 
         [0149]      E. coli  strain BL21 pLysS (Novagen) was transformed with expression plasmid. LB medium (2 L) containing 100 μg/ml ampicillin and 34 μg/ml chloramphenicol was inoculated with transformed cells, and the protein expression was induced by adding 1 mM isopropylthio-β-galactoside (IPTG) and carried out at 37° C. for 3 hours. The cells were harvested and dissolved in 70 ml lysis buffer containing 50 mM Tris-HCl pH 8.0, 0.6M NaCl, 1 mM EDTA, 5 mM β-mercaptoethanol, and protease inhibitors (Roche). The lysate was centrifuged at 38,000 g for 20 minutes, heated at 75° C. for 30 minutes, and centrifuged again at 38,000 g for 30 minutes. The supernatant was filtered through a 0.22 μm Millipore filter, diluted to 0.25M NaCl and applied on a Q-Sepharose column (1.6×17 cm), equilibrated with 50 mM Tris pH 7.5, containing 0.25M NaCl and 2 mM ME. After washing with the same buffer RFC-S was eluted with linear gradient of 0.25-1.0 M.  
         [0150]     Shown in  FIG. 10  is the expression and purification of RFC-S from  E. coli  cells. Cell lysate before induction (lane 2), cell lysate after induction (lane 3) and purified protein (lane 4) were analyzed by SDS-PAGE (10% gel) and visualized by Coomassie Blue G-250. Lane 1 is molecular size marker 10-225 kDa (Novagen).  
         M. kandleri  Replication Factor C Large Subunit RFC-L (MK0006)  
       [0000]     Construction of an Expression Vector for RFC-L  
         [0000]     pET21d-M.ka-AV19-RFC-L:  
         [0151]     1539 bp RFC-L cds was PCR-amplified from  M. kandleri  (av19) genomic DNA using following primers:  
                                                                 (SEQ ID No.:1711)                    5′-AATCCATGGTAGCACCGTTGGTCCCTTGGGTTGA               and                        (SEQ ID No.:1712)                    5′-ATAAAGCTTCAGAAGAACGCGTCTAACGTCCTCTGTTCA.              
 
         [0152]     NcoI-incompletely digested and HindIII-digested PCR fragment (NcoI and HindIII sites were introduced in the primers; additional NcoI site is presented in the cds) was cloned into NcoI, HindIII sites of pET21d vector. Sequencing of several inserts revealed clones carrying the correct sequence. The expressed protein contains an additional Met at the N-terminus.  
         [0000]     Expression and Purification of RFC-L  
         [0153]      E. coli  strain BL21 pLysS (Novagen) was transformed with expression plasmid. LB medium (2 L) containing 100 μg/ml ampicillin and 34 μg/ml chloramphenicol was inoculated with transformed cells, and the protein expression was induced by adding 1 mM isopropylthio-β-galactoside (IPTG) and carried out at 37° C. for 3 hours. The cells were harvested and dissolved in 60 ml lysis buffer containing 50 mM Tris-HCl pH 8.0, 0.6M NaCl, 1 mM EDTA, 5 mM β-mercaptoethanol, and protease inhibitors (Roche). The lysate was centrifuged at 38000 g for 20 minutes, filtered through a 0.22 μm Millipore filter, diluted to 0.5M NaCl and applied on a heparin high trap 5 ml column (APB), equilibrated with 50 mM Tris pH 7.5, containing 0.5 M NaCl and 2 mM ME. After washing with the same buffer RFC-L was eluted with shallow linear gradient of 0.5-1.0 M NaCl. Shown in  FIG. 11  is the expression and purification of RFC-L from  E. coli  cells. Cell lysate before induction (lane 2), cell lysate after induction (lane 3) and purified protein (lane 4) were analyzed by SDS-PAGE (10% gel) and visualized by Coomassie Blue G-250. Lane 1 is molecular size marker 10-225 kDa (Novagen).  
         M. kandleri  AV 19 DNA Polymerase Family B (Mka PolB) (MK1039)  
       [0000]     Construction of Expression Vector  
         [0154]     PET21d-Mka-AV19-PolB: 2490 bp PolB cds was PCR-amplified from  M. Kandleri  AV19 genomic DNA using following primers:  
                                                                 (SEQ ID No.:1713)                    5′TATCCATGGGGTTGCTCCGTACAGTGTGGGTAGATTAGCG               and                        (SEQ ID No.:1714)                    5′CTAGAATTCAGCCGAAGAACTGATCCAGCGTCTT.              
 
         [0155]     NcoI+EcoRI-digested PCR fragment (NcoI and EcoRI sites were introduced in the primers) was cloned into NcoI, EcoRI sites of pET21d vector. Sequencing of several inserts revealed clones carrying the correct sequence. The PolB protein contains a dipeptide Met-Gly at its N-terminus.  
         [0000]     Expression and Purification of Mka PolB  
         [0156]      E. coli  strain BL21 pLysS (Novagen) was transformed with expression plasmid. LB medium (2 L) containing 100 μg/ml ampicillin and 34 μg/ml chloramphenicol was inoculated with transformed cells, and the protein expression was induced by adding 1 mM isoprophylthio-β-galactoside (IPTG) and carried out at 37° C. for 3 hours. The cells were harvested and dissolved in 75 ml lysis buffer containing 50 mM Tris-HCl pH 8.0, 0.6 M NaCl. 1 mM EDTA, 5 mM β-mercaptoethanol, and protease inhibitors (Roche). The lysate was centrifuged at 38,000 g for 20 minutes, filtered through a 0.22 μm Millipore filter, diluted to 0.5M NaCl and applied on a heparin high trap 5 ml column (APB), equilibrated with 50 mM Tris pH 8.0, containing 0.5 M NaCl and 2 mM ME. After washing with the same buffer Pol B was eluted with 50 mM Tris pH 8.0, containing 0.75 M NaCl and 2 mM ME.  
         [0157]     Shown in  FIG. 12  is the expression and purification of PolB from  E. coli  cells. Cell lysate before induction (lane 2), cell lysate after induction (lane 3) and purified protein (lane 4) were analyzed by SDS-PAGE (10% gel) and visualized by Coomassie Blue G-250. Lane 1 is molecular size marker 10-225 kDa (Novagen).  
         [0000]     DNA Polymerase Activity of PolB  
         [0158]     A primer extension assay was applied with a fluorescent duplex substrate containing a primer-template junction (PTJ). The duplex shown in  FIG. 18  was prepared by annealing a 5′-end labeled with fluorescein 20-nt long primer with a 40-nt long template:  
         [0159]     DNA polymerase reaction mixtures (15-20 μl) contained dATP, dTTP, dCTP, and dGTP (1 mM each), 4.5 mM MgCl 2 , detergents Tween 20 and Nonidet P-40 (0.2% each), fixed concentrations of PTJ—duplex, other additions, as indicated, and appropriate amounts of polB in 30 mM Tris-HCl buffer pH 8.0 (25° C.). The background reaction mixtures contained all components except DNA polymerases. Primer extensions were carried out for a preset time at 75° C. in PTC-150 Minicycler (MJ Research, Inc.; Waltham, Mass.). 5 μl samples were removed and chilled to 4° C. followed by immediate addition of 20 μl of 20 mM EDTA. The samples were desalted by centrifugation through Sephadex G-50 spun columns, diluted, and analyzed on a ABI Prism 377 DNA sequencer (Applied BioSystems; Foster City, Calif.). For each sample, raw data were extracted from the sequencer trace files with the program Chromas 1.5 (Technelysium Pty Ltd., Australia), and the fluorescent signals were analyzed by our nonlinear regression data analysis programs written in Fortran. The programs applied Powell algorithms to approximate the signals by a number of Gaussian peaks and calculate integral fluorescent intensities for each product peak. The total amount of fluorescent products for each time of incubation was determined, and the initial rates of extension were calculated. PolB was found to carry out DNA synthesis at various conditions of primer extension assay.  
         [0000]     Studies of Thermostability of pol B DNA Polymerase  
         [0160]     To determine DNA polymerase activity and thermostability of DNA polymerase polB in various media. Proteins in 25 μl of 20 mM Tris-HCl buffer (pH 8.0 at 25° C.) containing indicated concentrations of salts and betaine were incubated in PTC-150 Minicycler (MJ Research) at 95° C. or 100° C. 4 μl samples were removed at defined times of incubation and assayed for primer extension activity. These activities and stabilities are shown in  FIG. 13 .  
         [0161]     As demonstrated in  FIG. 14 , 1 M Betaine was found to stabilize specifically polB DNA polymerase in the presence of potassium glutamate at 100° C. The stabilizing effect of betaine is diminished in the presence of organic solvents DMSO and formamide.  
         [0162]     It was found that potassium glutamate specifically activates polB DNA polymerase and produces about twenty-fold increase of polymerase activity at 0.8 M of the salt. See  FIG. 15 .  
         [0163]     Studies of Processivity of Pol B DNA Polymerase  
         [0164]     For processivity assays, the primer extension reactions were carried out and analyzed as described above, but after determination of the amount of extended products, the initial rates for appearance of each extended primer were calculated. Then the processivity for each position of the template was determined using equation:  
           p   n     =         ∑     i   =   1         n   max     -   n       ⁢     v   ⁡     (     I     n   +   i       )             ∑     i   =   0         n   max     -   n       ⁢     v   ⁡     (     I     n   +   i       )             ,       where   ⁢           ⁢     v   ⁡     (     I     n   +   i       )         =       ⅆ     I     n   +   i           ⅆ   t         ,       
 
 initial rate of appearance for each extended product, and the processivity equivalence parameter, P e , was calculated for each reaction. Results for various concentrations of potassium glutamate are shown above. 
 
         [0165]     Exonucleasease Activity of PolB  
         [0166]     A 3′→5′ exonuclease activity of polB polymerase was measured at the same conditions as in the primer extension assay, except omitting dideoxynucleotides. A fluorescent primer:  
                                           *FL-GTAATACGACTCACTATAGGG   (SEQ ID NO.:1715)              
 
 was incubated with the enzyme at defined times. Then, the amounts of formed products were calculated, and the initial rates of hydrolysis were found, as in case of primer extension. It is interesting that polB was able to cleave off only 9 nucleotides of the primer, that is, the 13-nt primer was the shortest substrate that polB could process. 
 
         [0167]     Performance of M.K. polB DNA Polymerase in Various Media.  
         [0168]     Initial rates of primer extension reactions shown below in Table 3 demonstrate abolishing of 3′→5′ exonuclease activity of M.K. polB DNA polymerase upon transformation of the enzyme into its glutamate form by buffer exchange on a Sephadex G50 column.  
                             TABLE 3                       Initial Rate of Primer Extension, μM/min                                    PolB; 0.5 M NaCl   0.123 ± 0.003           PolB; 0.5 M NaCl + PCNA   0.214 ± 0.014           PolB; 1 M KGlu   2.74 ± 0.18           PolB; 1 M KGlu; dUTP   1.82 ± 0.09           PolB; 1 M DPG   2.17 ± 0.16                      
 
         [0169]     The next two tables (Table 4 and 5) display effects of various media components on M.K. polB DNA polymerase activity. Initial rates of primer extension reaction were measured as described by Pavlov et al., 2002.  
                                               TABLE 4                           Initial Rate of Primer Extension, μM/min                0.5 M NaCl   1 M KGlu                            Pol; NaCl protein   0.15 ± 0.01   2.55 ± 0.31           Exo; NaCl protein   0.50 ± 0.06   1.07 ± 0.06           Pol; KGlu protein       2.74 ± 0.18           Exo; KGlu protein       0 ± 0                      
 
         [0170]    
       
         
               
             
               
               
               
             
               
               
               
             
           
               
                 TABLE 5 
               
             
             
               
                   
               
               
                   
               
               
                 Inhibition constants in different media 
               
             
          
           
               
                   
                 Chemical 
                 IC 50  (M) 
               
               
                   
                   
               
             
          
           
               
                   
                 NaCl 
                 0.55 
               
               
                   
                 KCl 
                 0.45 
               
               
                   
                 LiClO 4   
                 0.27 
               
               
                   
                 NH 4 Ac 
                 0.56 
               
               
                   
                 NH 4 OH 
                 &lt;0.03 
               
               
                   
                   
               
             
          
         
       
     
         [0171]     Conclusions: 
        1. KGlu inhibits the 3′-5′ exonuclease activity of Mka PolB, while NaCl stimulates it.     2. KGlu, diphosphoglycerate, and Mka PCNA (see below) increase the polymerase activity of PolB.     3. PolB can use dUTP for primer extensions.     4. PolB is resistant to aggressive chemicals.        
 
         [0176]     Activity of Mka PolB DNA Polymerase at Different Temperature  
                                           TABLE 6                           Initial Rate of Primer Extension, μM/min                t° C.   Initial Rates                            50   1.01 ± 0.06           55   1.08 ± 0.09           60   1.12 ± 0.08           65   1.23 ± 0.05           70   1.01 ± 0.07           75   0.95 ± 0.07           80   0.92 ± 0.07           85   0.94 ± 0.07           90   0.71 ± 0.05           95   0.62 ± 0.04           100   0.62 ± 0.06           105   0.55 ± 0.09                      
 
 Table 6 illustrates the dependency of initial rates of primer extension for Duplex 2 shown in  FIG. 17  on temperature of the reaction. Initial rates of primer extension reaction were measured as described by Pavlov et al., 2002. 
 
         [0177]     As once can see from Table 6, Mka PolB can extend primers at temperatures up to 105° C., i.e. above the melting temperature of the duplex.  
         [0178]      FIG. 18  shows the amplification of 110 nt region of ssDNA M13mp18(+) with ALF M13 Universal fluorescent primer (Amersham Pharmacia Biotech) and primer caggaaacagctatgacc (M13 reverse) in the presence of 1 M potassium glutamate with polB DNA polymerase. Cycling: 100° C. for 40 seconds; 50° C. for 30 seconds; 72° C. for 2 minutes; 30 cycles (3, 4, 5 6). The products shown in  FIG. 18  were resolved on a 10% sequencing gel with ABI PRISM 377 DNA sequencer.  
         M. kandleri  AV19 PCNA (MK1030)  
       [0000]     Construction of an Expression Vector for Mka DNA Polymerase Sliding Clamp (PCNA)  
         [0179]     pET21a-MKA-PCNA: PCNA was PCR-amplified from  M. kandleri  genomic DNA using following primers:  
                                                                 (SEQ ID No.:1716)                    5′- ATCATTCATATGGTGGAGTTCAGGGCCTACCAG               and                        (SEQ ID No.:1717)                    5′- AGATATGAATTCAAGGAGGAAGGGTTCACTCCT              
 
         [0180]     NdeI+EcoRI-digested PCR fragment (NdeI and EcoRI sites were introduced in the primers) was cloned into NdeI, EcoRI sites of the pET21a vector. Sequencing of several inserts revealed clones carrying the correct sequence.  
         [0181]     Expression and Purification of PCNA  
         [0182]      E. coli  strain BL21 pLysS (Novagen) was transformed with expression plasmid. LB medium (2 L) containing 100 μg/ml ampicillin and 34 μg/ml chloramphenicol was inoculated with transformed cells, and the protein expression was induced by adding 1 mM isopropylthio-β-galactoside (IPTG) and carried out at 37° C. for 3 hours. The cells were harvested and dissolved in 50 ml lysis buffer containing 50 mM Tris-HCl pH 8.0, 0.6 M NaCl, 1 mM EDTA, 5 mM β-mercaptoethanol, and protease inhibitors (Roche). The lysate was centrifuged at 38,000 g for 20 minutes, filtered through a 0.22 μm Millipore filter, diluted to 0.25 M NaCl and applied on a heparin high trap 5 ml column (APB), equilibrated with 50 mM Tris pH 8.0, containing 0.25 M NaCl and 2 mM ME. PCNA was eluted with the same buffer. Fractions containing PCNA were pooled, concentrated by Centriprep, followed by Centricon YM-30, and passed through a Superdex 200 (1.0×30 cm), equilibrated with 50 mM Tris-HCl pH 8.0, containing 0.5M NaCl and 2 mM MgCl 2 .  
         [0183]     Expression and purification of PCNA from  E. coli  cells is shown in  FIG. 19 . Cell lysate before induction (lane 2), cell lysate after induction (lane 3) and purified protein (lane 4) were analyzed by SDS-PAGE (10% gel) and visualized by Coomassie Blue G-250. Lane 1 is molecular size marker 10-225 kDa (Novagen).  
         [0000]     Interaction of polB with PCNA.  
         [0184]     PolB was incubated with PCNA (final concentration 5.6 μM subunits) in the presence of 100 mM NaCl. The polymerase activity was measured in the primer extension assay and compared to the activity without PCNA added. Even without clamp loader, the interaction of PCNA with PolB was detected as the initial rate of the primer extension increased 1.75 times. The most remarkable, however, was suppression of hydrolysis of the primer annealed to the duplex that occurs as the combined result of 3′-5′ exonuclease activity of polB, its sliding along PTJ, and partial melting of the duplex substrate in the active site of the enzyme shown in  FIG. 20 . This happens, most likely because PCNA anchors polB on the PTJ and/or prevents partial melting of the PTJ duplex.  
         M. kandleri  AV19 DNA topoisomerase IA (Topo I) (MK1604)  
       [0000]     Construction of an Expression Vector for Topo I  
         [0000]     pET21d-M.ka-AV19-Top1:  
         [0185]     1761 bp Top1 cds was PCR-amplified from  M. kandleri  genomic DNA using following primers:  
                                                                 (SEQ ID No.:1718)                    5′-TATCCATGGCCTCGTCGTCGAAGGAGACG               and                        (SEQ ID No.:1719)                    5′-TTAGAATTCAGACCACCTTGGCTGACTTCAACTTCTTG.              
 
         [0186]     NcoI+EcoRI-digested PCR fragment (NcoI and EcoRI sites were introduced in the primers) was cloned into NcoI, EcoRI sites of pET21d vector. Sequencing of several inserts revealed clones carrying the correct sequence.  
         [0187]     Expression, Purification, and Activity of Topo I  
         [0188]      E. coli  strain BL21 pLysS (Novagen) was transformed with expression plasmid. LB medium (2 L) containing 100 μg/ml ampicillin and 34 μg/ml chloramphenicol was inoculated with transformed cells, and the protein expression was induced by adding 1 mM isopropylthio-β-galactoside (IPTG) and carried out at 37° C. for 3 hours. The cells were harvested and dissolved in 50 ml lysis buffer containing 50 mM Tris-HCl pH 8.0, 0.6 M NaCl, 1 mM EDTA, 5 mM β-mercaptoethanol, and protease inhibitors (Roche). The lysate was centrifuged at 38000 g for 20 minutes, filtered through a 0.22 μm Millipore filter, diluted to 0.5 M NaCl and applied on a heparin high trap 5 ml column (APB), equilibrated with 50 mM Tris pH 8.0, containing 0.5 M NaCl and 2 mM ME. After washing the column with 50 mM Tris pH 8.0, containing 0.75 M NaCl and 2 mM ME, Topo I was eluted with 1.4 M NaCl in the same buffer.  
         [0189]     Expression and purification of Topo I from  E. coli  cells is shown in  FIG. 21 . Cell lysate before induction (lane 2), cell lysate after induction (lane 3) and purified protein (lane 4) were analyzed by SDS-PAGE (10% gel) and visualized by Coomassie Blue G-250. Lane 1 is molecular size marker 10-225 kDa (Novagen).  
         [0190]     Relaxation of closed circular pBR322 DNA by Mka Topo I in 100 mM NaCl (lane 2) and 1 M KGlu (lane 5) at 80° C. shown in  FIG. 22 . Topo I was incubated with DNA for 10 min. Topoisomers were separated in a 1% agarose gel.  
         M. kandleri  AV19 ATP-Dependent Helicase MCM2 — 2 (MK1120)  
       [0000]     Construction of an Expression Vector for MCM2 — 2  
         [0000]     PET21d-M.ka-AV19-MCM2 — 2:  
         [0191]     1179 bp MCM-2 cds was PCR-amplified from  M. kandleri  (av19) genomic DNA using following primers:  
                                                                 (SEQ ID No.:1720)                    5′-CCATCGGTTCCGGAGGGTAGAGAGAATACG               and                        (SEQ ID No.:1721)                    5′-ATTGAATTCGACTCAGGGTTTGAGCGACGAGATCCTG.              
 
 NcoI-incompletely digested and EcoRI-digested PCR fragment (2 NcoI sites are presented in the coding region of MCM-2 gene, from the first NcoI site the cds begins: CCATGG; the EcoRI site was introduced in the primer) was cloned into NcoI, EcoRI sites of pET21d vector. Sequencing of several inserts revealed clones carrying the correct sequence. 
 
         [0192]     Expression of MCM2 — 2.  E. coli  strain BL21 pLysS (Novagen) was transformed with expression plasmid. LB medium (2 L) containing 100 μg/ml ampicillin and 34 μg/ml chloramphenicol was inoculated with transformed cells, and the protein expression was induced by adding 1 mM isopropylthio-β-galactoside (IPTG) and carried out at 37° C. for 3 hours. The cells were harvested and dissolved in 60 ml lysis buffer containing 50 mM Tris-HCl pH 8.0, 0.6M NaCl, 1 mM EDTA, 5 mM β-mercaptoethanol, and protease inhibitors (Roche). The lysate was centrifuged at 38,000 g for 20 minutes, heated at 75° C. for 30 minutes, and centrifuged again at 38,000 g for 30 minutes.  
         [0193]     Expression and purification of MCM2 — 2 from  E coli  cells is shown in  FIG. 23 . Cell lysate before induction (lane 2) and after induction (lane 3) were analyzed by SDS-PAGE (10% gel) and visualized by Coomassie Blue G-250. Lane 1 is molecular size marker 10-225 kDa (Novagen).  
         M. kandleri  AV19 Eukaryotic-Type DNA Primase P41P46 (MK0586 and MK1394)  
       [0000]     Construction of Expression Vectors for p41 and p46 Subunits  
         [0000]     pET21d-M.ka-AV19-p41:  
         [0194]     948 bp p41 cds was PCR-amplified from  M. kandleri  (av19) genomic DNA using following primers:  
                                                                 (SEQ ID No.:1722)                    5′-TTACCATGGACTTCTATTCGCCAACCTTCCACAGC               and                        (SEQ ID No.:1723)                    5′-TAAGAATTCACGGCTTAAGCTCCCCCAGCACC.              
 
         [0195]     NcoI+EcoRI-digested PCR fragment (NcoI and EcoRI sites were introduced in the primers) was cloned into NcoI, EcoRI sites of pET21d vector. Sequencing of several inserts revealed clones carrying the correct sequence. Expression protein should contain Met instead of Leu at its N-terminus.  
         [0000]     pET21d-M.ka-AV19-p46:  
         [0196]     1218 bp p46 short variant cds was PCR-amplified from  M. kandleri  (av19) genomic DNA using following primers:  
                                                                 (SEQ ID No.:1724)                    5′-TATCCATGGGCTCATGGTTCCCCCACGCCCC               and                        (SEQ ID No.:1725)                    5′-ATAGAATTCATCCGTCGTCGGCCCTAGGTCG.              
 
         [0197]     NcoI+EcoRI-digested PCR fragment (NcoI and EcoRI sites were introduced in the primers) was cloned into NcoI, EcoRI sites of pET21d vector. Sequencing of several inserts revealed clones carrying the correct sequence. Expression protein should contain Met-Gly instead of Leu-Arg at its N-terminus.  
         [0000]     Expression of p41  
         [0198]      E. coli  strain BL21 pLysS (Novagen) was transformed with expression plasmid. LB medium (2 L) containing 100 μg/ml ampicillin and 34 μg/ml chloramphenicol was inoculated with transformed cells, and the protein expression was induced by adding 1 mM isopropylthio-β-galactoside (IPTG) and carried out at 37° C. for 3 hours. The cells were harvested and dissolved in 50 ml lysis buffer containing 50 mM Tris-HCl pH 8.0, 0.6M NaCl, 1 mM EDTA, 5 mM β-mercaptoethanol, and protease inhibitors (Roche). The lysate was centrifuged at 38000 g for 20 minutes. The supernatant was filtered through a 0.22 μm Millipore filter.  
         [0000]     Expression of p46  
         [0199]      E. coli  strain BL21 pLysS (Novagen) was transformed with expression plasmid. LB medium (2 L) containing 100 μg/ml ampicillin and 34 μg/ml chloramphenicol was inoculated with transformed cells, and the protein expression was induced by adding 1 mM isopropylthio-β-galactoside (IPTG) and carried out at 37° C. for 3 hours. The cells were harvested and dissolved in 50 ml lysis buffer containing 50 mM Tris-HCl pH 8.0, 0.6M NaCl, 1 mM EDTA, 5 mM β-mercaptoethanol, and protease inhibitors (Roche). The lysate was centrifuged at 38,000 g for 20 min, heated at 75° C. for 30 minutes, and centrifuged again at 38,000 g for 30 minutes. The supernatant was filtered through a 0.22 μm Millipore filter.  
         [0200]     Purification of p41p46 Complex  
         [0201]     p41 lysate was mixed with p46 lysate approximately 1:1 according to SDS-PAGE, heated at 80° C. for 15 minutes, centrifuged at 38000 g for 15 min, and applied on Heparin-Sepharose Hi Trap 1 ml equilibrated with 50 mM Tris pH 7.5, containing 0.5 M NaCl and 2 mM ME. After washing with the same buffer p41p46complex was eluted with linear gradient of 0.5-1.0 M NaCl.  
         [0202]     Purification of P41P46 complex from  E. coli  cells is shown in  FIG. 24 . P41 cell lysate (lane 2), P46 cell lysate (lane 3), P41P46 complex before (lane 4) and after purification (lane 5) were analyzed by SDS-PAGE (10% gel) and visualized by Coomassie Blue G-250. Lane 1 is molecular size marker 10-225 kDa (Novagen).  
         [0000]     Assay of Primase Activity of p41p46.  
         [0203]     Primase activity assay for complex p41p46.50 ng/μl single stranded M13 DNA (Amersham) were incubated with complex p41p46 at 75° C. for 45 minutes in the presence of dNTPs (1 mM each) and MgCl 2  (4.5 mM). Then the mixture was desalted using Sephadex G-50 spin column and any primer-template junctions formed by the primase were labeled with fluorescent dideoxinucleotides using SnapShot kit (ABI). The products were desalted with Sephadex G-50 spin columns and resolved on a sequencing gel using ABI 377 sequencer shown in  FIG. 25 .  
         [0204]     The foregoing description is considered as illustrative only of the principles of the invention. The words “comprise,” “comprising,” “include,” “including,” and “includes” when used in this specification and in the following claims are intended to specify the presence of one or more stated features, integers, components, or steps, but they do not preclude the presence or addition of one or more other features, integers, components, steps, or groups thereof. Furthermore, since a number of modifications and changes will readily occur to those skilled in the art, it is not desired to limit the invention to the exact construction and process shown described above. Accordingly, all suitable modifications and equivalents may be resorted to falling within the scope of the invention as defined by the claims which follow. 
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
         
 
                                                                                     TABLE 1                                       No. of                       SEQ ID               Amino           Homology   Functional       NO.   Start   Stop   Strand   Acids   Gene   Function   Group   Class                                0001   748   1806   −   352   RCL1   RNA 3′-terminal phosphate cyclase   COG0430   [A]       0002   1888   2403   −   171   IbpA   Molecular chaperone (small heat   COG0071   [O]                               shock protein)       0003   2357   3415   −   352       Predicted GTPase   COG1084   [R]       0004   3490   3807   +   105   RPP1A   Ribosomal protein   COG2058   [J]                               L12E/L44/L45/RPP1/RPP2       0005   3811   5343   −   510       Replication factor C (ATPase   COG0470   [L]                               involved in DNA replication)       0006   5349   7256   −   635       Replication factor C (ATPase   COG0470 &amp;   [L][L]                               involved in DNA replication) intein   COG1372                               containing       0007   7315   8682   −   455   TIP49   DNA helicase TIP49, TBP-interacting   COG1224   [K]                               protein       0008   8796   9161   +   121   DsrE   Uncharacterized conserved protein   COG1553   [P]                               involved in intracellular sulfur                               reduction       0009   9299   10450   +   383       Uncharacterized protein specific for                               M. kandleri, MK-36 family       0010   10400   11074   −   224       Predicted dinucleotide-utilizing   COG4015   [R]                               enzyme of the ThiF/HesA family       0011   11167   12018   +   283   Mtd   F420 dependent N5,N10-   COG1927   [C]                               methylenetetrahydromethanopterin                               dehydrogenase       0012   11999   12547   −   182       Uncharacterized protein conserved   COG4016   [S]                               in archaea       0013   12672   13748   +   358   Hmd   H2-forming N5,N10-   COG4074   [C]                               methylenetetrahydromethanopterin                               dehydrogenase       0014   13791   14549   +   252       Uncharacterized protein conserved   COG4017   [S]                               in archaea       0015   14518   15279   +   253       Uncharacterized conserved protein   COG0327   [S]       0016   15236   16306   +   356       Biotin synthase and related enzymes   COG0502   [H]       0017   16252   17787   +   511       Uncharacterized protein conserved   COG4018   [S]                               in archaea, FLPA ortholog       0018   17781   18263   +   160       Uncharacterized protein conserved   COG4019   [S]                               in archaea       0019   18347   19369   +   340       Collagenase and related proteases   COG0826   [O]       0020   19326   19685   +   119       Predicted metal-binding protein       0021   20108   20878   −   256   Pnp   5′-methylthioadenosine   COG0005   [F]                               phosphorylase       0022   20875   21456   −   193   Cmk   Cytidylate kinase   COG1102   [F]       0023   21460   21801   −   113   RPL34A   Ribosomal protein L34E   COG2174   [J]       0024   21809   22345   −   178       Predicted membrane protein   COG1422   [S]       0025   22359   22934   −   191   AdkA   Archaeal adenylate kinase   COG2019   [F]       0026   22954   24330   −   458   SecY   Preprotein translocase subunit SecY   COG0201   [U]       0027   24397   24861   −   154   RplO   Ribosomal protein L15   COG0200   [J]       0028   24876   25325   −   149   RpmD   Ribosomal protein L30/L7E   COG1841   [J]       0029   25473   26153   −   226   RpsE   Ribosomal protein S5   COG0098   [J]       0030   26170   26778   −   202   RplR   Ribosomal protein L18   COG0256   [J]       0031   26782   27231   −   149   RPL19A   Ribosomal protein L19E   COG2147   [J]       0032   27295   27900   −   201       C4-type Zn finger   COG1779   [R]       0033   27917   28900   −   327       2-phosphoglycerate kinase &amp;   COG2074 &amp;   [G]                               Predicted small molecule binding   COG1827   [R]                               protein (contains 3H domain)       0034   28904   29251   −   115       Uncharacterized conserved protein   COG2450   [S]       0035   29245   30336   −   363       Uncharacterized conserved protein   COG3367   [S]       0036   30390   30980   −   196       GTPase SAR1 and related small G   COG1100   [R]                               proteins       0037   31183   31749   +   188       Predicted hydrolase of HD   COG1896   [R]                               superfamily       0038   31721   32782   +   353   PelA   Predicted RNA-binding protein   COG1537   [R]                               pelota       0039   33253   34011   −   252       RecA-superfamily ATPase   COG0467   [T]                               implicated in signal transduction       0040   34081   35229   +   382       Uncharacterized conserved protein   COG1602   [S]       0041   35263   37083   +   606       Uncharacterized conserved protein   COG1542   [S]       0042   37451   38404   −   317       Uncharacterized protein       0043   38495   39829   −   444       tRNA and rRNA cytosine-C5-   COG0144   [J]                               methylases       0044   40642   41649   −   335       Fe—S oxidoreductase similar to   COG1242   [R]                               Oxygen-independent                               coproporphyrinogen III oxidase (like                               hemN)       0045   41815   42918   +   367       Predicted GTPase of the YlqF family   COG1161   [R]       0046   43093   43638   +   181       SAM-dependent methyltransferase   COG0500   [QR]       0047   43671   44753   −   360       Pyruvate-formate lyase-activating   COG1180   [O]                               enzyme       0048   44786   45367   +   193       Uncharacterized conserved protein   COG1590   [S]       0049   45367   49032   +   1221   RgyB   Reverse gyrase, subunit B   COG1110   [L]       0050   49029   49949   +   306       Uncharacterized protein       0051   49918   50835   −   305       Predicted ATPase of the PP-loop   COG0037   [D]                               superfamily implicated in cell cycle                               control       0052   50862   51494   +   210   GlpG   Predicted membrane serine protease   COG0705   [R]                               of the Rhomboid superfamily       0053   51991   53284   +   431   AmtB   Ammonia permease   COG0004   [P]       0054   53306   53659   +   117       Nitrogen regulatory protein PII   COG0347   [E]       0055   53735   54652   −   305       Fe—S oxidoreductase   COG0731   [C]       0056   55284   55847   −   187       Uncharacterized protein conserved   COG1772   [S]                               in archaea       0057   55840   56433   −   197       Uncharacterized conserved protein   COG1628   [S]       0058   56430   56768   −   112   RPB11   DNA-directed RNA polymerase,   COG1761   [K]                               subunit L       0059   56784   57464   −   226       Uncharacterized protein conserved   COG3286   [S]                               in archaea       0060   57457   58047   −   196       Predicted RNA-binding protein   COG1096   [J]                               (consists of S1 domain and a Zn-                               ribbon domain)       0061   58044   59066   −   340   RecJ   Single-stranded DNA-specific   COG0608   [L]                               exonuclease       0062   59083   59697   −   204       Predicted RNA methylase   COG2263   [J]       0063   59694   59882   −   62       Zn-ribbon containing protein       0064   59908   60720   +   270       Uncharacterized protein       0065   60717   61094   −   125       Uncharacterized conserved protein   COG4744   [S]       0066   61097   61705   −   202   TolQ   Biopolymer transport proteins   COG0811   [U]       0067   61681   62895   −   404       Predicted transporter   COG4827   [R]       0068   62910   63524   −   204       Uncharacterized protein       0069   63592   63867   −   91       Uncharacterized protein       0070   63864   65960   −   698       Superfamily I DNA/RNA helicase   COG1112   [L]       0071   66184   66945   +   253       ATP-utilizing enzymes of the PP-   COG1606   [R]                               loop superfamily       0072   66957   68126   −   389       Uncharacterized protein specific for                               M. kandleri, MK-21 family       0073   68133   69011   −   292   NadA   Quinolinate synthase   COG0379   [H]       0074   69027   69896   −   289       Predicted metal-dependent   COG1831   [R]                               hydrolase of the urease superfamily       0075   69998   70933   +   311       Uncharacterized protein       0076   70930   71757   +   275       Uncharacterized domain specific for                               M. kandleri, MK-33 family       0077   71931   73088   +   385       Predicted GTPase or GTP-binding   COG1341   [R]                               protein       0078   73121   74119   +   332       Predicted carbohydrate kinase of the   COG4020   [S]                               FGGY family       0079   74116   74928   +   270   TyrA_1   Prephenate dehydratase   COG0077   [E]       0080   74941   75492   +   183   PorG_1   Pyruvate: ferredoxin oxidoreductase,   COG1014   [C]                               gamma subunit       0081   75485   75754   +   89   PorD   Pyruvate: ferredoxin oxidoreductase,   COG1144   [C]                               delta subunit       0082   75767   76918   +   383   PorA_1   Pyruvate: ferredoxin oxidoreductase,   COG0674   [C]                               alpha subunit       0083   76931   77821   +   296   PorB_1   Pyruvate: ferredoxin oxidoreductase,   COG1013   [C]                               beta subunit       0084   77794   78321   +   175       Fe—S-cluster-containing hydrogenase   COG1142   [C]                               component       0085   78242   79153   +   303   TtdA   Tartrate dehydratase alpha   COG1951   [C]                               subunit/Fumarate hydratase class I,                               N-terminal domain       0086   79158   79691   +   177   FumA   Tartrate dehydratase beta   COG1838   [C]                               subunit/Fumarate hydratase class I,                               C-terminal domain       0087   79695   80291   +   198   purO   Archaeal IMP cyclohydrolase   COG3363   [F]       0088   80293   82308   −   671       Predicted RNA-binding protein   COG1293   [K]                               homologous to eukaryotic snRNP       0089   82341   83522   −   393       FOG: CBS domain   COG0517   [R]       0090   83620   83895   +   91       Uncharacterized membrane protein,                               conserved in archaea       0091   83902   85701   +   599       Predicted ATPase, RNase L inhibitor   COG1245   [R]                               (RLI) homolog       0092   86099   86650   −   183       Predicted phosphoesterase   COG0622   [R]       0093   86682   87470   −   262       Uncharacterized conserved protein   COG4021   [S]       0094   87467   88255   −   262       Predicted dinucleotide-utilizing   COG1712   [R]                               enzyme       0095   88185   88820   −   211       Uncharacterized conserved protein   COG2428   [S]       0096   88832   89203   −   123       Uncharacterized conserved protein   COG1873   [S]       0097   89216   90763   +   515       Predicted carbamoyl transferase,   COG2192   [O]                               NodU family       0098   90768   91475   +   235   RibD   2,5-diamino-6-ribosylamino-4(3H)-   COG1985   [H]                               pyrimidinone 5′-phosphate                               reductase, riboflavin biosynthesis       0099   91472   91828   +   118       Zn-ribbon-containing protein       0100   91983   93164   +   393       Uncharacterized protein specific for                               M. kandleri, MK-36 family       0101   93378   93962   +   194   Tmk   Thymidylate kinase   COG0125   [F]       0102   93969   94385   +   138       Holliday junction resolvase, archaeal   COG1591   [L]                               type       0103   94354   95916   −   520   AsnB   Asparagine synthase (glutamine-   COG0367   [E]                               hydrolyzing)       0104   95989   98838   +   949       Uncharacterized protein specific for                               M. kandleri, MK-40 family       0105   98775   99845   −   356       Diverged homolog of ATP-                               dependent DNA ligase (eukaryotic                               ligase III)       0106   99868   101157   −   429   ThiC   Thiamine biosynthesis protein ThiC   COG0422   [H]       0107   101154   102512   −   452       Predicted diverged member of                               adenylate cyclase 3 family       0108   102514   103230   −   238       Uncharacterized protein conserved                               in archaea       0109   103269   104672   +   467   LysC   Aspartokinase   COG0527   [E]       0110   104669   105400   +   243       Uncharacterized protein       0111   105387   107522   −   711       Superfamily II helicase   COG1204   [R]       0112   107561   108058   +   165   PaaY   Carbonic   COG0663   [R]                               anhydrases/acetyltransferases,                               isoleucine patch superfamily       0113   108066   109103   −   345       Predicted sugar kinase of the   COG1548   [KG]                               RNAseH/HSP70 fold       0114   109078   110001   −   307       Predicted ATP-utilizing enzymes of   COG1821   [R]                               the ATP-grasp superfamily       0115   110027   111160   +   377       Uncharacterized conserved protein   COG1944   [S]       0116   111223   112113   −   296   Ftr_1   Formylmethanofuran:tetrahydromethanopterin   COG2037   [C]                               formyltransferase       0117   112165   113037   −   290   AroE   Shikimate 5-dehydrogenase   COG0169   [E]       0118   113009   113827   −   272       Calcineurin superfamily phosphatase   COG0622   [R]                               (nuclease) with Zn-cluster       0119   113841   114335   −   164   UbiC   4-hydroxybenzoate synthetase   COG3161   [H]                               (chorismate lyase)       0120   114352   115302   −   316       Uncharacterized archaeal coiled-coil   COG1340   [S]                               protein       0121   115299   115952   −   217   SerB   Phosphoserine phosphatase   COG0560   [E]       0122   115928   117214   −   428   GlyA   Glycine/serine   COG0112   [E]                               hydroxymethyltransferase       0123   117235   117816   +   193       Uncharacterized protein       0124   117823   118356   +   177       Ferredoxin domain containing   COG4739   [S]                               protein       0125   118374   118637   +   87       Zn-ribbon containing protein       0126   118826   120259   +   477       Kef-type K+ transport systems (NAD-   COG1226 &amp;   [P][R]                               binding component fused to domain   COG0618                               related to exopolyphosphatase)       0127   120262   122115   −   617   GlmS   glucosamine-fructose-6-phosphate   COG0449   [M]                               aminotransferase       0128   122121   123176   −   351       Acetylornithine   COG0624   [E]                               deacetylase/Succinyl-                               diaminopimelate desuccinylase and                               related deacylases       0129   123173   125095   −   640   GatE   Archaeal Glu-tRNAGln   COG2511   [J]                               amidotransferase subunit E                               (contains GAD domain)       0130   125187   125582   +   131   Ada   Methylated DNA-protein cysteine   COG0350   [L]                               methyltransferase       0131   125594   126139   +   181       Uncharacterized conserved protein   COG2029   [S]       0132   126133   127611   +   492   FrdB/   Succinate dehydrogenase/fumarate   COG0479 &amp;   [C][C]                           GlpC   reductase Fe—S protein   COG0247       0133   127591   128607   −   338   TruB   Pseudouridine synthase of the TruB   COG0130   [J]                               family       0134   128665   134793   −   2042       Cobalamin biosynthesis protein   COG1429   [H]                               CobN and related Mg-chelatases       0135   134868   136871   −   667       Terpene cyclase/mutase family                               protein       0136   137011   137391   −   126       Predicted transcriptional regulator   COG0640   [K]       0137   137551   138318   −   255       Uncharacterized conserved protein   COG2106   [S]       0138   138349   139011   +   220   ComB   2-phosphosulfolactate phosphatase   COG2045   [HR]       0139   139012   139761   +   249       Uncharacterized conserved protein,   COG1916   [S]                               PrgY homolog (pheromone                               shutdown protein)       0140   139843   140517   +   224       Uncharacterized protein conserved   COG1810   [S]                               in archaea       0141   140548   141339   −   263       Predicted permease   COG0730   [R]       0142   141415   141891   +   158       Universal stress protein UspA and   COG0589   [T]                               related nucleotide-binding proteins       0143   141888   142646   −   252       Predicted permease   COG0730   [R]       0144   142704   143494   −   263       Predicted ATPase of the PP-loop   COG0037   [D]                               superfamily implicated in cell cycle                               control       0145   143437   143949   +   170       Uncharacterized conserved protein   COG2410   [S]       0146   143918   146485   −   855       Predicted P-loop ATPase fused to an   COG1444   [R]                               acetyltransferase       0147   146611   147321   +   236       Uncharacterized protein conserved                               in archaea       0148   147400   148779   −   459       Selenocysteine-specific translation   COG3276   [J]                               elongation factor       0149   148789   149439   −   216       Uncharacterized membrane protein       0150   149446   150267   −   273       Uncharacterized protein conserved   COG4022   [S]                               in archaea       0151   150225   150746   +   173       Uncharacterized conserved protein   COG1720   [S]       0152   150700   152415   −   571   GRS1   Glycyl-tRNA synthetase, class II   COG0423   [J]       0153   152432   153412   −   326   SgbH   3-hexulose-6-phosphate synthase   COG0269   [G]       0154   153397   154548   −   383   TRM1_1   N2,N2-dimethylguanosine tRNA   COG1867   [J]                               methyltransferase       0155   154583   154855   −   90       Ribosomal protein L35AE/L33A   COG2451   [J]       0156   154883   156067   +   394       Predicted pyridoxal-phosphate-   COG0399   [M]                               dependent enzyme apparently                               involved in regulation of cell wall                               biogenesis       0157   156089   158347   +   752       Archaea-specific RecJ-like   COG1107   [L]                               exonuclease, contains DnaJ-type Zn                               finger domain       0158   158344   158832   −   162   SrtA   Sortase (surface protein   COG3764   [M]                               transpeptidase)       0159   158829   159656   −   275       Predicted membrane protein       0160   159680   160726   −   348       Uncharacterized protein conserved   COG1627   [S]                               in archaea       0161   160771   161502   −   243   PssA   Phosphatidylserine synthase   COG1183   [I]       0162   161509   162153   −   214   Psd   Phosphatidylserine decarboxylase   COG0688   [I]       0163   162159   162707   −   182       SAM-dependent methyltransferase   COG0500   [QR]       0164   162731   163357   +   208       GTPase SAR1 and related small G   COG1100   [R]                               proteins       0165   163354   163716   +   120       Uncharacterized protein conserved   COG3365   [S]                               in archaea       0166   163730   163984   +   84       Zn-ribbon containing protein   COG3364   [R]       0167   163989   164609   +   206       Uncharacterized protein conserved                               in archaea       0168   164625   165806   +   393   MreB   Actin-like ATPase involved in cell   COG1077   [D]                               morphogenesis       0169   165843   166553   +   236       Histidinol phosphatase and related   COG1387   [ER]                               hydrolases of the PHP family       0170   166637   167686   +   349       tRNA and rRNA cytosine-C5-   COG0144   [J]                               methylases       0171   167695   168651   +   318   HtpX   Zn-dependent protease with   COG0501   [O]                               chaperone function       0172   168617   169261   −   214       Predicted metal-dependent                               hydrolase       0173   169255   170073   −   272   HisF   Imidazoleglycerol-phosphate   COG0107   [E]                               synthase       0174   170173   170856   +   227       Uncharacterized conserved protein   COG2454   [S]       0175   170934   171410   +   158   TroR   Mn-dependent transcriptional   COG1321   [K]                               regulator       0176   171517   171996   +   159       Uncharacterized protein       0177   172421   172690   +   89       Predicted membrane protein       0178   172865   174169   −   434       Coenzyme F420-reducing   COG3259   [C]                               hydrogenase, alpha subunit       0179   174173   175090   −   305       Coenzyme F420-reducing   COG1941   [C]                               hydrogenase, gamma subunit       0180   175215   175787   +   190   CbiM   Cobalamin biosynthesis protein   COG0310   [P]                               CbiM       0181   175784   176476   +   230   CbiQ   ABC-type cobalt transport system,   COG0619   [P]                               permease component       0182   176505   177311   +   268   CbiO   ABC-type cobalt transport system,   COG1122   [P]                               ATPase component       0183   177298   177972   +   224       Protein similar to creatinine   COG1402   [R]                               amidohydrolase       0184   177969   178136   +   55       Uncharacterized protein       0185   178176   178400   +   74       Uncharacterized protein       0186   178822   179454   +   210   RnhB   Ribonuclease HII   COG0164   [L]       0187   179476   180135   +   219       Pyruvate-formate lyase-activating   COG1180   [O]                               enzyme       0188   180142   181521   +   459   Tgt   Queuine/archaeosine tRNA-   COG0343   [J]                               ribosyltransferase       0189   181481   182362   +   293   TRM1_2   N2,N2-dimethylguanosine tRNA   COG1867   [J]                               methyltransferase       0190   182418   184016   +   532       Uncharacterized protein conserved   COG1892   [S]                               in archaea       0191   184291   185067   −   258       Uncharacterized protein       0192   185064   187520   −   818   Chll/ChlD   Mg-chelatase subunit ChlI and Chld   COG1239 &amp;   [H][H]                               (MoxR-like ATPase and vWF   COG1240                               domain) similar to subunits of a Ni-                               chelatase for the biosynthesis of the                               Ni-containing coenzyme F430, which                               is essential for the production of                               methane in methanogens       0193   187517   188218   −   233   Nth_1   Predicted EndoIII-related   COG0177   [L]                               endonuclease       0194   188360   189619   −   419       HD superfamily phosphohydrolase   COG1078   [R]       0195   189564   190313   −   249       Uncharacterized conserved protein   COG2457   [S]       0196   190289   191185   −   298   CitG_1   Triphosphoribosyl-dephospho-CoA   COG1767   [H]                               synthetase       0197   191179   191640   −   153   PgpB   Membrane-associated phospholipid   COG0671   [I]                               phosphatase       0198   191625   192632   −   335   HemB   Delta-aminolevulinic acid   COG0113   [H]                               dehydratase       0199   192583   193491   +   302       Uncharacterized protein       0200   193462   194676   −   404   HemA   Glutamyl-tRNA reductase   COG0373   [H]       0201   194763   195011   +   82       Uncharacterized protein       0202   195008   195703   −   231   Mra1   Uncharacterized conserved protein   COG1756   [S]       0203   195719   196417   +   232       Predicted hydrolase of the HAD   COG0561   [R]                               superfamily       0204   196414   197445   +   343   RecJ_1   Single-stranded DNA-specific   COG0608   [L]                               exonuclease       0205   197414   199021   −   535   PyrG   CTP synthase (UTP-ammonia lyase)   COG0504   [F]       0206   199348   200073   +   241       Uncharacterized protein conserved   COG2122   [S]                               in archaea       0207   200076   200687   −   203       Predicted GTPase of the YihA family   COG0218   [R]       0208   200743   200916   −   57       Preprotein translocase subunit   COG4023   [U]                               Sec61beta       0209   201121   201396   +   91       Uncharacterized protein       0210   201559   202800   −   413       Diverged homolog of ATP-                               dependent DNA ligase (eukaryotic                               ligase III)       0211   202797   203468   −   223       Uncharacterized protein conserved   COG4024   [S]                               in archaea       0212   203539   204414   −   291       Uncharacterized membrane protein,   COG4025   [S]                               conserved in archaea       0213   204416   205297   −   293       Predicted hydrolase of the metallo-   COG2248   [R]                               beta-lactamase superfamily       0214   205420   205839   −   139       Predicted metal-dependent protease   COG1310   [R]                               of the PAD1/JAB1 superfamily       0215   205772   206662   −   296       Predicted membrane protein       0216   206731   207078   +   115       Predicted regulator of Ras-like   COG2018   [R]                               GTPase activity, member of the                               Roadblock/LC7/MgIB family       0217   207252   207995   +   247       Uncharacterized protein       0218   207997   208806   +   269       ATPase involved in chromosome   COG0455   [D]                               partitioning       0219   208803   209303   −   166       Predicted RNA-binding protein   COG2016   [J]                               containing PUA domain       0220   209340   209561   +   73   LSM1   Small nuclear ribonucleoprotein   COG1958   [K]                               (snRNP) homolog       0221   209582   209770   +   62   RPL37A   Ribosomal protein L37E   COG2126   [J]       0222   209784   210659   +   291       TOPRIM-domain-containing protein,   COG4026   [R]                               potential nuclease       0223   210649   211632   +   327   PepP   Xaa-Pro aminopeptidase   COG0006   [E]       0224   211590   212726   +   378   CobT   NaMN:DMB   COG2038   [H]                               phosphoribosyltransferase       0225   212723   213457   −   244       Uncharacterized membrane protein                               specific for M. kandleri, MK-4 family       0226   213461   214513   −   350   HypD   Hydrogenase maturation factor   COG0409   [O]       0227   214461   214739   −   92   HypC   Hydrogenase maturation factor   COG0298   [O]       0228   214814   215236   +   140       Uncharacterized conserved protein   COG1371   [S]       0229   215254   216432   +   392       Archaea-specific pyridoxal   COG1103   [R]                               phosphate-dependent enzyme       0230   216609   217232   +   207       Predicted RNA methylase       0231   217222   217764   −   180       Predicted transcriptional regulator   COG1318   [K]       0232   217843   218598   +   251       Predicted metal-dependent   COG1099   [R]                               hydrolase of the TIM-barrel fold       0233   218648   219319   +   223       Predicted dinucleotide-binding   COG2085   [R]                               enzyme       0234   219392   220681   +   429   UbiD   Predicted decarboxylase related 3-   COG0043   [H]                               polyprenyl-4-hydroxybenzoate                               decarboxylase       0235   220673   221713   −   346   PurA   Adenylosuccinate synthase   COG0104   [F]       0236   221605   223494   −   629       Uncharacterized protein       0237   223440   225296   −   618       Uncharacterized secreted protein       0238   225321   226688   +   455   GatA   Asp-tRNAAsn/Glu-tRNAGln   COG0154   [J]                               amidotransferase A subunit       0239   227527   227967   +   146       Predicted SAM-dependent   COG0500   [QR]                               methyltransferase       0240   228106   228978   −   290       ATPase involved in chromosome   COG0489   [D]                               partitioning       0241   229171   230037   −   288       Uncharacterized membrane protein,                               conserved in archaea       0242   230076   231260   +   394       Predicted membrane protein       0243   231242   232369   −   375       Fe—S oxidoreductase, related to   COG1625   [C]                               NifB/MoaA family       0244   232648   234678   −   676       Distinct Superfamily II helicase   COG1205   [R]                               family with a unique C-terminal                               domain including a metal-binding                               cysteine cluster       0245   234728   235990   +   420   CysH   3′-phosphoadenosine 5′-   COG4027 &amp;   [S][EH]                               phosphosulfate sulfotransferase   COG0175                               (PAPS reductase)/FAD synthetase                               fused to uncharacterized archaeal                               protein       0246   236115   236423   −   102   RpsJ   Ribosomal protein S10   COG0051   [J]       0247   236467   237738   −   423       Translation elongation factor EF-   COG5256   [J]                               1alpha (GTPase)       0248   237821   238774   −   317       Predicted dehydrogenase   COG0673   [R]       0249   238965   240974   −   669   HdrA_1   Heterodisulfide reductase, subunit A   COG1148   [C]       0250   241089   241838   −   249       Uncharacterized protein       0251   241914   242435   +   173   RplP   Ribosomal protein L16/L10E   COG0197   [J]       0252   242469   244781   +   770   PpsA   Phosphoenolpyruvate   COG0574   [G]                               synthase/pyruvate phosphate                               dikinase       0253   244787   245512   +   241       Predicted transcriptional regulator   COG1378   [K]       0254   245475   245990   −   171       Predicted HD superfamily hydrolase   COG1418   [R]       0255   246012   246296   −   94   EFB1   Translation elongation factor EF-   COG2092   [J]                               1beta       0256   246301   246495   −   64       Predicted Zn-ribbon-containing RNA-   COG2888   [J]                               binding protein with a function in                               translation       0257   246666   246899   −   77       Predicted redox protein, regulator of   COG0425   [O]                               disulfide bond formation       0258   247069   248334   +   421   HgdB   Benzoyl-CoA reductase/2-   COG1775   [E]                               hydroxyglutaryl-CoA dehydratase                               subunit, BcrC/BadD/HgdB       0259   248342   249646   −   434   FwdB_1   Formylmethanofuran dehydrogenase   COG1029   [C]                               subunit B       0260   249749   250504   −   251       Activator of 2-hydroxyglutaryl-CoA   COG1924   [I]                               dehydratase, contains a HSP70-                               class ATPase domain       0261   250695   251156   +   153       Uncharacterized membrane protein,                               conserved in archaea       0262   251171   251644   +   157       Predicted transporter component   COG2391   [R]       0263   251649   252227   +   192       Uncharacterized protein conserved                               in archaea       0264   252347   253048   +   233       Predicted sugar kinase   COG0063   [G]       0265   253054   255024   −   656   HdrA_2   Heterodisulfide reductase, subunit A,   COG1148   [C]                               polyferredoxin       0266   255031   256479   −   482       Coenzyme F420-reducing   COG3259   [C]                               hdrogenase, alpha subunit       0267   256476   257390   −   304       Coenzyme F420-reducing   COG1941   [C]                               hydrogenase, gamma subunit       0268   257387   257812   −   141   FlpD_1   Coenzyme F420-reducing   COG1908   [C]                               hydrogenase, delta subunit       0269   257952   259379   +   475       Predicted membrane protein       0270   259341   259781   −   146       Uncharacterized conserved protein   COG1617   [S]       0271   260022   261596   +   524   PheS   Phenylalanyl-tRNA synthetase alpha   COG0016   [J]                               subunit       0272   261597   262133   −   178       Uncharacterized protein       0273   262262   262552   +   96       Uncharacterized conserved protein   COG1872   [S]       0274   263009   263827   +   272       Uncharacterized protein       0275   263828   265357   −   509       Isopropylmalate/homocitrate/citramalate   COG0119   [E]                               synthase homolog       0276   265405   266217   −   270       Predicted P-loop ATPase/GTPase   COG4028   [R]       0277   266246   266977   +   243       Predicted Fe—S oxidoreductase   COG5014   [R]       0278   266967   268979   +   670       Predicted membrane protein, family                               MK-41 family       0279   269014   271053   +   679       Predicted membrane protein, family                               MK-41 family       0280   271207   272499   −   430   HemL   Glutamate-1-semialdehyde   COG0001   [H]                               aminotransferase       0281   272912   273337   −   141   RibH   Riboflavin synthase beta-chain   COG0054   [H]       0282   273412   274092   +   226   Pcm   Protein-L-isoaspartate   COG2518   [O]                               carboxylmethyltransferase       0283   274537   274878   +   113       Uncharacterized protein conserved   COG4043   [S]                               in archaea       0284   275404   276174   −   256       Metal-dependent hydrolases of the   COG1235   [R]                               beta-lactamase superfamily I       0285   276198   277166   −   322       Uncharacterized protein conserved   COG4079   [S]                               in archaea       0286   277208   278248   −   346       Pyruvate-formate lyase-activating   COG1180   [O]                               enzyme       0287   278245   278508   −   87   PaaD   Predicted metal-sulfur cluster   COG2151   [R]                               biosynthetic enzyme (MinD N-                               terminal domain family)       0288   278515   278901   −   128       Flavodoxins   COG0716   [C]       0289   278976   280052   −   358   RgyA   Reverse gyrase, subunit A   COG1110   [L]       0290   280321   280542   +   73       Uncharacterized protein       0291   280561   281142   −   193   DCD-   Deoxycytidine   COG0717   [F]                           DUT   deaminase/diphosphatase       0292   281158   282030   +   290       Predicted phosphohydrolase   COG1409   [R]       0293   282024   282554   −   176       Uncharacterized conserved protein   COG1641   [S]       0294   282582   283844   +   420       Uncharacterized membrane protein   COG3174   [S]       0295   283841   285190   −   449       tRNA/rRNA cytosine-C5-methylase   COG0144   [J]       0296   285197   285631   −   144       Predicted diguamylate cyclase,                               diverged member of the GGDEF                               superfamily       0297   285628   287196   −   522       Phosphoglycerate dehydrogenase   COG0111   [E]                               and related dehydrogenases       0298   287326   287943   −   205       Uncharacterized protein specific for                               M. kandleri, MK-1 family       0299   288089   289126   −   345       Uncharacterized secreted protein                               specific for M. kandleri, MK-3 family       0300   289372   290193   −   273       Uncharacterized protein       0301   290810   291202   +   130       Predicted RNA-binding protein                               containing PIN domain, a fragment       0302   291417   292477   +   353       Predicted RNA-binding protein                               containing PIN domain, a fragment       0303   292704   293645   +   313       Predicted cysteine protease of the   COG1305   [E]                               transglutaminase-like superfamily       0304   293608   294210   +   200       Uncharacterized protein       0305   294271   295311   +   346       Uncharacterized protein       0306   295669   296193   +   174       Uncharacterized protein       0307   296467   297540   +   357   FwdF_1   Probable formylmethanofuran   COG1145   [C]                               dehydrogenase subunit F, ferredoxin                               containing       0308   297654   298370   −   238       Uncharacterized protein       0309   298367   299322   −   321       ATPase involved in chromosome   COG1192   [D]                               partitioning       0310   299623   300867   −   414       Orphan DOD family homing   COG1372   [L]                               endonuclease       0311   302118   302261   −   47       Uncharacterized protein       0312   302397   303113   +   238       Uncharacterized protein specific for                               M. kandleri, MK-42 family       0313   303210   303731   +   173       Uncharacterized protein specific for                               M. kandleri, MK-22 family       0314   304168   305175   +   335   FocA   Transporter of the formate/nitrite   COG2116   [P]                               trasnporter family       0315   306790   307817   +   342       Predicted hydrolase of the metallo-   COG0595   [R]                               beta-lactamase superfamily, a                               fragment       0316   307991   308224   +   77       Uncharacterized protein       0317   309026   309403   −   125       Adenine-specific DNA methylase   COG1743   [L]                               containing a Zn-ribbon       0318   309400   310002   −   200       Adenine-specific DNA methylase   COG1743   [L]                               containing a Zn-ribbon       0319   310314   310514   −   66       Phosphoglycerate dehydrogenase   COG0111   [E]                               and related dehydrogenases       0320   310502   311260   −   252   SerA   Phosphoglycerate dehydrogenase   COG0111   [E]                               and related dehydrogenases       0321   311717   313774   +   685   FdhA   Selenocysteine-containing anaerobic   COG0243   [C]                               formate dehydrogenase, subunit                               alpha       0322   313780   314913   +   377       Coenzyme F420-reducing   COG1035   [C]                               hydrogenase, beta subunit       0323   315226   315678   +   150   Fwd_F2   Probable formylmethanofuran   COG1145   [C]                               dehydrogenase subunit F, ferredoxin                               containing       0324   315855   316253   −   132       Fragment of predicted                               dehydrogenase related to                               phosphoglycerate dehydrogenase       0325   316385   316765   −   126       Uncharacterized protein specific for                               M. kandleri, MK-1 family       0326   316791   318491   +   566       Uncharacterized protein specific for                               M. kandleri, MK-5 family       0327   318525   319349   +   274       Predicted membrane protein       0328   319527   320099   +   190       Predicted membrane protein       0329   320696   321142   +   148       Predicted membrane protein       0330   321611   322570   −   319       Uncharacterized secreted protein                               specific for M. kandleri, MK-30 family       0331   323201   323818   +   205       Uncharacterized protein specific for                               M. kandleri, MK-1 family       0332   324061   324486   −   141       Uncharacterized protein conserved   COG4029   [S]                               in archaea       0333   324530   325426   +   298   ThrB   Homoserine kinase   COG0083   [E]       0334   325541   326770   −   409   CbiD   Cobalamin biosynthesis protein CbiD   COG1903   [H]       0335   326767   327753   −   328   GCN3   Translation initiation factor eIF-2B   COG0182   [J]                               alpha subunit       0336   327856   328425   +   189       Uncharacterized protein       0337   328419   329402   −   327       Predicted transcriptonal regulator   COG1693   [S]                               consisting of wHTH DNA-binding                               domain and an uncharacterized                               domain conserved in archaea       0338   329455   330930   −   491   GlnA   Glutamine synthetase   COG0174   [E]       0339   330946   332115   +   389       Predicted membane protein       0340   332123   333190   −   355       Predicted Fe—S oxidoreductase   COG1244   [R]       0341   333200   333739   +   179   SEN2_1   tRNA splicing endonuclease   COG1676   [J]       0342   333753   333998   +   81       Predicted transcriptional regulator                               containing DNA-binding HTH domain       0343   334027   335151   +   374   TrpS   Tryptophanyl-tRNA synthetase   COG0180   [J]       0344   335153   336226   +   357       Predicted 23S rRNA methylase   COG1818 &amp;   [R][J]                               containing THUMP domain   COG0293       0345   336446   336976   +   176       Uncharacterized protein       0346   336954   337934   +   326       Uncharacterized protein conserved   COG4030   [S]                               in archaea       0347   337941   339344   −   467       Predicted ABC-type ATPase   COG3044   [R]       0348   339352   339930   −   192       Uncharacterized protein       0349   339944   340672   −   242       Uncharacterized protein       0350   340738   340962   +   74       Uncharacterized protein conserved   COG1531   [S]                               in archaea       0351   340922   341869   −   315       Predicted DNA-binding protein   COG1571   [R]                               containing a Zn-ribbon       0352   341898   342389   +   163       Uncharacterized protein       0353   342379   343095   −   238       Uncharacterized domain conserved   COG4031   [R]                               in archaea fused to a metal-binding                               domain       0354   343122   343445   +   107       Uncharacterized protein       0355   343442   344674   −   410   HMG1   Hydroxymethylglutaryl-CoA   COG1257   [I]                               reductase       0356   345316   345639   −   107       Predicted membrane protein       0357   345630   346286   −   218       Peroxiredoxin, predicted regulator of   COG0425 &amp;   [O]                               disulfide bond formation   COG2044   [R]       0358   346686   347828   −   380       Ferredoxin fused to an   COG1900 &amp;   [S][C]                               uncharacterized conserved domain   COG1146       0359   348126   348380   −   84   GatC   Asp-tRNAAsn/Glu-tRNAGln   COG0721   [J]                               amidotransferase C subunit       0360   348428   349369   −   313   AmpS   Leucyl aminopeptidase   COG2309   [E]                               (aminopeptidase T)       0361   349585   350058   −   157       Archaeal riboflavin synthase   COG1731   [H]       0362   350055   351050   −   331       Predicted metal-binding protein,                               conserved in archaea       0363   351081   352025   +   314   GuaA_1   PP-ATPase subunit of GMP   COG0519   [F]                               synthase       0364   352038   352766   +   242   HisA   Phosphoribosylformimino-5-   COG0106   [E]                               aminoimidazole carboxamide                               ribonucleotide (ProFAR) isomerase       0365   352763   353614   −   283   HisG   ATP phosphoribosyltransferase   COG0040   [E]       0366   353673   354968   +   431       Predicted metal-dependent   COG0402   [FR]                               hydrolase related to cytosine                               deaminase       0367   355449   356759   −   436       Uncharacterized protein conserved                               in archaea       0368   356998   358272   +   424       S-adenosylhomocysteine hydrolase   COG0499   [H]       0369   358478   358597   +   39       Uncharacterized protein       0370   359581   360552   +   323       tRNA/rRNA cytosine-C5-methylase   COG0144   [J]       0371   360613   361065   +   150       Uncharacterized protein       0372   361116   362186   −   356   MurG   UDP-N-acetylglucosamine:LPS N-   COG0707   [M]                               acetylglucosamine transferase       0373   362211   363419   +   402       Predicted GTPase, probable   COG0012   [J]                               translation factor       0374   363447   363887   +   146       Uncharacterized protein       0375   364113   364475   −   120   GimC   Prefoldin, chaperonin cofactor   COG1382   [O]       0376   364476   364727   −   83       Uncharacterized protein conserved   COG2892   [S]                               in archaea       0377   364743   365321   −   192   IMP4   Predicted exosome subunit   COG2136   [J]                               containing the IMP4 domain present                               in small nuclear ribonucleoprotein       0378   365318   365473   −   51   RPC10   DNA-directed RNA polymerase   COG1996   [K]                               subunit RPC10 (contains C4-type                               Zn-finger)       0379   365476   365745   −   89   RPL43A   Ribosomal protein L37AE/L43A   COG1997   [J]       0380   365802   366605   −   267       Predicted exosome subunit,   COG2123   [J]                               predicted exoribonuclease related to                               RNase PH       0381   366607   367326   −   239   Rph   Predicted exosome subunit, RNase   COG0689   [J]                               PH       0382   367335   368054   −   239   RRP4   Predicted exosome subunit, RNA-   COG1097   [J]                               binding protein Rrp4 (contain S1                               domain and KH domain)       0383   368062   369129   −   355       Predicted hydrolase related to   COG1363   [G]                               cellulase M       0384   369130   369852   −   240       Predicted exosome subunit   COG1500   [J]       0385   369855   370595   −   246   HslV_1   Protease subunit of the proteasome   COG0638   [O]       0386   370595   371089   −   164   POP5   Predicted exosome subunit, RNase   COG1369   [J]                               P subunit P14       0387   371086   371820   −   244   RPP30   Ribonuclease P subunit Rpp30   COG1603   [J]       0388   371817   372278   −   153       Predicted exosome subunit   COG1325   [J]       0389   372312   372905   −   197   RPL15A   Ribosomal protein L15E   COG1632   [J]       0390   372970   373710   −   246       Predicted HD-superfamily hydrolase   COG3481   [R]       0391   373774   375273   +   499       Isopropylmalate synthase   COG0119   [E]       0392   375270   376295   −   341   ComC   L-sulfolactate dehydrogenase   COG2055   [C]       0393   376299   376865   −   188   ComE   Sulfopyruvate decarboxylase, beta   COG0028   [EH]                               subunit       0394   376933   377703   +   256   ComA   (2R)-phospho-3-sulfolactate   COG1809   [S]                               synthase (PSL synthase)       0395   377707   378210   +   167   ComD   Sulfopyruvate decarboxylase, alpha   COG4032   [R]                               subunit       0396   378195   379127   −   310       SAM-dependent methyltransferase   COG0500   [QR]       0397   379182   379682   −   166   SEN2_2   tRNA splicing endonuclease   COG1676   [J]       0398   379633   379872   −   79       Ribosomal protein S4 and related   COG0522   [J]                               proteins       0399   379869   380348   −   159       Uncharacterized protein conserved   COG1931   [S]                               in archaea       0400   380305   380895   −   196   CoaE   Dephospho-CoA kinase   COG0237   [H]       0401   380949   382022   −   357       Uncharacterized conserved protein   COG1415   [S]       0402   382222   383223   +   333       Predicted RNA-binding protein   COG1818   [R]                               containing THUMP domain       0403   383306   384133   +   275   TrpA   Tryptophan synthase alpha chain   COG0159   [E]       0404   385121   386080   −   319   ECM27_1   Ca2+/Na+ antiporter   COG0530   [P]       0405   386095   386403   +   102       Zn-ribbon-containing protein       0406   386375   386872   +   165   MobA   Molybdopterin-guanine dinucleotide   COG0746   [H]                               biosynthesis protein A       0407   386862   388859   −   665       Uncharacterized protein conserved   COG2433   [S]                               in archaea       0408   388923   389306   +   127       Uncharacterized membrane   COG1714   [S]                               protein/domain       0409   389293   389832   −   179       Predicted intracellular   COG0693   [R]                               protease/amidase       0410   389846   390271   +   141       Uncharacterized protein conserved   COG4081   [S]                               in archaea       0411   390268   390561   +   97       Uncharacterized protein conserved   COG4033   [S]                               in archaea       0412   390558   391289   −   243   RplB   Ribosomal protein L2   COG0090   [J]       0413   391302   391589   −   95   RplW   Ribosomal protein L23   COG0089   [J]       0414   391593   392375   −   260   RplD   Ribosomal protein L4   COG0088   [J]       0415   392390   393475   −   361   RplC   Ribosomal protein L3   COG0087   [J]       0416   393619   394368   +   249       Uncharacterized protein       0417   394373   394654   +   93   RPL42A   Ribosomal protein L44E   COG1631   [J]       0418   394669   394890   +   73   RPS27A   Ribosomal protein S27E   COG2051   [J]       0419   394890   395693   +   267   SUI2   Translation initiation factor elF2-   COG1093   [J]                               alpha       0420   395697   395897   +   66       Predicted Zn-ribbon-containing RNA-   COG2260   [J]                               binding protein       0421   395901   396710   +   269       Uncharacterized enzyme of the ATP-   COG2047   [R]                               grasp superfamily       0422   397017   397583   +   188       Uncharacterized membrane protein       0423   397587   398081   +   164       Uncharacterized membrane protein,   COG4083   [S]                               conserved in archaea       0424   398083   399336   +   417       Uncharacterized conserved protein   COG1379   [S]       0425   399333   400784   +   483       Predicted metal-dependent                               hydrolase of the TIM-barrel fold       0426   400786   401517   +   243       Predicted metal-dependent   COG2159   [R]                               hydrolase of the TIM-barrel fold       0427   401719   402249   +   176       Uncharacterized conserved protein       0428   402254   402685   +   143       Uncharacterized conserved protein   COG2138   [S]       0429   402699   403346   +   215   AroD   3-dehydroquinate dehydratase   COG0710   [E]       0430   403335   404072   −   245       Flavoprotein involved in thiazole   COG1635   [H]                               biosynthesis       0431   404095   404466   −   123       Uncharacterized protein conserved                               in archaea       0432   404463   404834   −   123       Uncharacterized protein       0433   404865   405650   −   261   SurE   Predicted acid phosphatase   COG0496   [R]       0434   405568   406407   −   279   DapF   Diaminopimelate epimerase   COG0253   [E]       0435   406436   407173   −   245   DapD   Tetrahydrodipicolinate N-   COG2171   [E]                               succinyltransferase       0436   407170   407748   −   192   PabA   Anthranilate/para-aminobenzoate   COG0512   [EH]                               synthase component II       0437   407723   409129   −   468   TrpE   Anthranilate/para-aminobenzoate   COG0147   [EH]                               synthase component I       0438   409120   409710   −   196       Uncharacterized membrane protein   COG1300   [S]       0439   409925   411559   −   544       Phenylalanyl-tRNA synthetase alpha   COG2024   [J]                               subunit, archaeal type       0440   411681   412184   +   167       Uncharacterized protein       0441   412195   412410   +   71       Uncharacterized protein       0442   412377   413771   +   464       Uncharacterized protein       0443   413745   414398   −   217       Predicted RNA-binding protein of the   COG2178   [J]                               translin family       0444   414419   415777   −   452       tRNA/rRNA cytosine-C5-methylase   COG0144   [J]       0445   415803   416762   +   319       Uncharacterized protein conserved   COG4034   [S]                               in archaea       0446   416913   417761   +   282   NadC   Nicotinate-nucleotide   COG0157   [H]                               pyrophosphorylase       0447   417779   418756   −   325       Uncharacterized protein       0448   418732   419226   −   164   IlvB_1   Acetolactate synthase large subunit   COG0028   [EH]       0449   419733   420248   +   171       Predicted transcription factor,   COG1813   [K]                               homolog of eukaryotic MBF1       0450   420252   420827   −   191       Uncharacterized protein       0451   420814   422439   −   541   FtsA   Actin-like ATPase involved in cell   COG0849   [D]       0452   422444   422755   −   103       Predicted pyrophosphatase   COG1694   [R]       0453   422752   423300   −   182       SAM-dependent methyltransferase   COG0500   [QR]       0454   423263   423655   −   130       Uncharacterized protein conserved   COG1844   [S]                               in archaea       0455   423708   424130   +   140       Uncharacterized protein conserved   COG4921   [S]                               in archaea       0456   424099   425370   +   423       GTPase of the HfIX family   COG2262   [R]       0457   425367   425804   −   145       Predicted transcription regulator                               containing the wHTH DNA-binding                               domain       0458   425875   426513   −   212       FOG: CBS domain   COG0517   [R]       0459   426513   427271   −   252       Ferredoxin   COG1145   [C]       0460   427268   427711   −   147   EhaP   Ferredoxin   COG1145   [C]       0461   427686   428825   −   379   EhbK   Ferredoxin   COG1145   [C]       0462   428829   429407   −   192   EhaQ   Ferredoxin   COG1145   [C]       0463   429389   430618   −   409   EhaO   Ni,Fe-hydrogenase III large subunit   COG3261   [C]       0464   430599   431087   −   162   EhaN   Ni,Fe-hydrogenase III small subunit   COG3260   [C]       0465   431084   431524   −   146   EhaM   Uncharacterized protein conserved   COG4084   [S]                               in archaea       0466   431521   431865   −   114   EhaL   Uncharacterized membrane protein,   COG4035   [S]                               conserved in archaea       0467   431862   432101   −   79       Uncharacterized protein       0468   432112   432963   −   283   EhaJ   Membrane protein related to formate   COG0650   [C]                               hydrogenlyase subunit 4       0469   432967   433170   −   67       Uncharacterized protein       0470   433183   433854   −   223   EhaH   Uncharacterized membrane protein,   COG4078   [S]                               conserved in archaea       0471   433838   434515   −   225   EhaG   Uncharacterized membrane protein,   COG4036   [S]                               conserved in archaea       0472   434512   435021   −   169   EhaF   Uncharacterized membrane protein,   COG4037   [S]                               conserved in archaea       0473   434978   435265   −   95   EhaE   Uncharacterized membrane protein,   COG4038   [S]                               conserved in archaea       0474   435258   435500   −   80   EhaD   Uncharacterized membrane protein,   COG4039   [S]                               conserved in archaea       0475   435497   435760   −   87   EhaC   Uncharacterized membrane protein,   COG4040   [S]                               conserved in archaea       0476   435757   436278   −   173   EhaB   Uncharacterized membrane protein,   COG4041   [S]                               conserved in archaea       0477   436275   436568   −   97   EhaA   Uncharacterized membrane protein,   COG4042   [S]                               conserved in archaea       0478   436592   437665   +   357       Predicted ATPase, MoxR-like family   COG0714   [R]                               of the AAA+ class       0479   438675   440018   +   447       Uncharacterized protein containing a   COG2425   [R]                               von Willebrand factor type A (vWA)                               domain       0480   440015   440614   −   199       Uncharacterized protein       0481   440625   441635   +   336       Predicted NTPase       0482   441586   442755   −   389       Predicted transcriptional regulators,   COG2896 &amp;   [H][K]                               consists of a molybdenum cofactor   COG1522                               biosynthesis enzyme fused to a HTH                               DNA-binding domain       0483   442817   444034   −   405   LysA   Diaminopimelate decarboxylase   COG0019   [E]       0484   444079   444621   −   180       Uncharacterized protein conserved   COG4077   [S]                               in archaea       0485   444618   445595   −   325       Uncharacterized conserved protein   COG1469   [S]       0486   445677   449426   +   1249       ATPases of the AAA+ class &amp;   COG0464 &amp;   [O][L]                               Intein/homing endonuclease   COG1372       0487   449457   449915   +   152       Uncharacterized conserved protein   COG1656   [S]       0488   449908   450531   +   207       Uncharacterized conserved protein   COG2078   [S]       0489   450514   451131   −   205       Uncharacterized proteins, LmbE   COG2120   [S]                               homologs       0490   451128   452138   −   336       Glycosyltransferase, probably   COG1215   [M]                               involved in cell wall biogenesis       0491   452156   453241   −   361   CarA   Carbamoylphosphate synthase small   COG0505   [EF]                               subunit       0492   453622   454674   +   350       Archaea-specific enzyme related to   COG1411 &amp;   [R][S]                               ProFAR isomerase (HisA) and   COG4043                               containing an additional                               uncharacterized domain       0493   454678   455469   −   263       Uncharacterized protein conserved   COG4044   [S]                               in archaea       0494   455483   456004   −   173       Predicted HD superfamily hydrolase   COG1418   [R]       0495   456001   456582   −   193   TFA1   Transcription initiation factor IIE,   COG1675   [K]                               large subunit       0496   456587   457279   −   230       Uncharacterized protein       0497   457283   459457   −   724   PurL_2   Phosphoribosylformylglycinamidine   COG0046   [F]                               (FGAM) synthase, synthetase                               domain       0498   459523   460449   −   308       Fe—S oxidoreductase   COG0247   [C]       0499   460425   461879   −   484       Predicted ribonuclease of the G/E   COG1530   [J]                               family       0500   461906   462208   +   100   HisI_1   Phosphoribosyl-ATP   COG0140   [E]                               pyrophosphohydrolase       0501   462591   463937   +   448       Uncharacterized FAD-dependent   COG2509   [R]                               dehydrogenase       0502   463950   464894   +   314       Uncharacterized protein conserved                               in archaea       0503   465077   466090   +   337       Predicted aminopeptidase   COG2234   [R]       0504   466093   466626   +   177       Amidase related to nicotinamidase   COG1335   [Q]       0505   466623   467993   +   456   cDPGS   Cyclic 2,3-diphosphoglycerate-   COG2403   [R]                               synthetase       0506   467990   468223   −   77   HHT1_1   Histone H3/H4   COG2036   [L]       0507   468287   469069   +   260       Predicted nuclease of the RecB   COG1637   [L]                               family       0508   469072   469722   +   216   TrpF   Phosphoribosylanthranilate   COG0135   [E]                               isomerase       0509   469706   473605   −   1299       Predicted protein of the CobN/Mg-   COG1429   [H]                               chelatase family       0510   473846   475135   +   429       Predicted Zn-dependent                               metallopeptidase       0511   475141   476415   +   424       Terpene cyclase/mutase family   COG1657   [I]                               protein       0512   476375   477415   −   346   Top6A   DNA topoisomerase VI, subunit A   COG1697   [L]       0513   477452   478060   −   202       Predicted RNA-binding protein   COG1094   [R]                               containing KH domain)       0514   478065   478856   −   263   RIO1_1   Serine/threonine protein kinase   COG1718   [TD]                               involved in cell cycle control       0515   478853   479188   −   111   InfA   Translation initiation factor IF-1   COG0361   [J]       0516   479449   480423   −   324   TyrS   Tyrosyl-tRNA synthetase   COG0162   [J]       0517   480456   481520   −   354   NMD3   NMD protein affecting ribosome   COG1499   [J]                               stability and mRNA decay       0518   481521   482639   −   372       Uncharacterized protein conserved   COG4046   [S]                               in archaea       0519   483150   483854   −   234   LasT   rRNA methylase   COG0565   [J]       0520   483880   485811   +   643       ABC-type ATPase fused to a   COG2401   [R]                               predicted acetyltransferase domain       0521   485808   486257   −   149       Universal stress protein UspA and   COG0589   [T]                               related nucleotide-binding proteins       0522   486337   486723   +   128       Zn-finger-containing protein   COG2158   [R]       0523   486677   487123   −   148       Uncharacterized protein conserved   COG4933   [S]                               in archaea       0524   487264   488313   −   349   Mer   Coenzyme F420-dependent N5,N10-   COG2141   [C]                               methylene tetrahydromethanopterin                               reductase       0525   488504   489094   +   196       FOG: CBS domain   COG0517   [R]       0526   489122   489958   +   278       FOG: CBS domain   COG0517   [R]       0527   489930   492113   −   727       Uncharacterized membrane protein                               specific for M. kandleri, MK-13 family       0528   492151   493311   +   386       ATP-dependent DNA ligase,   COG1423   [L]                               homolog of eukaryotic ligase III       0529   493316   493792   +   158       Soluble P-type ATPase   COG4087   [R]       0530   493786   495066   +   426   PyrC   Dihydroorotase   COG0044   [F]       0531   495059   496756   +   565   IlvB_2   Acetolactate synthase, large subunit   COG0028   [EH]       0532   497119   492505   +   128       Rubrerythrin   COG1592   [C]       0533   497572   498342   +   256       Predicted metal-dependent   COG1099   [R]                               hydrolase of the TIM-barrel fold       0534   498533   499327   +   264       Uncharacterized protein conserved   COG1810   [S]                               in archaea       0535   499336   499764   −   142       Uncharacterized protein       0536   499901   501817   +   638       6Fe—6S prismane cluster-containing   COG1151   [C]                               carbon monoxide dehydrogenase                               catalytic subunit       0537   501838   502950   +   370       Coenzyme F420-reducing   COG3259   [C]                               hydrogenase, alpha subunit       0538   502964   503680   +   238       Coenzyme F420-reducing   COG1941   [C]                               hydrogenase, gamma subunit       0539   503796   504623   +   275       Coenzyme F420-reducing   COG1035   [C]                               hydrogenase, beta subunit       0540   504665   505129   +   154       Uncharacterized protein       0541   505144   505872   +   242       Uncharacterized protein conserved   COG4047   [S]                               in archaea       0542   506098   506835   +   245       Predicted transcriptional regulator   COG0640 &amp;   [K][R]                               consisting of a V4R domain and a   COG1719                               DNA-binding HTH domain       0543   506807   507148   −   113       Uncharacterized conserved protein,   COG0599   [S]                               homolog of gamma-                               carboxymuconolactone                               decarboxylase subunit       0544   507396   509270   +   624   ThrS   Threonyl-tRNA synthetase   COG0441   [J]       0545   509272   509775   −   167   IlvH   Acetolactate synthase, small subunit   COG0440   [E]       0546   509917   510690   +   257   TatD   Mg-dependent DNase   COG0084   [L]       0547   510899   511126   +   75       Uncharacterized protein       0548   511128   511655   +   175       Predicted Zn-dependent protease   COG1913   [R]       0549   511613   512170   +   185       Acetyltransferase   COG0456   [R]       0550   512386   513675   +   429   GltB_1   Glutamate synthase subunit 2   COG0069   [E]       0551   513689   514252   +   187   GuaA_2   Glutamine amidotransferase subunit   COG0518   [F]                               of GMP synthase       0552   514237   515541   +   434   NhaP   NhaP-type Na+/H+ or K+/H+   COG0025   [P]                               antiporter       0553   515607   516128   +   173   MoaB   Molybdopterin biosynthesis enzyme   COG0521   [H]       0554   516136   516606   −   156   MoaC   Molybdenum cofactor biosynthesis   COG0315   [H]                               enzyme       0555   518513   518920   +   135       DNA endonuclease related to intein-   COG3780   [L]                               encoded endonucleases       0556   519350   520219   −   289       RecA-superfamily ATPase   COG0467   [T]                               implicated in signal transduction       0557   520203   520772   −   189       Uncharacterized protein conserved   COG1790   [S]                               in archaea       0558   521047   522033   +   328       beta-Ribofuranosylaminobenzene 5′-   COG1907   [R]                               phosphate synthase (beta-RFAP                               synthase)       0559   522045   523307   +   420   SIK1   Protein implicated in ribosomal   COG1498   [J]                               biogenesis, Nop56p homolog       0560   523355   524053   +   232   NOP1   Fibrillarin-like rRNA methylase   COG1889   [J]       0561   524303   525274   +   323   PitA   Phosphate/sulphate permeases   COG0306   [P]       0562   525271   525885   +   204       Uncharacterized protein       0563   525882   526838   +   318   PyrD   Dihydroorotate dehydrogenase   COG0167   [F]       0564   526826   527614   +   262   PyrK   Dihydroorotate dehydrogenase   COG0543   [HC]                               electron transfer subunit similar to 2-                               polyprenylphenol hydroxylase and                               related flavodoxin oxidoreductases       0565   527589   528335   +   248       Glycosyltransferase involved in cell   COG0463   [M]                               wall biogenesis       0566   528389   529435   +   348   Exo   5′-3′ exonuclease   COG0258   [L]       0567   529503   530324   −   273       Uncharacterized membrane protein,   COG3366   [S]                               conserved in archaea       0568   530382   531287   +   301       L-alanine-DL-glutamate epimerase   COG4948   [MR]                               and related enzymes of enolase                               superfamily       0569   531423   532460   +   345       Uncharacterized conserved protein   COG3367   [S]       0570   532442   532792   −   116       Uncharacterized protein conserved   COG4048   [S]                               in archaea       0571   532866   533444   +   192       Uncharacterized metal-binding   COG4887   [R]                               protein conserved in archaea       0572   533451   534368   −   305   HdrB   Heterodisulfide reductase, subunit B   COG2048   [C]       0573   534381   534959   −   192   HdrC   Heterodisulfide reductase, subunit C   COG1150   [C]       0574   535060   535818   +   252       Transcriptional regulator of the LysR   COG0583   [K]                               family       0575   536146   536853   −   235       Uncharacterized protein conserved   COG2043   [S]                               in archaea       0576   536956   537345   +   129       Predicted transcriptional regulator   COG3355   [K]       0577   537359   537568   +   69       Predicted nucleic-acid-binding   COG4049   [R]                               protein containing an archaeal-type                               C2H2 Zn-finger       0578   537647   538099   −   150   TagD   Cytidylyltransferase   COG0615   [MI]       0579   538169   538615   +   148       Uncharacterized protein conserved   COG4050   [S]                               in archaea       0580   538628   539851   +   407       Activator of 2-hydroxyglutaryl-CoA   COG1924   [I]                               dehydratase (HSP70-class ATPase                               domain)       0581   539864   540490   +   208       Uncharacterized protein conserved   COG4051   [S]                               in archaea       0582   540487   541335   +   282       Predicted Fe—S oxidoreductase   COG0535   [R]       0583   541340   542266   +   308       Uncharacterized protein conserved   COG4052   [R]                               in archaea, related to methyl                               coenzyme M reductase II, operon                               protein C (mtrC)       0584   542479   543207   −   242       Uncharacterized protein specific for                               M. kandleri, MK-1 family       0585   543481   544767   +   428       Uncharacterized protein       0586   545004   545954   +   316   PRI1   Eukaryotic-type DNA primase,   COG1467   [L]                               catalytic (small) subunit       0587   545951   546523   +   190       Uncharacterized conserved protein   COG1920   [S]       0588   546629   547708   +   359       Predicted ATP-utilizing enzyme of   COG1759   [R]                               the ATP-grasp superfamily (probably                               carboligase)       0589   547818   549116   +   432   ThiD   Hydroxymethylpyrimidine/phosphomethylpyrimidine   COG0351 &amp;   [H][S]                               kinase fused to   COG1992                               uncharacterized conserved domain       0590   549121   549732   +   203       Uncharacterized protein       0591   549969   550763   +   264       Uncharacterized secreted protein                               specific for M. kandleri with repeats,                               MK-6 family       0592   550754   551515   +   253       Uncharacterized protein specific for                               M. kandleri with repeats, MK-6 family       0593   551518   551976   +   152       Uncharacterized protein specific for                               M. kandleri, MK-6 family       0594   552664   552933   +   89       Uncharacterized protein       0595   553054   553923   +   289       Predicted archaea-specific   COG2521   [R]                               methyltransferase       0596   553892   554356   −   154       Uncharacterized conserved protein   COG1833   [S]       0597   554373   556742   +   789       Uncharacterized membrane protein                               specific for M. kandleri, MK-13 family       0598   556733   557212   +   159       Uncharacterized protein       0599   557225   558235   +   336       Predicted methyltransferase   COG2520   [R]       0600   558229   558702   −   157       RecB-family nuclease   COG4080   [L]       0601   558753   559712   +   319       ABC-type   COG0715   [P]                               nitrate/sulfonate/bicarbonate                               transport systems, periplasmic                               components       0602   559712   560467   +   251       ABC-type   COG0600   [P]                               nitrate/sulfonate/bicarbonate                               transport system, permease                               component       0603   560458   561198   +   246       ABC-type   COG1116   [P]                               nitrate/sulfonate/bicarbonate                               transport system, ATPase                               component       0604   561299   562033   +   244       tRNA-dihydrouridine synthase   COG0042   [J]       0605   562156   563580   −   474       Transposase and inactivated   COG0675   [L]                               derivatives       0606   563941   565068   +   375   Kch_1   Kef-type K+ transport systems,   COG1226 &amp;   [P][R]                               predicted NAD-binding component &amp;   COG1827                               Predicted small molecule binding                               protein (contains 3H domain)       0607   566155   567084   −   309   ThiL   Thiamine monophosphate kinase   COG0611   [H]       0608   567068   567601   +   177   NIP7   Predicted RNA-binding protein   COG1374   [J]                               involved in ribosomal biogenesis,                               contains PUA domain       0609   567603   568250   +   215       Predicted metabolic regulator   COG1707   [R]                               containing the ACT domain       0610   568264   568827   +   187       Adenine/guanine   COG0503   [F]                               phosphoribosyltransferases and                               related PRPP-binding proteins       0611   568818   569834   −   338       Uncharacterized protein conserved   COG1665   [S]                               in archaea       0612   569848   570273   +   141       Predicted DNA-binding protein with   COG1661   [R]                               PD1-like DNA-binding motif       0613   570239   571111   −   290   Map   Methionine aminopeptidase   COG0024   [J]       0614   571138   571800   +   220       Uncharacterized protein       0615   572038   572349   −   103       Predicted metal-binding protein   COG1745   [R]                               conserved in archaea       0616   572365   573780   −   471   LonB   Predicted ATP-dependent protease   COG1067   [O]       0617   573932   575161   −   409   DnaG   DNA primase (bacterial type)   COG0358   [L]       0618   575280   576332   −   350   GapA   Glyceraldehyde-3-phosphate   COG0057   [G]                               dehydrogenase       0619   576853   577878   −   341   SUA7_1   Transcription initiation factor IIB   COG1405   [K]       0620   578231   579271   −   346   SelA   Selenocysteine synthase   COG1921   [E]       0621   579226   580800   −   524       Predicted RNA modification enzyme   COG5270 &amp;   [J][EH]                               consisting of a 3-phosphoadenosine   COG0175                               5-phosphosulfate sulfotransferase                               fused to RNA-binding PUA domain       0622   580781   582307   −   508   ArgH   Argininosuccinate lyase   COG0165   [E]       0623   582471   583118   +   215       Predicted cysteine protease of the   COG1305   [E]                               transglutaminase-like supefamily       0624   583203   583934   +   243       Uncharacterized protein conserved   COG1667   [S]                               in archaea       0625   583941   584888   +   315   Mch   Methenyltetrahydromethanopterin   COG3252   [H]                               cyclohydrolase       0626   588697   589611   +   304       Uncharacterized protein specific for                               M. kandleri, MK-7 family       0627   589834   590232   −   132   FlpD_2   Coenzyme F420-reducing   COG1908   [C]                               hydrogenase, delta subunit       0628   590310   591596   +   428   AroA   5-enolpyruvylshikimate-3-phosphate   COG0128   [E]                               synthase       0629   591588   592031   −   147       Predicted hydrocarbon binding   COG1719   [R]                               protein (contains V4R domain)       0630   592104   592511   −   135       Predicted hydrocarbon binding   COG1719   [R]                               protein (contains V4R domain)       0631   592609   593769   +   386   AroC   Chorismate synthase   COG0082   [E]       0632   593764   594639   −   291       Predicted hydrocarbon binding   COG1719   [R]                               protein (contains V4R domain)       0633   594757   595908   +   383       Aspartate aminotransferase   COG0075   [E]       0634   595894   596667   −   257       Uncharacterized protein conserved   COG4053   [S]                               in archaea       0635   596667   597305   +   212   SUA5   Translation factor (SUA5)   COG0009   [J]       0636   597298   597756   +   152       Uncharacterized protein conserved   COG4090   [S]                               in archaea       0637   597753   598430   +   225       SAM-dependent methyltransferase   COG0500   [QR]       0638   598427   598936   +   169       Uncharacterized conserved protein   COG2042   [S]       0639   598998   600539   −   513       Predicted membrane protein       0640   600529   601014   −   161       Uncharacterized protein       0641   601207   601356   +   49   RPL40A   Ribosomal protein L40E   COG1552   [J]       0642   601360   602079   +   239       Predicted phosphate-binding   COG1646   [R]                               enzyme of the TIM-barrel fold       0643   602066   602473   −   135       Uncharacterized protein       0644   602534   603211   +   225       Predicted ATPase of the PP-loop   COG2102   [R]                               superfamily       0645   603358   604410   +   350       Uncharacterized protein       0646   604733   604954   −   73       Uncharacterized protein       0647   605491   606189   +   232       Uncharacterized protein specific for                               M. kandleri, MK-1 family       0648   606223   608511   −   762   HypF   Hydrogenase maturation factor   COG0068   [O]       0649   608508   609632   −   374       Uncharacterized protein       0650   609636   610853   −   405       Fe—S oxidoreductase, related to   COG1625   [C]                               NifB/MoaA family       0651   611026   612360   +   444   McrB   Methyl coenzyme M reductase, beta   COG4054   [H]                               subunit       0652   612470   612991   +   173   McrD   Methyl coenzyme M reductase,   COG4055   [H]                               subunit D       0653   613000   613608   +   202   McrC   Methyl coenzyme M reductase,   COG4056   [H]                               subunit C       0654   613750   614523   +   257   McrG   Methyl coenzyme M reductase,   COG4057   [H]                               gamma subunit       0655   614620   616281   +   553   McrA   Methyl coenzyme M reductase,   COG4058   [H]                               alpha subunit       0656   616411   617307   +   298   MtrE   N5-methyl-   COG4059   [H]                               tetrahydromethanopterin:coenzyme                               M methyltransferase, subunit E       0657   617423   618100   +   225   MtrD   N5-methyl-   COG4060   [H]                               tetrahydromethanopterin:coenzyme                               M methyltransferase, subunit D       0658   618120   618932   +   270   MtrC   N5-methyl-   COG4061   [H]                               tetrahydromethanopterin:coenzyme                               M methyltransferase, subunit C       0659   618946   619284   +   112   MtrB   N5-methyl-   COG4062   [H]                               tetrahydromethanopterin:coenzyme                               M methyltransferase, subunit B       0660   619299   620057   +   252   MtrA   N5-methyl-   COG4063   [H]                               tetrahydromethanopterin:coenzyme                               M methyltransferase, subunit A       0661   620071   620295   +   74   MtrG   N5-methyl-   COG4064   [H]                               tetrahydromethanopterin:coenzyme                               M methyltransferase, subunit G       0662   620318   621286   +   322   MtrH   N5-methyl-   COG1962   [H]                               tetrahydromethanopterin:coenzyme                               M methyltransferase, subunit H       0663   621086   622561   −   491       Predicted protein of the CobN/Mg-   COG1429   [H]                               chelatase family, a fragment       0664   622607   624328   +   573       Predicted protein of the CobN/Mg-   COG1429   [H]                               chelatase family, a fragment       0665   624364   625800   +   478       Uncharacterized protein conserved   COG4065   [S]                               in archaea       0666   625919   626347   +   142       Uncharacterized protein conserved   COG4066   [S]                               in archaea       0667   626344   627258   +   304   MetE   Methionine synthase II (cobalamin-   COG0620   [E]                               independent)       0668   627325   627636   +   103       Uncharacterized protein conserved                               in archaea       0669   627780   628319   −   179       Membrane-associated phospholipid   COG0671   [I]                               phosphatase       0670   628363   628776   −   137       Predicted NADH-flavin reductase   COG2510   [S]       0671   628773   629018   −   81       Uncharacterized protein       0672   629019   630314   −   431       Pyridoxal-phosphate-dependent   COG0076   [E]                               enzyme related to glutamate                               decarboxylase       0673   630694   631617   +   307       tRNA/rRNA cytosine-C5-methylase   COG0144   [J]       0674   631691   632797   +   368       RIO1-like serine/threonine protein   COG0478   [T]                               kinase fused to an N-terminal DNA-                               binding HTH domain       0675   632724   633431   +   235       NCAIR mutase   COG1691   [R]       0676   633524   634726   +   400       Uncharacterized conserved protein   COG0585   [S]       0677   634723   634887   −   54       Zn-ribbon-containing protein       0678   634980   635999   +   339   TrpD   Anthranilate   COG0547   [E]                               phosphoribosyltransferase       0679   636060   639833   −   1257   FusA   Translation elongation and release   COG0480 &amp;   [J][L]                               factor (GTPase), contains an intein   COG1372       0680   639848   640441   −   197   RpsG   Ribosomal protein S7   COG0049   [J]       0681   640545   640988   −   147   RpsL   Ribosomal protein S12   COG0048   [J]       0682   641007   641435   −   142   NusA_1   Transcription elongation factor NusA   COG0195   [K]       0683   641451   641780   −   109   RPL30   Ribosomal protein L30E   COG1911   [J]       0684   642269   643558   −   429   RpoC_1   DNA-directed RNA polymerase   COG0086   [K]                               largest subunit, the N-terminal part       0685   643555   646416   −   953   RpoC_2   DNA-directed RNA polymerase   COG0086   [K]                               largest subunit, the C-terminal part       0686   646413   648335   −   640   RpoB_1   DNA-directed RNA polymerase   COG0085   [K]                               second-largest subunit, the N-                               terminal part       0687   648385   649962   −   525   RpoB_2   DNA-directed RNA polymerase   COG0085   [K]                               second-largest subunit, the N-                               terminal part       0688   649995   650273   −   92   RPB5   DNA-directed RNA polymerase   COG2012   [K]                               subunit H       0689   650240   650781   −   180       Ferredoxin   COG1145   [C]       0690   650789   653419   −   876   SbcC   SMC1-family ATPase involved in   COG0419   [L]                               DNA repair       0691   653427   654782   −   451   SbcD   DNA repair exonuclease of the   COG0420   [L]                               SbcD/Mre11-family       0692   654785   656368   −   527       Predicted P-loop ATPase   COG0433   [R]       0693   656349   657518   −   389       Uncharacterized protein conserved                               in archaea       0694   657749   658219   −   156       Uncharacterized protein       0695   658227   658802   −   191       Uncharacterized protein       0696   658768   659217   −   149       Uncharacterized conserved protein   COG1991   [S]       0697   659236   661821   +   861       Uncharacterized protein       0698   661961   663658   −   565       Uncharacterized secreted protein       0699   663655   664569   −   304       Uncharacterized secreted protein       0700   664566   664736   −   56       Uncharacterized secreted protein       0701   664747   664935   −   62       Predicted secreted protein specific                               for M. kandleri, MK-18 family       0702   664932   665126   −   64       Predicted secreted protein specific                               for M. kandleri, MK-19 family       0703   665111   666085   −   324   PppA   Type II secretory pathway, prepilin   COG1989   [NOU]                               signal peptidase PulO and related                               peptidases       0704   666091   667089   −   332       Uncharacterized protein       0705   668048   669025   −   325       Flp pilus assembly protein TadC   COG2064   [NU]       0706   669056   670144   −   362       Flp pilus assembly protein TadC   COG2064   [NU]       0707   670334   672142   −   602       Flp pilus assembly protein, ATPase   COG4962   [U]                               CpaF       0708   672151   673908   −   585       Predicted AAA+ class ATPase with   COG0606   [O]                               chaperone activity       0709   673914   674513   −   199   RsmC   16S RNA G1207 methylase RsmC   COG2813   [J]       0710   675105   676400   −   431   AsnS   Aspartyl/asparaginyl-tRNA   COG0017   [J]                               synthetases       0711   676444   677739   −   431   HisD   Histidinol dehydrogenase   COG0141   [E]       0712   677717   678481   −   254       Uncharacterized protein conserved   COG1701   [S]                               in archaea       0713   678478   679608   −   376   Dfp   Phosphopantothenoylcysteine   COG0452   [H]                               synthetase/decarboxylase       0714   679601   680143   −   180   NusA_2   Transcription elongation factor NusA   COG0195   [K]       0715   680294   680575   +   93   Ssh10b_1   Archaea-specific DNA-binding   COG1581   [K]                               protein       0716   680541   682988   −   815       Uncharacterized protein specific for                               M. kandleri, MK-40 family       0717   682947   685229   +   760   CdhA_1   CO dehydrogenase/acetyl-CoA   COG1152   [C]                               synthase alpha subunit       0718   685235   685714   +   159   CdhB   CO dehydrogenase/acetyl-CoA   COG1880   [C]                               synthase epsilon subunit       0719   685725   687623   +   632   CdhA_1   CO dehydrogenase/acetyl-CoA   COG1152   [C]                               synthase alpha subunit       0720   687632   689035   +   467   CdhC   CO dehydrogenase/acetyl-CoA   COG1614   [C]                               synthase beta subunit       0721   689032   689805   +   257   CooC_1   CO dehydrogenase maturation factor   COG3640   [D]       0722   689798   691000   +   400   CdhD   CO dehydrogenase/acetyl-CoA   COG2069   [C]                               synthase delta subunit (corrinoid Fe—                               S protein)       0723   691014   692402   +   462   CdhE   CO dehydrogenase/acetyl-CoA   COG1456   [C]                               synthase gamma subunit (corrinoid                               Fe—S protein)       0724   692457   693386   +   309       Nucleoside-diphosphate-sugar   COG0451   [MG]                               epimerase       0725   693426   693929   +   167   HycB   Fe—S-cluster-containing hydrogenase   COG1142   [C]                               component       0726   693907   694650   +   247   CooC_2   CO dehydrogenase maturation factor   COG3640   [D]       0727   694590   694850   +   86       Ferredoxin   COG1146   [C]       0728   694843   695961   +   372   PorA_2   Pyruvate: ferredoxin oxidoreductase,   COG0674   [C]                               alpha subunit       0729   695958   696773   +   271   PorB_2   Pyruvate: ferredoxin oxidoreductase,   COG1013   [C]                               beta subunit       0730   696757   697287   +   176   PorG_2   Pyruvate: ferredoxin oxidoreductase,   COG1014   [C]                               gamma subunit       0731   697284   698363   +   359   SucC   Succinyl-CoA synthetase beta   COG0045   [C]                               subunit       0732   698367   699230   +   287   SucD   Succinyl-CoA synthetase alpha   COG0074   [C]                               subunit       0733   699231   700091   +   286       Predicted archaea-specific kinase of   COG1829   [R]                               the sugar kinase superfamily       0734   700084   700260   +   58       Predicted RNA-binding protein   COG1532   [R]       0735   700349   701005   −   218   PyrF   Orotidine-5′-phosphate   COG0284   [F]                               decarboxylase       0736   700981   701478   −   165       Uncharacterized protein       0737   701479   702372   −   297   DYS1   Deoxyhypusine synthase   COG1899   [O]       0738   702369   703142   −   257   SpeB   Agmatinase   COG0010   [E]       0739   703117   703527   −   136   Efp   Translation initiation factor elF-5A   COG0231   [J]       0740   703599   704051   +   150   SpeA   Pyruvoyl-dependent arginine   COG1945   [S]                               decarboxylase (PvlArgDC)                               [Contains: Pyruvoyl-dependent                               arginine decarboxylase beta subunit;                               Pyruvoyl-dependent arginine                               decarboxylase alpha subunit]       0741   704058   705071   +   337   SuhB   Archaea-specific fructose-1,6-   COG0483 &amp;   [G]                               bisphosphatase fused to predicted   COG1694   [R]                               pyrophosphatase of the PRA-PH                               family       0742   705044   705874   +   276       Predicted sugar kinase   COG0061   [G]       0743   705968   706243   −   91   HHT1_2   Histones H3/H4   COG2036   [L]       0744   706262   706693   +   143       Predicted nuclei-acid-binding protein,   COG1439   [R]                               consists of a PIN domain and a Zn-                               ribbon       0745   706675   707529   +   284       Predicted metalloprotease fused to   COG4067 &amp;   [O]                               aspartyl protease   COG4740   [R]       0746   707526   708443   +   305   HemC   Porphobilinogen deaminase   COG0181   [H]       0747   708436   709227   +   263   DPH5   Methyltransferase involved in   COG1798   [J]                               diphthamide biosynthesis       0748   709231   709587   +   118       Uncharacterized protein conserved   COG1885   [S]                               in archaea       0749   709592   710701   −   369       Uncharacterized protein conserved                               in archaea, possible membrane                               metallohydrolase       0750   710703   711950   −   415       Uncharacterized protein conserved                               in archaea, Zn-ribbon domain                               containing       0751   711973   712422   −   149       Uncharacterized protein conserved                               in archaea       0752   712425   713867   −   480   MurE_1   UDP-N-acetylmuramyl tripeptide   COG0769   [M]                               synthase       0753   713877   714947   −   356   MraY   UDP-N-acetylmuramyl pentapeptide   COG0472   [M]                               phosphotransferase       0754   714964   716103   −   379   CarB_1   Carbamoylphosphate synthase large   COG0458   [EF]                               subunit       0755   716100   717638   −   512   MurC   UDP-N-acetylmuramate-alanine   COG0773   [M]                               ligase       0756   717691   718695   −   334       Predicted ATPase of the PP-loop   COG0037   [D]                               superfamily implicated in cell cycle                               control       0757   718688   720403   −   571   GlnS   Glutamyl-tRNA synthetase   COG0008   [J]       0758   720849   722627   −   592   ArgS   Arginyl-tRNA synthetase   COG0018   [J]       0759   722643   723872   −   409   eRF1   Peptide chain release factor eRF1   COG1503   [J]       0760   723901   724572   +   223   PyrH   Uridylate kinase   COG0528   [F]       0761   724579   724770   +   63       Zn-ribbon containing protein   COG4068   [S]       0762   724738   725484   −   248       Predicted RNA methylase   COG4076   [R]       0763   725481   726020   −   179       Uncharacterized conserved protein   COG1432   [S]       0764   726042   726800   −   252       Uncharacterized protein       0765   726742   727086   −   114       Uncharacterized protein       0766   727083   728198   −   371   PhoH   Phosphate starvation-inducible   COG1702   [T]                               protein PhoH, predicted ATPase       0767   728211   729026   −   271   UppS   Undecaprenyl pyrophosphate   COG0020   [I]                               synthase       0768   729066   729563   +   165       Predicted phosphoesterase   COG0622   [R]       0769   729717   730787   +   356       tRNA/rRNA cytosine-C5-methylase   COG0144   [J]       0770   730816   731811   +   331       Predicted integral membrane protein   COG0392   [S]       0771   732207   734036   +   609       Predicted acyltransferase   COG4801   [R]       0772   734033   734974   −   313       Carbonic   COG0663   [R]                               anhydrases/acetyltransferase                               homolog, isoleucine patch                               superfamily       0773   735042   735533   −   163       Uncharacterized protein conserved   COG4072   [S]                               in archaea       0774   735536   736510   −   324   IspA   Geranylgeranyl pyrophosphate   COG0142   [H]                               synthase       0775   736523   737884   −   453       Predicted hydrolase of the metallo-   COG0595   [R]                               beta-lactamase superfamily       0776   737872   738996   −   374   LldD   L-lactate dehydrogenase (FMN-   COG1304   [C]                               dependent)       0777   738974   739693   −   239       Predicted archaeal kinase   COG1608   [R]       0778   739816   740862   +   348   ThiI_1   Thiamine biosynthesis ATP   COG0301   [H]                               pyrophosphatase       0779   740929   741837   +   302       FOG: CBS domain   COG0517   [R]       0780   741887   743083   +   398       Uncharacterized conserved protein   COG3287   [S]       0781   743138   743650   +   170   LeuD_1   3-isopropylmalate dehydratase small   COG0066   [E]                               subunit       0782   743656   744663   +   335   LeuB_1   Isocitrate/isopropylmalate   COG0473   [E]                               dehydrogenase       0783   744973   745683   +   236       Uncharacterized protein       0784   745708   746904   +   398   TrpB   Tryptophan synthase beta chain   COG0133   [E]       0785   746905   747300   −   131       Predicted hydrocarbon binding   COG1719   [R]                               protein (contains V4R domain)       0786   747316   747681   +   121       Uncharacterized protein conserved   COG2098   [S]                               in archaea       0787   747678   748961   +   427       Protein containing   COG0615 &amp;   [MI]                               cytidylyltransferase domain and   COG1323   [R]                               predicted nucleotidyltransferase                               (HIG superfamily) domain       0788   748958   750166   +   402       Fe—S oxidoreductase family protein   COG1032   [C]       0789   750112   750972   +   286       Possible metal-dependent hydrolase       0790   750903   751583   −   226   PurL_1   Phosphoribosylformylglycinamidine   COG0047   [F]                               (FGAM) synthase, glutamine                               amidotransferase subunit       0791   751653   751907   −   84   PurS   Phosphoribosylformylglycinamidine   COG1828   [F]                               (FGAM) synthase, PurS subunit       0792   751904   752647   −   247   PurC   Phosphoribosylaminoimidazolesuccinocarboxamide   COG0152   [F]                               (SAICAR) synthase       0793   752727   753977   +   416       Uncharacterized conserved protein   COG3287   [S]       0794   753993   755180   +   395       Uncharacterized protein conserved   COG4069   [S]                               in archaea       0795   755237   756220   +   327       Selenophosphate synthetase   COG2144   [R]       0796   756217   757752   +   511       Predicted peptidyl-prolyl cis-trans   COG4070   [O]                               isomerase (rotamase), cyclophilin                               family       0797   757749   759056   +   435       Fe—S oxidoreductase   COG1032   [C]       0798   759053   760315   +   420   TyrA_2   Prephenate dehydrogenase   COG0287   [E]       0799   760363   762369   −   668       Coenzyme F420-reducing   COG1035 &amp;   [C][C]                               hydrogenase, beta subunit fused to   COG2221                               oxidoreductase related to Nitrite                               reductase and Dissimilatory sulfite                               reductase (desulfoviridin), alpha and                               beta subunits       0800   762431   762814   +   127       Predicted transcriptional regulator   COG3355   [K]                               containing a wHTH DNA-binding                               domain       0801   762811   763422   +   203       Oxidoreductase related to Nitrite   COG2221   [C]                               reductase and Dissimilatory sulfite                               reductase (desulfoviridin), alpha and                               beta subunits       0802   763376   764641   −   421       Uncharacterized protein       0803   764701   765237   +   178       SpoU-like RNA methylase   COG1303   [S]       0804   765234   765932   +   232   ApaH   Diadenosine tetraphosphatase   COG0639   [T]       0805   765929   766717   −   262       Uncharacterized protein       0806   766921   768012   −   363       Possible Zn-dependent                               metallohydrolase       0807   768031   768816   +   261       Uncharacterized conserved protein   COG1912   [S]       0808   768856   770355   −   499       Short chain dehydrogenase fused to   COG0062 &amp;   [S][G]                               sugar kinase   COG0063       0809   770475   771254   +   259       ABC-type antimicrobial peptide   COG1136   [V]                               transport system, ATPase                               component       0810   771251   771961   +   236   HypB_1   Ni2+-binding GTPase involved in   COG0378   [OK]                               regulation of expression and                               maturation of urease and                               hydrogenase       0811   771930   772610   +   226       Predicted Fe—S protein   COG2000   [R]       0812   772762   773676   −   304       Uncharacterized conserved protein   COG1578   [S]       0813   773691   774935   −   414       Predicted membrane-associated Zn-   COG0750   [M]                               dependent protease       0814   774937   775368   −   143       Uncharacterized conserved protein   COG0432   [S]       0815   775372   776106   +   244   MscS   Small-conductance   COG0668   [M]                               mechanosensitive channel       0816   776227   777129   +   300   Ftr_2   Formylmethanofuran:tetrahydromethanopterin   COG2037   [C]                               formyltransferase       0817   777133   778026   +   297       Sugar kinase of the ribokinase family   COG0524   [G]       0818   778042   778800   −   252       Organic-radical-activating enzyme   COG0602   [O]       0819   778761   779243   −   160       6-pyruvoyl-tetrahydropterin synthase   COG0720   [H]       0820   779435   781207   +   590   PheT   Phenylalanyl-tRNA synthetase beta   COG0072   [J]                               subunit       0821   781211   782434   +   407   FtsZ_1   FtsZ GTPase involved in cell division   COG0206   [D]       0822   782450   782635   +   61   Sss1   Protein translocase subunit Sss1   COG2443   [U]       0823   782651   783142   +   163   NusG   Transcription antiterminator NusG   COG0250   [K]       0824   783170   783670   +   166   RplK   Ribosomal protein L11   COG0080   [J]       0825   783684   784328   +   214   RplA   Ribosomal protein L1   COG0081   [J]       0826   784328   785416   +   362   RplJ   Ribosomal protein L10   COG0244   [J]       0827   785439   785981   +   180       Predicted nucleotide kinase   COG1618   [J]       0828   785987   787657   +   556   SdhA   Succinate dehydrogenase/fumarate   COG1053   [C]                               reductase, flavoprotein subunit       0829   787632   789431   −   599   AdeC   Adenine deaminase   COG1001   [F]       0830   789454   790515   −   353       Uncharacterized protein specific for                               M. kandleri, MK-25 family       0831   790663   791670   −   335       Uncharacterized membrane protein                               specific for M. kandleri, MK-24 family       0832   791741   792721   −   326   IlvC   Ketol-acid reductoisomerase   COG0059   [EH]       0833   792735   793019   −   94   RPL14A   Ribosomal protein L14E   COG2163   [J]       0834   793046   794548   +   500       Uncharacterized membrane protein       0835   794560   797016   +   818       Archaea-specific Superfamily II   COG1202   [R]                               helicase       0836   797005   798327   −   440       Uncharacterized protein       0837   798324   798665   −   113       Uncharacterized protein       0838   798710   799576   +   288       Uncharacterized protein conserved   COG4071   [S]                               in archaea       0839   799566   800123   −   185   SPT15   Transcription initiation factor TFIID   COG2101   [K]                               (TATA-binding protein)       0840   800146   801222   −   358       Predicted molecular chaperone   COG2377   [O]                               distantly related to HSP70-fold                               metalloproteases       0841   801199   801678   +   159   RplV   Ribosomal protein L22   COG0091   [J]       0842   801692   802375   +   227   RpsC   Ribosomal protein S3   COG0092   [J]       0843   802379   802612   +   77   RpmC   Ribosomal protein L29   COG0255   [J]       0844   802632   802952   +   106   SUI1   Translation initiation factor (SUI1)   COG0023   [J]       0845   802945   803634   −   229       SAM-dependent methyltransferase   COG0500   [QR]       0846   803550   803876   +   108   POP4_1   RNAse P subunit P29   COG1588   [J]       0847   803850   804587   −   245       Membrane protease subunit,   COG0330   [O]                               stomatin/prohibitin homolog       0848   804584   805012   −   142       Membrane protein implicated in   COG1585   [OU]                               regulation of membrane protease                               activity       0849   805062   806366   +   434   Lpd   Dihydrolipoamide dehydrogenase   COG1249   [C]       0850   806368   808374   −   668   MetG   Methionyl-tRNA synthetase   COG0143 &amp;   [J][R]                                   COG0073       0851   808381   809715   −   444       Uncharacterized membrane protein                               specific for M. kandleri, MK-15 family       0852   809802   810416   −   204       Uncharacterized protein       0853   810419   811066   −   215       Uncharacterized membrane protein                               specific for M. kandleri, MK-15 family       0854   811293   812264   −   323       Predicted UDP-N-acetylglucosamine                               2-epimerase of the MurG family       0855   812269   812874   −   201   HisB   Imidazoleglycerol-phosphate   COG0131   [E]                               dehydratase       0856   812939   813283   +   114       Predicted RNA-binding protein   COG4085   [R]                               containing a TRAM domain       0857   813255   814070   +   271       Uncharacterized protein       0858   814061   814984   −   307   SUA7_2   Transcription initiation factor IIB   COG1405   [K]       0859   815000   815284   −   94   GAR1   RNA-binding protein involved in   COG3277   [J]                               rRNA processing       0860   815362   815964   −   200       Ferredoxin   COG1146   [C]       0861   815970   816254   +   94       Uncharacterized protein       0862   816285   817220   +   311   PhoU   Phosphate uptake regulator   COG0704   [P]       0863   817232   817948   +   238   FtsZ_2   FtsZ GTPase involved in cell division   COG0206   [D]       0864   817961   818197   +   78       Predicted DNA-binding protein       0865   818237   819400   +   387       Predicted kinase related to thiamine   COG1364   [E]                               pyrophosphokinase       0866   819624   820862   +   412       Uncharacterized conserved protein   COG1915   [S]       0867   820834   821088   −   84       Uncharacterized protein conserved   COG4082                               in archaea       0868   821117   822100   +   327       2-Phosphoglycerate kinase   COG2074   [G]       0869   822107   822523   +   138       CBS-domain-containing protein   COG0517   [R]       0870   822747   823631   −   294       Uncharacterized protein       0871   823635   824180   −   181   CyaB   Adenylate cyclase, class 2   COG1437   [F]                               (thermophilic)       0872   824222   825364   −   380   EriC   Chloride channel protein EriC   COG0038   [P]       0873   825400   825711   +   103   CpsB_1   Mannose-6-phosphate isomerase   COG0662   [G]       0874   825979   826695   +   238       Acetyltransferase (the isoleucine   COG0110   [R]                               patch superfamily)       0875   826703   827305   +   200       Uncharacterized protein       0876   827312   828238   +   308   CitG_2   Triphosphoribosyl-dephospho-CoA   COG1767   [H]                               synthetase       0877   828174   828677   +   167       Uncharacterized protein       0878   828838   830148   +   436   RPT1   ATP-dependent 26S proteasome   COG1222   [O]                               regulatory subunit       0879   830233   831030   +   265       Uncharacterized protein       0880   830924   831646   +   240       Glycosyltransferase involved in cell   COG0463   [M]                               wall biogenesis       0881   831689   833029   +   446       NAD(FAD)-dependent   COG0446   [R]                               dehydrogenase       0882   833026   833541   +   171       Permease related to cation   COG1824   [P]                               transporters       0883   833538   834059   +   173       Permease related to cation   COG1824   [P]                               transporters       0884   834071   834661   +   196       Uncharacterized conserved protein   COG3273   [S]       0885   834663   834959   +   98       Predicted transcriptional regulator   COG3357   [K]                               consisting of an HTH domain fused                               to a Zn-ribbon       0886   834949   835605   −   218       Uncharacterized protein       0887   835602   836366   −   254       Uncharacterized protein       0888   836360   837130   −   256   TruA   Pseudouridylate synthase (tRNA   COG0101   [J]                               psi55)       0889   837127   838032   −   301       Predicted enzyme related to   COG2144   [R]                               selenophosphate synthetase       0890   838029   839210   −   393       Predicted membrane protein   COG1784   [S]       0891   839229   839777   +   182       Predicted membrane protein       0892   839829   841106   −   425       Nucleoside-diphosphate-sugar   COG1208   [MJ]                               pyrophosphorylase involved in                               lipopolysaccharide                               biosynthesis/translation initiation                               factor elF2B subunit       0893   841103   842461   −   452   CpsG_1   Phosphomannomutase   COG1109   [G]       0894   842475   843281   +   268       Predicted DNA-modification   COG1041   [L]                               methylase       0895   843334   844707   −   457       Fe—S oxidoreductase similar to Mg-   COG1032   [C]                               protoporphyrin IX monomethyl ester                               oxidative cyclase-related protein                               and subunits of a Ni-chelatase for                               the biosynthesis of the Ni-containing                               coenzyme F430, which is essential                               for the production of methane in                               methanogens       0896   844704   846110   −   468       Fe—S oxidoreductase fused to a   COG4001 &amp;   [R][R]                               metal-binding domain   COG0535       0897   846128   847237   −   369   ThiH_1   Predicted enzyme related to   COG1060   [HR]                               thiamine biosynthesis enzyme ThiH       0898   847218   848360   −   380   ThiH_2   Predicted enzyme related to   COG1060   [HR]                               thiamine biosynthesis enzyme ThiH       0899   848389   851631   +   1080   IleS   Isoleucyl-tRNA synthetase   COG0060   [J]       0900   851628   854384   +   918   AlaS   Alanyl-tRNA synthetase   COG0013   [J]       0901   854758   856533   −   591   NrdD   Oxygen-sensitive ribonucleoside-   COG1328   [F]                               triphosphate reductase       0902   856681   858303   −   540       Uncharacterized protein       0903   858399   858818   +   139       Ferredoxin   COG1145   [C]       0904   858815   859825   +   336       Predicted protease of the   COG0826   [O]                               collagenase family       0905   859827   860189   +   120       Predicted metal-binding protein       0906   860186   860890   +   234       Predicted protease of the   COG0826   [O]                               collagenase family       0907   860862   862367   −   501       prdicted regulatory protein consisting   COG1900 &amp;   [S][R]                               of a uncharacterized conserved   COG0517                               domain fused to a CBS domain       0908   862342   863466   −   374   Thil_2   ATP pyrophosphatase involved in   COG0301   [H]                               thiamine biosynthesis       0909   863512   864411   +   299       Uncharacterized conserved protein   COG2013   [S]       0910   864567   866477   −   636       Predicted membrane protein, MK-44                               family       0911   866594   868288   −   564   CarB_2   Carbamoylphosphate synthase large   COG0458   [EF]                               subunit       0912   868674   869447   +   257       Uncharacterized protein       0913   869366   870883   +   505       Predicted membrane protein       0914   870784   873003   −   739       Predicted membrane protein, MK-44                               family       0915   872967   873524   −   185       Uncharacterized protein       0916   873521   874090   −   189       Predicted membrane protein       0917   874490   875560   −   356       Nucleoside-diphosphate-sugar   COG1208   [MJ]                               pyrophosphorylase involved in                               lipopolysaccharide                               biosynthesis/translation initiation                               factor elF2B subunit       0918   875582   876487   −   301   AgaS   Predicted phosphosugar isomerase   COG2222   [M]       0919   876477   876932   −   151       Uncharacterized membrane protein   COG2246   [S]       0920   876957   878327   +   456   CpsG_2   Phosphomannomutase   COG1109   [G]       0921   878332   879759   +   475   Top6B   DNA topoisomerase VI, subunit B   COG1389   [L]       0922   880054   881355   +   433       Uncharacterized protein specific for                               M. kandleri, MK-19 family       0923   881345   881530   −   61       Uncharacterized protein       0924   882370   883326   +   318       Uncharacterized protein conserved   COG3366   [S]                               in archaea       0925   883220   884197   −   325       Uncharacterized protein specific for                               M. kandleri, MK-36 family       0926   884275   885705   +   476   MurE_1   UDP-N-acetylmuramyl tripeptide   COG0769   [M]                               synthase       0927   885706   886470   +   254       Uncharacterized protein conserved                               in archaea       0928   886477   887508   +   343   PflX   Uncharacterized Fe—S protein PflX,   COG1313   [R]                               homolog of pyruvate formate lyase                               activating protein       0929   887505   888422   −   305       Coenzyme F420-reducing   COG1035   [C]                               hydrogenase, beta subunit       0930   888425   889183   −   252       Coenzyme F420-reducing   COG1941   [C]                               hydrogenase, gamma subunit       0931   889351   890601   −   416       Coenzyme F420-reducing   COG3259   [C]                               hydrogenase, alpha subunit       0932   890735   892306   +   523       Fe—S oxidoreductase family protein   COG1032   [C]       0933   892458   893501   −   347       Predicted hydrolase of the metallo-                               beta-lactamase superfamily,                               contains a Zn-ribbon       0934   893506   894342   −   278   KsgA   Dimethyladenosine transferase   COG0030   [J]                               (rRNA methylase)       0935   894329   895165   −   278       Predicted RNA-binding protein,   COG2131 &amp;   [F][R]                               contains THUMP domain   COG1818       0936   895204   895467   +   87       CBS-domain-containing protein   COG0517   [R]       0937   895592   896863   −   423       Uncharacterized protein specific for                               M. kandleri, MK-21 family       0938   896885   897463   −   192   Isf   Iron-sulfur flavoprotein similar to   COG0655   [R]                               Multimeric flavodoxin WrbA       0939   897491   898330   +   279       Uncharacterized protein conserved   COG1650   [S]                               in archaea       0940   898801   899631   −   276       Predicted SAM-dependent   COG2520   [R]                               methyltransferase       0941   899633   900397   −   254       Phosphate acetyltransferase family   COG4002   [R]                               enzyme       0942   901574   902758   +   394   ArgG   Argininosuccinate synthase   COG0137   [E]       0943   902832   903947   −   371       ABC-type multidrug transport   COG0842   [V]                               system, permease subunit       0944   903932   904639   −   235       ABC-type multidrug transport   COG1131   [V]                               system, ATPase subunit       0945   904797   905420   −   207       Uncharacterized protein specific for                               M. kandleri, MK-1 family       0946   905879   906190   +   103       Uncharacterized membrane protein                               specific for M. kandleri, MK-4 family       0947   906696   908201   +   501       Uncharacterized secreted protein                               specific for M. kandleri, contains                               repeats, MK-5 family       0948   908194   910293   +   699       Uncharacterized protein specific for                               M. kandleri, MK-5 family       0949   910269   911270   +   333       Predicted membrane protein       0950   911951   912499   −   182       Predicted phosphatase homologous   COG2110   [R]                               to the C-terminal domain of histone                               macroH2A1       0951   912898   913887   +   329   ECM27_2   Ca2+/Na+ antiporter   COG0530   [P]       0952   914028   915068   +   346       Pyruvate-formate lyase-activating   COG1180   [O]                               enzyme       0953   915262   916077   +   271   UbiA   4-hydroxybenzoate   COG0382   [H]                               polyprenyltransferase       0954   916066   917193   −   375       Archaeal fructose 1,6-   COG1980   [G]                               bisphosphatase       0955   917240   917590   −   116   EGD2   Transcription factor homologous to   COG1308   [K]                               NACalpha-BTF3       0956   917639   918091   −   150       Prefoldin, molecular chaperone   COG1370   [O]                               implicated in de novo protein folding,                               alpha subunit       0957   918107   919444   +   445   TldD   Predicted Zn-dependent protease of   COG0312   [R]                               TldD family       0958   919444   920673   +   409   PmbA   Inactivated homologs of predicted   COG0312   [R]                               Zn-dependent protease of TldD                               family (PmbA subfamily protein)       0959   920942   921322   +   126       Uncharacterized protein       0960   921362   922747   +   461   GatB   Asp-tRNAAsn/Glu-tRNAGln   COG0064   [J]                               amidotransferase B subunit (PET112                               homolog)       0961   922744   923442   −   232   SpeE   Spermidine synthase or similar   COG0421   [E]                               enzyme that uses putrescine       0962   923454   923702   +   82       Uncharacterized protein conserved   COG4003   [S]                               in archaea       0963   923724   924575   +   283       Predicted dioxygenase   COG1355   [R]       0964   924582   925004   +   140       Uncharacterized membrane protein       0965   925021   926991   +   656   MCM2_1   Predicted ATPase involved in   COG1241   [L]                               replication control, Cdc46/Mcm                               family       0966   926988   927662   +   224       Uncharacterized protein conserved   COG3390   [S]                               in archaea       0967   927666   928082   +   138   GCD7   Translation initiation factor elF-2   COG1601   [J]       0968   928083   928427   +   114       Uncharacterized conserved protein   COG2412   [S]       0969   928424   929482   +   352       Predicted N6-adenine-specific RNA   COG0116   [L]                               methylase containing THUMP                               domain       0970   929468   930193   −   241       Predicted hydrolase of the HAD   COG1011   [R]                               superfamily       0971   930168   930926   +   252       Uncharacterized conserved protein   COG1478   [S]       0972   931280   932956   +   558       Uncharacterized protein specific for                               M. kandleri, MK-8 family       0973   932946   934205   +   419       Uncharacterized protein specific for                               M. kandleri with repeats, MK-6 family       0974   934272   935483   +   403   ThrC   Threonine synthase   COG0498   [E]       0975   935967   936332   −   121       Uncharacterized conserved protein       0976   936332   938134   +   600       Predicted membrane protein   COG3356   [S]       0977   938193   939227   +   344       Glycosyl transferase, related to   COG1819   [GC]                               UDP-glucuronosyltransferase       0978   939220   939801   +   193   SEC59   Dolichol kinase   COG0170   [I]       0979   939803   940735   +   310       Uncharacterized membrane protein                               specific for M. kandleri, MK-15 family       0980   941177   942388   −   403       Predicted Fe—S oxidoreductase   COG0535   [R]       0981   942395   943513   −   372       Predicted membrane-associated Zn-   COG0750   [M]                               dependent protease       0982   943478   944167   +   229       Predicted nucleotidyltransferase of   COG2413   [R]                               the DNA polymerase beta                               superfamily       0983   944171   944794   +   207       Predicted archaea-specific RNA-   COG2517   [R]                               binding protein containing a C-                               terminal EMAP domain       0984   944800   945213   +   137       Transcriptional regulator containing   COG1846   [K]                               DNA-binding HTH domain       0985   945361   945537   −   58       Uncharacterized protein       0986   945634   947301   +   555   LysS   Lysyl-tRNA synthetase (class I)   COG1384   [J]       0987   947313   948383   +   356       Fe—S protein related to pyruvate   COG2108   [R]                               formate-lyase activating enzyme       0988   948365   948892   +   175       Uncharacterized protein       0989   948921   950180   +   419       Predicted Fe—S oxidoreductase   COG2100   [R]       0990   950200   950649   +   149   RpsS   Ribosomal protein S19   COG0185   [J]       0991   950650   951324   −   224       Uncharacterized protein       0992   951376   952827   +   483       Fe—S oxidoreductase similar to Mg-   COG1032   [C]                               protoporphyrin IX monomethyl ester                               oxidative cyclase-related protein                               and subunits of a Ni-chelatase for                               the biosynthesis of the Ni-containing                               coenzyme F430, which is essential                               for the production of methane in                               methanogens       0993   952778   953764   −   328   ERG12   Mevalonate kinase   COG1577   [I]       0994   953789   954649   +   286       Uncharacterized protein conserved   COG1667   [S]                               in archaea       0995   954953   956260   +   435   MurD_1   UDP-N-acetylmuramoylalanine-D-   COG0771   [M]                               glutamate ligase       0996   956267   957001   +   244       Archaea-specific enzyme of the   COG1938   [R]                               ATP-grasp superfamily       0997   957063   957452   +   129       Uncharacterized conserved protein   COG1935   [S]       0998   957638   958237   +   199       Predicted cysteine protease of the   COG1305   [E]                               transglutaminase-like superfamily       0999   958234   959913   −   559   CDC9   ATP-dependent DNA ligase   COG1793   [L]       1000   960189   961070   +   293       Predicted serine/threonine protein   COG0478   [T]                               kinase       1001   961247   962146   +   299       Ferredoxin   COG1145   [C]       1002   962187   962981   +   264   MhpD   2-keto-4-pentenoate hydratase   COG0179   [Q]                               hydratase       1003   963347   964648   −   433       Predicted DNA-binding protein   COG1571   [R]                               containing a Zn-ribbon       1004   964675   964869   +   64       Uncharacterized protein       1005   964874   965851   +   325       Predicted transcriptional regulator   COG1395   [K]                               containing a cHTH DNA-binding                               domain       1006   965913   967550   +   545   GroL   HSP60 family chaperonin   COG0459   [O]       1007   967621   967887   −   88       Uncharacterized archaeal membrane   COG2034   [S]                               protein       1008   967906   968730   +   274   SecF   Preprotein translocase subunit SecF   COG0341   [U]       1009   968734   969945   +   403   SecD   Preprotein translocase subunit SecD   COG0342   [U]       1010   969971   971443   +   490   TrkG   Membrane subunit of a Trk-type K+   COG0168   [P]       1011   971489   972157   +   222   TrkA   NAD-binding component of a K+   COG0569   [P]       1012   972487   974457   +   656   NtpI   Archaeal/vacuolar-type H+-ATPase   COG1269   [C]                               subunit I       1013   974472   977537   +   1021   NtpK   Archaeal/vacuolar-type H+-ATPase   COG0636   [C]                               subunit K       1014   977572   978174   +   200   NtpE   Archaeal/vacuolar-type H+-ATPase   COG1390   [C]                               subunit E       1015   978178   979302   +   374   NtpC   Archaeal/vacuolar-type H+-ATPase   COG1527   [C]                               subunit C       1016   979315   979653   +   112   NtpF   Archaeal/vacuolar-type H+-ATPase   COG1436   [C]                               subunit F       1017   979665   981443   +   592   NtpA   Archaeal/vacuolar-type H+-ATPase   COG1155   [C]                               subunit A       1018   981484   982095   +   203       Uncharacterized conserved protein   COG1901   [S]       1019   982627   982932   −   101       Uncharacterized conserved protein   COG0011   [S]       1020   982920   983942   −   340       Uncharacterized protein       1021   983976   984734   +   252       Sugar phosphate   COG1082   [G]                               isomerase/epimerase       1022   984769   984969   −   66       Predicted RNA-binding protein,   COG3269   [R]                               contains TRAM domain       1023   985170   985793   −   207       Acyl-CoA synthetase (NDP forming)   COG1042   [C]       1024   985790   986929   −   379       Pyridoxal-phosphate-dependent   COG0436   [E]                               aminotransferase       1025   986956   987471   +   171       Predicted transcriptional regulator of                               amino acid metabolism consisting of                               an ACT domain and a DNA-binding                               HTH domain       1026   987473   988462   +   329       Uncharacterized conserved protein   COG2419   [S]       1027   988455   989405   +   316       Pyruvate-formate lyase-activating   COG1180   [O]                               enzyme       1028   989456   989920   +   154       ADP-ribose pyrophosphatase   COG1051   [F]       1029   989917   990534   +   205       Uncharacterized protein       1030   990746   991507   +   253   DnaN   DNA polymerase sliding clamp   COG0592   [L]                               (PCNA)       1031   991571   992038   −   155   LepB   Type I signal peptidase   COG0681   [U]       1032   992204   993154   +   316   RadA_1   RadA recombinase   COG0468   [L]       1033   993238   994077   −   279       Metal-dependent hydrolase of the   COG1234   [R]                               beta-lactamase superfamily       1034   994067   995521   −   484       Uncharacterized protein       1035   995608   998340   +   910   Lhr   Lhr-like Superfamily II helicase   COG1201   [R]       1036   998337   999296   −   319       Uncharacterized protein specific for                               M. kandleri, MK-38 family       1037   999306   999872   −   188   CobL_1   Precorrin-6B methylase   COG2242   [H]       1038   999865   1000527   +   220   CobF   Precorrin-2 methylase   COG2243   [H]       1039   1000589   1003081   +   830   PolB   B family DNA polymerase   COG0417   [L]       1040   1003150   1004791   +   546       Fe—S oxidoreductase   COG1031   [C]       1041   1004793   1009553   −   1586       Predicted protein of the CobN/Mg-   COG1429   [H]                               chelatase family       1042   1009534   1009770   −   78       Uncharacterized protein       1043   1010030   1010881   +   283       Squalene cyclase   COG1657   [I]       1044   1010902   1011384   +   160       Uncharacterized protein       1045   1011565   1013082   +   505       Uncharacterized protein       1046   1013137   1013823   −   228       L-alanine-DL-glutamate epimerase   COG4948   [MR]                               and related enzymes of enolase                               superfamily       1047   1013993   1015405   +   470   MurD_2   UDP-N-acetylmuramoylalanine-D-   COG0771   [M]                               glutamate ligase       1048   1015395   1016936   +   513   HyuB   N-methylhydantoinase B   COG0146   [EQ]       1049   1016944   1017231   +   95       Predicted pyrophosphatase   COG1694   [R]       1050   1017228   1018340   +   370       Predicted metal-dependent   COG0402   [FR]                               hydrolase related to cytosine                               deaminase       1051   1018337   1018726   +   129       Predicted nucleotide-binding protein   COG0589   [T]                               related to universal stress protein,                               UspA       1052   1018718   1020367   −   549   ELP3   ELP3 component of the RNA   COG1243   [KB]                               polymerase II complex, consists of                               an N-terminal BioB/LipA-like domain                               and a C-terminal histone acetylase                               domain       1053   1020723   1021256   +   177       Zn-dependent protease   COG1994   [R]       1054   1021422   1022354   −   310       Predicted ATPase of the PP-loop   COG0037   [D]                               superfamily implicated in cell cycle                               control       1055   1022751   1023809   +   352       Predicted deacetylase   COG0123   [BQ]       1056   1024357   1026507   −   716       Predicted exporter of the RND   COG1033   [R]                               superfamily       1057   1026786   1027487   +   233       Zn-ribbon-containing-protein       1058   1027491   1028459   +   322       Fe—S oxidoreductase   COG4004 &amp;   [S][C]                                   COG0731       1059   1028450   1028851   −   133       Uncharacterized membrane protein       1060   1028915   1029487   +   190       Predicted nucleotide kinase related   COG1936   [F]                               to CMP and AMP kinase       1061   1029500   1030444   +   314       Acetyltransferase (the isoleucine   COG0110   [R]                               patch superfamily)       1062   1030519   1031127   +   202   PDX2   Predicted glutamine   COG0311   [H]                               amidotransferase involved in                               pyridoxine biosynthesis       1063   1031140   1032081   +   313   GltB_2   Glutamate synthase subunit 1   COG0067   [E]       1064   1032078   1032770   +   230   GltB_3   Glutamate synthase subunit 3   COG0070   [E]       1065   1032777   1033466   +   229       Predicted PP-loop superfamily   COG0603   [R]                               ATPase       1066   1033579   1033920   +   113       Uncharacterized protein       1067   1033966   1035177   +   403       Predicted SAM-dependent   COG1092   [R]                               methyltransferase       1068   1035174   1036619   −   481       Uncharacterized membrane protein                               specific for M. kandleri, MK-25 family       1069   1036609   1037562   −   317   Mdh   NADPH-dependent L-malate   COG0039   [C]                               dehydrogenase       1070   1037571   1038509   −   312   ArgF   Ornithine carbamoyltransferase   COG0078   [E]       1071   1038509   1039858   −   449   PurD   Phosphoribosylamine-glycine ligase   COG0151   [F]       1072   1039833   1040384   −   183   PyrE   Orotate phosphoribosyltransferase   COG0461   [F]       1073   1040378   1040899   −   173   CdsA   CDP-diglyceride synthetase   COG0575   [I]       1074   1040918   1042417   +   499       Predicted Fe—S oxidoreductase   COG1964   [R]       1075   1042423   1043175   +   250   SIR2   NAD-dependent protein deacetylase,   COG0846   [K]                               SIR2 family       1076   1043739   1044446   −   235       Uncharacterized Rossman fold   COG1634   [R]                               enzyme       1077   1044460   1045491   +   343   ArgC   Acetylglutamate semialdehyde   COG0002   [E]                               dehydrogenase       1078   1045573   1046004   −   143       Predicted hydrocarbon binding   COG1719   [R]                               protein (contains V4R domain)       1079   1046073   1046807   −   244       Metal-dependent hydrolases of the   COG1237   [R]                               beta-lactamase superfamily II       1080   1047394   1047978   +   194   MobB   Molybdopterin-guanine dinucleotide   COG1763   [H]                               biosynthesis protein       1081   1048183   1049454   −   423   MiaB   2-methylthioadenine synthetase   COG0621   [J]       1082   1049460   1050929   −   489       Uncharacterized membrane protein                               specific for M. kandleri, MK-16 family       1083   1050955   1052430   −   491       Predicted glycosyltransferase   COG0438   [M]       1084   1052589   1054142   −   517       Queuine tRNA-ribosyltransferase,   COG1549   [J]                               contains RNA-binding PUA domain       1085   1054126   1055544   −   472   PurB   Adenylosuccinate lyase   COG0015   [F]       1086   1055634   1056806   −   390       Ferredoxin domain fused to   COG1145 &amp;   [C][R]                               pyruvate-formate lyase-activating   COG0535                               enzyme       1087   1056850   1057029   −   59       Nitrogen regulatory protein PII   COG0347   [E]                               homolog       1088   1057581   1058501   +   306       Uncharacterized protein conserved   COG3366   [S]                               in archaea       1089   1058600   1058881   +   93   Ssh10b_2   Archaea-specific DNA-binding   COG1581   [K]                               protein       1090   1058918   1059742   +   274       CBS-domain-containing protein   COG0517   [R]       1091   1059786   1061828   +   680   HyuA_1   N-methylhydantoinase A   COG0145   [EQ]       1092   1061983   1062237   +   84       Uncharacterized protein       1093   1062427   1063875   −   482   HyuA_2   N-methylhydantoinase A   COG0145   [EQ]       1094   1063943   1064371   −   142       Uncharacterized domain specific for                               M. kandleri, MK_11       1095   1064771   1065691   −   306       Uncharacterized protein       1096   1066239   1067360   −   373       Uncharacterized protein specific for                               M. kandleri, MK-7 family       1097   1067565   1067867   −   100       Uncharacterized protein specific for                               M. kandleri, MK-45 family       1098   1067881   1068231   −   116       Uncharacterized protein specific for                               M. kandleri, MK-35 family       1099   1068430   1069563   −   377       Uncharacterized protein specific for                               M. kandleri, MK-7 family       1100   1070068   1071114   +   348       Predicted extracellular   COG2342   [G]                               polysaccharide hydrolase of the                               endo alpha-1,4                               polygalactosaminidase family       1101   1071283   1072530   +   415       Uncharacterized protein specific for                               M. kandleri, MK-32 family       1102   1072764   1073159   −   131   Fur_1   Predicted transcriptional regulator   COG0640   [K]                               containing a HTH DNA-binding                               domain       1103   1073510   1074421   +   303       Predicted ATPase of the PP-loop   COG0037   [D]                               superfamily implicated in cell cycle                               control       1104   1074418   1075152   −   244       Uncharacterized membrane protein                               specific for M. kandleri, MK-4 family       1105   1075156   1076343   −   395       Uncharacterized conserved protein   COG1641   [S]       1106   1076417   1076743   +   108       Nitrogen regulatory protein PII   COG4075   [S]                               homolog       1107   1076740   1077711   −   323       Predicted metabolic regulator   COG1719   [R]                               containing two V4R domains       1108   1077887   1079302   −   471       NAD-dependent aldehyde   COG1012   [C]                               dehydrogenase       1109   1079336   1080184   −   282       Uncharacterized protein       1110   1080370   1081089   −   239       Uncharacterized protein       1111   1081197   1082513   +   438       Uncharacterized protein       1112   1082635   1084164   −   509       Uncharacterized protein specific for                               M. kandleri, MK-8 family       1113   1084374   1084985   −   203       Uncharacterized protein specific for                               M. kandleri, MK-22 family       1114   1085323   1086447   −   374       Uncharacterized secreted protein                               specific for M. kandleri with repeats,                               MK-6 family       1115   1086530   1088314   −   594       Uncharacterized secreted protein                               specific for M. kandleri with repeats,                               MK-6 family       1116   1088392   1090035   −   547       Uncharacterized protein specific for                               M. kandleri, MK-8 family       1117   1090497   1090760   −   87       Uncharacterized protein       1118   1090917   1091960   −   347       Uncharacterized protein       1119   1091917   1092153   −   78       Uncharacterized protein       1120   1092364   1093884   −   506   MCM2_2   Predicted ATPase involved in   COG1241   [L]                               replication control, Cdc46/Mcm                               family       1121   1095025   1095999   +   324       Uncharacterized protein specific for                               M. kandleri, MK-23 family       1122   1096289   1097245   +   318   HmdIII   N5,N10-   COG4007   [R]                               methylenetetrahydromethanopterin                               dehydrogenase (H2-forming)       1123   1097550   1097834   −   94       Uncharacterized protein conserved                               in archaea       1124   1098197   1099186   +   329       Uncharacterized membrane protein       1125   1099190   1100172   −   327       Predicted extracellular   COG2342   [G]                               polysaccharide hydrolase of the                               Endo alpha-1,4                               polygalactosaminidase family       1126   1101061   1101891   −   276   FtsZ_3   FtsZ GTPase involved in cell division   COG0206   [D]       1127   1102191   1102478   +   95       Predicted membrane protein       1128   1102596   1103690   −   364       Permease of the major facilitator   COG0477   [GEPR]                               superfamily       1129   1104523   1105320   +   265       Predicted protease or amidase   COG0693   [R]       1130   1105400   1105687   +   95       Uncharacterized protein       1131   1107532   1108419   −   295       Uncharacterized protein specific for                               M. kandleri, MK-23 family       1132   1109620   1110027   +   135       Uncharacterized conserved protein   COG2250   [S]                               related to C-terminal domain of                               eukaryotic chaperone, SACSIN       1133   1110240   1110470   −   76       Uncharacterized protein       1134   1113424   1114281   +   285       Uncharacterized protein       1135   1114332   1115444   +   370       Permease of the major facilitator   COG0477   [GEPR]                               superfamily       1136   1115624   1116253   +   209       Uncharacterized protein specific for                               M. kandleri, MK-1 family       1137   1116295   1116663   −   122       Predicted nucleotidyltransferase of   COG1708   [R]                               the DNA polymerase beta                               superfamily       1138   1116684   1116905   +   73       Uncharacterized conserved protein   COG2250   [S]                               related to C-terminal domain of                               eukaryotic chaperone, SACSIN       1139   1116898   1117071   +   57       Uncharacterized protein       1140   1117134   1117373   −   79       Uncharacterized protein       1141   1117370   1117810   −   146       Uncharacterized membrane protein                               specific for M. kandleri, MK-17 family       1142   1117919   1118431   −   170       Uncharacterized protein specific for                               M. kandleri, MK-22 family       1143   1119001   1119915   −   304       Uncharacterized protein       1144   1120281   1121489   −   402       Predicted membrane protein       1145   1122067   1122807   +   246       Predicted membrane protein       1146   1122763   1123665   −   300       Uncharacterized membrane protein                               specific for M. kandleri, MK-9 family       1147   1125171   1125659   −   162       Uncharacterized protein specific for                               M. kandleri, MK-5 family       1148   1125923   1130821   +   1632       Uncharacterized secreted protein                               specific for M. kandleri with repeats,                               MK-5 family       1149   1130814   1136363   +   1849       Uncharacterized secreted protein                               specific for M. kandleri with repeats,                               MK-5 family       1150   1136364   1137101   +   245       Predicted membrane protein       1151   1137105   1137752   +   215       Predicted membrane protein       1152   1138095   1138991   +   298       Uncharacterized membrane protein                               specific for M. kandleri, MK-9 family       1153   1139217   1139651   +   144       Predicted membrane protein       1154   1139945   1141204   +   419       Uncharacterized membrane protein                               specific for M. kandleri, MK-9 family       1155   1141640   1142470   +   276       Uncharacterized membrane protein       1156   1142499   1142942   +   147       Uncharacterized protein specific for                               M. kandleri, MK-24 family       1157   1143512   1144135   −   207       Uncharacterized protein specific for                               M. kandleri, MK-1 family       1158   1144383   1145600   −   405       Uncharacterized membrane protein                               specific for M. kandleri, MK-9 family       1159   1145844   1146677   +   277       Uncharacterized membrane protein                               specific for M. kandleri, MK-26 family       1160   1146822   1147688   +   288       Uncharacterized membrane protein                               specific for M. kandleri, MK-26 family       1161   1148015   1148680   +   221       Uncharacterized membrane protein                               specific for M. kandleri, MK-9 family       1162   1148705   1149403   +   232       Uncharacterized membrane protein                               specific for M. kandleri, MK-17 family       1163   1149695   1150318   −   207       Uncharacterized protein specific for                               M. kandleri, MK-1 family       1164   1151111   1151647   −   178       Thermonuclease   COG1525   [L]       1165   1151966   1152913   −   315       Uncharacterized protein       1166   1152967   1154208   −   413       Uncharacterized conserved protein   COG3287   [S]       1167   1155432   1156157   +   241       Uncharacterized protein       1168   1156220   1157155   +   311       Uncharacterized secreted protein                               specific for M. kandleri, MK-6 family       1169   1158073   1158933   −   286       Uncharacterized protein       1170   1160085   1161410   −   441       Fusion of at least two                               uncharacterized domain specific for                               M. kandleri, MK-12 family       1171   1161703   1162374   −   223       Predicted membrane-bound metal-   COG1988   [R]                               dependent hydrolase       1172   1162560   1163432   +   290       Uncharacterized protein       1173   1163540   1164262   +   240       Uncharacterized protein specific for                               M. kandleri, MK-27 family       1174   1165552   1166187   +   211       Predicted membrane protein       1175   1167028   1167396   −   122       Uncharacterized protein       1176   1167393   1167758   −   121       Uncharacterized protein       1177   1168689   1171121   +   810       Protein containing a metal-binding                               domain shared with                               formylmethanofuran dehydrogenase                               subunit E       1178   1171194   1174100   +   968       Uncharacterized protein conserved                               in archaea       1179   1174103   1174543   −   146       Uncharacterized protein       1180   1174740   1175693   −   317       Uncharacterized protein       1181   1176046   1176945   +   299       Uncharacterized protein specific for                               M. kandleri, MK-7 family       1182   1177071   1177787   −   238       Uncharacterized protein specific for                               M. kandleri, MK-27 family       1183   1178571   1179359   −   262       Polyferredoxin   COG0348   [C]       1184   1179463   1179858   −   131       Uncharacterized protein       1185   1179906   1180262   −   118       Uncharacterized protein       1186   1181791   1182024   +   77       Uncharacterized protein specific for                               M. kandleri, MK-20 family       1187   1182514   1183490   +   325       Predicted extracellular   COG2342   [G]                               polysaccharide hydrolase of the                               endo alpha-1,4                               polygalactosaminidase family       1188   1183487   1183930   +   147       Uncharacterized protein       1189   1184101   1185807   −   568       ATPase subunit of an ABC-type   COG1123   [R]                               transport system, contains a                               duplicated ATPase domain       1190   1185746   1186216   −   156       Uncharacterized protein       1191   1186199   1186804   +   201       Membrane-associated phospholipid   COG0671   [I]                               phosphatase       1192   1186783   1187529   +   248       Uncharacterized conserved protein   COG0327   [S]       1193   1187747   1189015   +   422       Predicted phosphoglycerate mutase,   COG3635   [G]                               AP superfamily       1194   1189020   1189562   +   180       Predicted membrane protein   COG1238   [S]       1195   1189569   1190054   +   161   PurE   Phosphoribosylcarboxyaminoimidazole   COG0041   [F]                               (NCAIR) mutase       1196   1190035   1190634   −   199   CobH   Precorrin isomerase   COG2082   [H]       1197   1190631   1192280   −   549   IlvD   Dihydroxyacid dehydratase   COG0129   [EG]       1198   1192330   1192938   +   202       Integral membrane protein of the   COG2095   [U]                               MarC family       1199   1192943   1194109   +   388       Predicted GTPase of the OBG/HflX   COG1163   [R]                               superfamily       1200   1194106   1194801   +   231       Uncharacterized, MobA-related   COG2068   [R]                               protein       1201   1194798   1194998   −   66   TatA   Sec-independent protein secretion   COG1826   [U]                               pathway component       1202   1195047   1195664   −   205   HyaB   Ni,Fe-hydrogenase I large subunit   COG0374   [C]       1203   1195681   1196247   −   188       Uncharacterized protein       1204   1196692   1196952   −   86       Uncharacterized protein       1205   1196967   1197401   −   144       Uncharacterized protein       1206   1197474   1197980   −   168   LeuD_2   3-isopropylmalate dehydratase small   COG0066   [E]                               subunit       1207   1197964   1198437   −   157       Predicted membrane protein   COG3431   [S]       1208   1198443   1199651   −   402   LeuC_2   3-isopropylmalate dehydratase large   COG0065   [E]                               subunit       1209   1200171   1201364   −   397   LeuA   Isopropylmalate synthase   COG0119   [E]       1210   1201369   1201722   −   117       Uncharacterized conserved protein   COG1993   [S]       1211   1201704   1202099   −   131   CrcB   Integral membrane protein possibly   COG0239   [D]                               involved in chromosome                               condensation       1212   1202106   1202915   −   269       Uncharacterized bacitracin   COG1968   [V]                               resistance protein       1213   1203140   1203412   +   90       Predicted metabolic regulator   COG3830   [T]                               containing an ACT domain       1214   1203418   1204770   +   450       Uncharacterized conserved protein   COG2848   [S]       1215   1204838   1205845   +   335   LeuB_2   Isopropylmalate dehydrogenase   COG0473   [E]       1216   1206266   1206589   +   107   POP4_2   RNAse P subunit P29   COG1588   [J]       1217   1206586   1206942   +   118   RpsQ   Ribosomal protein S17   COG0186   [J]       1218   1206955   1207356   +   133   RplN   Ribosomal protein L14   COG0093   [J]       1219   1207371   1207820   +   149   RplX   Ribosomal protein L24   COG0198   [J]       1220   1207835   1208617   +   260   RPS4A   Ribosomal protein S4E   COG1471   [J]       1221   1208630   1209190   +   186   RplE   Ribosomal protein L5   COG0094   [J]       1222   1209205   1209351   +   48   RpsN   Ribosomal protein S14   COG0199   [J]       1223   1209368   1209760   +   130   RpsH   Ribosomal protein S8   COG0096   [J]       1224   1209774   1210388   +   204   RplF   Ribosomal protein L6   COG0097   [J]       1225   1210401   1210796   +   131   RPL32   Ribosomal protein L32E   COG1717   [J]       1226   1210813   1211850   −   345   PurM   Phosphoribosylaminoimidazol (AIR)   COG0150   [F]                               synthetase       1227   1211864   1213822   −   652       Predicted metal-dependent RNase,   COG1782   [R]                               consists of a metallo-beta-lactamase                               domain and an RNA-binding KH                               domain       1228   1213888   1214520   −   210   HslV_2   Protease subunit of the proteasome   COG0638   [O]       1229   1214563   1216020   −   485   ProS   Prolyl-tRNA synthetase   COG0442   [J]       1230   1215994   1217055   +   353   GldA   Glycerol dehydrogenase   COG0371   [C]       1231   1217045   1217704   −   219   SlpA   FKBP-type peptidyl-prolyl cis-trans   COG1047   [O]                               isomerase       1232   1217710   1218660   −   316   SufB   ABC-type transport system involved   COG0719   [O]                               in Fe—S cluster assembly, permease                               component       1233   1218618   1219331   −   237   SufC   ABC-type transport system involved   COG0396   [O]                               in Fe—S cluster assembly, ATPase                               component       1234   1219555   1220589   +   344       Uncharacterized protein       1235   1220565   1221341   −   258       Predicted endonuclease of the RecB   COG4998   [L]                               family       1236   1221500   1222936   −   478       Acetolactate synthase large subunit   COG0028   [EH]                               homolog       1237   1222933   1223619   −   228       Predicted DNA-binding protein   COG1458   [R]                               containing PIN domain       1238   1223616   1224314   −   232       Uncharacterized protein       1239   1224388   1225167   −   259       MinD superfamily P-loop ATPase   COG1149   [C]                               containing an inserted ferredoxin                               domain       1240   1225182   1225970   −   262       MinD superfamily P-loop ATPase   COG1149   [C]                               containing an inserted ferredoxin                               domain       1241   1225978   1226307   −   109       Uncharacterized conserved protein   COG1433   [S]       1242   1226308   1226547   −   79       Zn-ribbon-containing protein       1243   1226554   1226736   −   60       Ferredoxin   COG1145   [C]       1244   1226760   1227170   −   136       Uncharacterized protein conserved                               in archaea       1245   1227252   1227620   +   122       CBS-domain   COG0517   [R]       1246   1227625   1228965   +   446       Acyl-CoA synthetase (NDP forming)   COG1042   [C]       1247   1228998   1229237   +   79   FeoA   Ferrous ion uptake system subunit   COG1918   [P]       1248   1229242   1231194   +   650   FeoB   Ferrous ion uptake system subunit,   COG0370   [P]                               predicted GTPase       1249   1231755   1232132   −   125       Rubrerythrin   COG1592   [C]       1250   1232451   1232984   −   177       Uncharacterized membrane protein       1251   1234371   1235411   −   346       Uncharacterized protein       1252   1236233   1236910   −   225       Uncharacterized protein specific for                               M. kandleri, MK-1 family       1253   1237175   1240579   +   1134       Uncharacterized secreted protein                               specific for M. kandleri, MK-28 family       1254   1241043   1241195   +   50       Uncharacterized protein       1255   1241416   1241982   +   188       Predicted RNA-binding protein                               containing PIN domain       1256   1241966   1242934   −   322       Uncharacterized domain specific for                               M. kandleri, MK-34 family       1257   1243554   1244471   −   305       Uncharacterized protein       1258   1244552   1245679   +   375       Predicted hydrolase of the metallo-   COG0595   [R]                               beta-lactamase superfamily fused to                               a uncharacterized domain       1259   1245681   1248527   −   948       Adenine-specific DNA methylase   COG1743   [L]                               containing a Zn-ribbon       1260   1248593   1250761   +   722       Predicted ATPase of the AAA+ class   COG1483   [R]       1261   1253762   1254154   +   130   Fur_2   Fe2+/Zn2+ uptake regulator similar   COG0640   [K]                               to transcriptional regulators       1262   1254242   1255155   +   303       ATPase involved in chromosome   COG1192   [D]                               partitioning       1263   1255170   1255841   +   223       Uncharacterized protein specific for                               M. kandleri, MK-29 family       1264   1255904   1257532   +   542       Uncharacterized protein specific for                               M. kandleri, MK-37 family       1265   1257546   1258277   +   243       Uncharacterized protein       1266   1258311   1259615   +   434       Uncharacterized protein specific for                               M. kandleri, MK-37 family       1267   1259840   1261165   +   441       Uncharacterized protein specific for                               M. kandleri, MK-37 family       1268   1261784   1263256   −   490       Uncharacterized secreted protein                               specific for M. kandleri, MK-28 family       1269   1264021   1264473   +   150       Uncharacterized protein specific for                               M. kandleri, MK-1 family       1270   1264935   1265888   −   317       Uncharacterized protein       1271   1266112   1267695   −   527       Uncharacterized protein       1272   1267711   1269366   −   551       Uncharacterized protein       1273   1269348   1270529   −   393       Uncharacterized secreted protein                               specific for M. kandleri, MK-5 family       1274   1270586   1271590   −   334       Predicted hydrolase of the metallo-   COG0595   [R]                               beta-lactamase superfamily       1275   1271731   1272240   −   169       Uncharacterized protein conserved   COG1795   [S]                               in archaea       1276   1272292   1273644   −   450       Fusion of at least two                               uncharacterized domain specific for                               M. kandleri, MK-12 family       1277   1274035   1274772   +   245       Uncharacterized protein specific for                               M. kandleri, MK-14 family       1278   1275808   1277502   −   564       Uncharacterized protein specific for                               M. kandleri, MK-19 family       1279   1277672   1278295   +   207       Uncharacterized protein       1280   1278820   1279008   +   62       Uncharacterized protein       1281   1279599   1280219   −   206       Uncharacterized protein specific for                               M. kandleri, MK-14 family       1282   1280956   1281933   −   325       Uncharacterized protein conserved                               in archaea       1283   1282214   1283809   −   531       Fusion of at least two                               uncharacterized domain specific for                               M. kandleri, MK-2 family       1284   1283981   1284406   −   141       Uncharacterized conserved protein   COG2250   [S]                               related to C-terminal domain of                               eukaryotic chaperone, SACSIN       1285   1284412   1284786   +   124       Predicted nucleotidyltransferase of   COG1708   [R]                               the DNA polymerase beta family       1286   1285068   1286045   +   325       Uncharacterized secreted protein                               specific for M. kandleri, MK-30 family       1287   1286185   1286763   −   192       Uncharacterized protein specific for                               M. kandleri, MK-1 family       1288   1287009   1287983   −   324       Uncharacterized secreted protein                               specific for M. kandleri, MK-3 family       1289   1288128   1290386   +   752       Adenine-specific DNA methylase   COG1743   [L]                               containing a Zn-ribbon       1290   1290370   1291122   +   250       Uncharacterized protein       1291   1291279   1291923   −   214       Uncharacterized protein specific for                               M. kandleri, MK-1 family       1292   1292092   1292835   −   247       Predicted nucleotidyltransferase of   COG1708 &amp;   [R][S]                               the DNA polymerase beta   COG2250                               supefamily fused to an                               Uncharacterized conserved protein                               related to C-terminal domain of                               eukaryotic chaperone, SACSIN       1293   1292953   1294143   +   396       Uncharacterized protein conserved   COG4006   [S]                               in archaea       1294   1294371   1295660   +   429       Uncharacterized protein       1295   1295771   1296877   −   368       Uncharacterized secreted protein                               specific for M. kandleri, MK-3 family       1296   1298182   1300266   −   694       Predicted component of a   COG1336 &amp;   [L][L]                               thermophile-specific DNA repair   COG1604                               system, contains two domains of the                               RAMP family       1297   1301091   1303472   +   793       Predicted DNA-dependent DNA   COG1353   [R]                               polymerase, component of a                               thermophile-specific DNA repair                               system       1298   1303469   1304803   +   444       Uncharacterized protein       1299   1304800   1305828   +   342       Predicted component of a   COG1336   [L]                               thermophile-specific DNA repair                               system, contains a RAMP domain       1300   1308020   1308490   −   156       Uncharacterized protein       1301   1308525   1310213   −   562       Squalene cyclase   COG1657   [I]       1302   1311974   1312216   +   80       Uncharacterized protein       1303   1312185   1313237   −   350       Uncharacterized domain specific for                               M. kandleri, MK-11 family       1304   1313373   1314599   −   408       Uncharacterized protein specific for                               M. kandleri, MK-14 family       1305   1314596   1316125   −   509       Uncharacterized membrane protein                               specific for M. kandleri, MK-16 family       1306   1316132   1317607   −   491       Predicted glycosyltransferase   COG0438   [M]       1307   1319237   1319530   −   97       Predicted nucleotidyltransferase of   COG1708   [R]                               the DNA polymerase beta                               superfamily       1308   1319573   1321492   −   639       Predicted P-loop ATPase       1309   1322642   1323265   +   207       Uncharacterized protein specific for                               M. kandleri, MK-1 family       1310   1324335   1324640   −   101       Uncharacterized protein predicted to   COG1343   [L]                               be involved in DNA repair       1311   1324652   1326787   −   711       Homolog of the eukaryotic argonaute   COG1431   [J]                               protein, implicated in translation or                               RNA processing       1312   1326771   1327766   −   331       Uncharacterized protein predicted to   COG1518   [L]                               be involved in DNA repair       1313   1329452   1330918   −   488       Uncharacterized domain specific for                               M. kandleri, MK-11 family       1314   1331274   1334015   +   913       Predicted DNA-dependent DNA   COG1353   [R]                               polymerase, component of a                               thermophile-specific DNA repair                               system       1315   1334017   1334541   +   174       Uncharacterized protein predicted to   COG1421   [L]                               be involved in DNA repair       1316   1334554   1335609   +   351       Predicted component of a   COG1337   [L]                               thermophile-specific DNA repair                               system, contains a RAMP domain       1317   1335611   1336702   +   363       Uncharacterized protein       1318   1336699   1338027   +   442       Uncharacterized protein       1319   1338024   1339115   +   363       Predicted component of a                               thermophile-specific DNA repair                               system, contains a RAMP domain       1320   1339214   1339987   +   257       Predicted xylanase/chitin   COG0726   [G]                               deacetylase family enzyme       1321   1340038   1340202   +   54       Uncharacterized protein       1322   1340374   1340895   +   173       Predicted membrane protein       1323   1340890   1341540   −   216       Metal-dependent hydrolase of the   COG1237   [R]                               beta-lactamase superfamily       1324   1342074   1342703   +   209       Uncharacterized membrane protein                               specific for M. kandleri, MK-31 family       1325   1342985   1343332   +   115       Predicted regulator of Ras-like   COG2018   [R]                               GTPase activity, member of the                               Roadblock/LC7/MgIB family       1326   1344045   1344728   +   227       Uncharacterized domain specific for                               M. kandleri, MK-12 family       1327   1344701   1345228   +   175       Uncharacterized domain specific for                               M. kandleri, MK-12 family       1328   1345308   1345556   −   82       Uncharacterized protein       1329   1345608   1346639   −   343       Uncharacterized protein specific for                               M. kandleri, MK-32 family       1330   1346857   1349094   −   745       Predicted membrane protein       1331   1349240   1350568   −   442       Uncharacterized domain specific for                               M. kandleri, MK-11 family       1332   1351003   1351692   +   229       Uncharacterized protein       1333   1351717   1352718   +   333       Uncharacterized domain specific for                               M. kandleri, MK-2 family       1334   1352753   1353799   −   348       Predicted membrane-bound metal-   COG1988   [R]                               dependent hydrolase       1335   1353804   1354355   −   183       Zn-dependent hydrolase   COG0491   [R]       1336   1354689   1355963   −   424       Uncharacterized protein specific for                               M. kandleri, MK-42 family       1337   1356271   1356459   −   62       Uncharacterized protein       1338   1356793   1357287   −   164       Uncharacterized protein       1339   1357826   1360414   −   862       Uncharacterized protein specific for                               M. kandleri, contains two domains of                               the MK-3 family       1340   1360653   1361492   +   279       Uncharacterized protein       1341   1361489   1361719   +   76       Uncharacterized protein       1342   1361829   1362332   +   167       Uncharacterized membrane protein                               specific for M. kandleri, MK-31 family       1343   1364466   1365077   +   203       Uncharacterized protein specific for                               M. kandleri, MK-1 family       1344   1365140   1366013   +   290       Uncharacterized domain specific for                               M. kandleri, MK-34 family, a fragment       1345   1366319   1367176   −   285       Fe—S oxidoreductase   COG0535   [R]       1346   1367297   1368256   −   319       Uncharacterized secreted protein                               specific for M. kandleri, MK-3 family       1347   1368270   1368527   −   85       Uncharacterized protein       1348   1369122   1369865   −   247       Uncharacterized domain specific for                               M. kandleri, MK-2 family       1349   1369858   1370589   −   243       Uncharacterized domain specific for                               M. kandleri, MK-2 family       1350   1370729   1371478   −   249       Predicted cysteine protease of the   COG1305   [E]                               transglutaminase-like superfamily       1351   1371767   1375339   −   1190       Predicted protein of CobN/Mg-   COG1429   [H]                               chelatase family       1352   1375488   1376102   +   204       Uncharacterized protein specific for                               M. kandleri, MK-35 family       1353   1376114   1376947   +   277       Uncharacterized protein specific for                               M. kandleri, MK-45 family       1354   1376796   1377713   +   305       Uncharacterized membrane protein                               specific for M. kandleri, MK-10 family       1355   1378052   1378888   +   278       Uncharacterized membrane protein                               specific for M. kandleri, MK-10 family       1356   1379071   1380000   +   309       Uncharacterized membrane protein                               specific for M. kandleri, MK-10 family       1357   1380143   1380862   +   239       Uncharacterized membrane protein                               specific for M. kandleri, MK-10 family       1358   1381069   1381686   +   205       Putative component of a threonine   COG1280   [E]                               efflux system       1359   1381905   1382150   −   81       Uncharacterized protein       1360   1382453   1383180   +   242       Uncharacterized membrane protein                               specific for M. kandleri, MK-10 family,                               a fragment       1361   1384064   1385821   +   585       Calcineurin superfamily phosphatase                               or nuclease       1362   1385837   1386457   −   206   Nth_2   A/G-specific DNA glycosylase   COG0177   [L]       1363   1387524   1389643   +   706       Predicted membrane protein                               specific for M. kandleri, MK-13 family,                               a frameshift       1364   1389932   1392763   +   943   LeuS   Leucyl-tRNA synthetase   COG0495   [J]       1365   1392767   1393741   −   324   HmdII   N5,N10-   COG4007   [R]                               methylenetetrahydromethanopterin                               dehydrogenase (H2-forming)       1366   1393825   1395282   −   485   CCA1   tRNA nucleotidyltransferase (CCA-   COG1746   [J]                               adding enzyme)       1367   1395443   1396009   −   188   LigT   2′-5′ RNA ligase   COG1514   [J]       1368   1396144   1397154   +   336       Predicted ATPase of the AAA+ class   COG1223   [R]       1369   1397219   1398223   −   334   SelD   Selenophosphate synthase   COG0709   [E]       1370   1398408   1399037   −   209   ThyA   Thymidylate synthase   COG0207   [F]       1371   1399129   1400016   −   295   SNZ1   Pyridoxine biosynthesis enzyme   COG0214   [H]       1372   1400084   1400647   +   187       Small, Ras-like GTPase   COG2229   [R]       1373   1400669   1401601   +   310       Uncharacterized protein       1374   1401670   1402089   +   139       Uncharacterized protein       1375   1402137   1402895   +   252   CobM   Precorrin-4 methylase   COG2875   [H]       1376   1403490   1404254   +   254   CobJ   Precorrin-3B methylase   COG1010   [H]       1377   1404218   1404622   −   134       Predicted nucleic-acid-binding   COG1545   [R]                               protein containing a Zn-ribbon       1378   1404635   1405819   −   394       Acetyl-CoA acetyltransferase   COG0183   [I]       1379   1405824   1406876   −   350   PksG   3-hydroxy-3-methylglutaryl CoA   COG3425   [I]                               synthase       1380   1406873   1407622   −   249       Predicted transcriptional regulator   COG1709   [K]                               containing a DNA-binding HTH                               domain       1381   1407623   1409290   +   555       Glycosyltransferase involved in cell   COG0463   [M]                               wall biogenesis       1382   1409287   1410831   +   514       Fe—S oxidoreductase   COG1032   [C]       1383   1410810   1411397   −   195       Uncharacterized membrane protein   COG1814   [S]       1384   1411404   1411694   −   96       Uncharacterized protein conserved   COG1888   [S]                               in archaea       1385   1411726   1412775   +   349   NifD   Nitrogenase molybdenum-iron   COG2710   [C]                               subunit       1386   1412760   1413503   −   247   CitT   Di- and tricarboxylate transporter   COG0471   [P]       1387   1413918   1414901   +   327       Predicted integral membrane protein   COG0392   [S]       1388   1414907   1415602   +   231       Predicted ICC-like   COG1407   [R]                               phosphoesterases       1389   1415734   1416798   +   354   Asd   Aspartate-semialdehyde   COG0136   [E]       1390   1416789   1417262   −   157       Predicted Rossmann fold nucleotide-   COG1611   [R]                               binding protein       1391   1417522   1418286   +   254   TrpC   Indole-3-glycerol phosphate   COG0134   [E]                               synthase       1392   1418283   1419104   +   273       Uncharacterized domain specific for                               M. kandleri, MK-33 family       1393   1419288   1419860   −   190       Uncharacterized protein conserved   COG4073   [S]                               in archaea       1394   1419851   1421071   +   406   PRI2   Eukaryotic-type DNA primase, large   COG2219   [L]                               subunit       1395   1421041   1421427   −   128       Zn-ribbon-containing protein       1396   1421429   1422007   −   192       Uncharacterized protein       1397   1422004   1422678   −   224   RibB   3,4-dihydroxy-2-butanone 4-   COG0108   [H]                               phosphate synthase       1398   1422654   1423097   −   147       Transcriptional regulator of the   COG1339   [K]                               riboflavin/FAD biosynthetic operon       1399   1423066   1423941   −   291   RIO1_2   Serine/threonine protein kinase   COG1718   [TD]                               involved in cell cycle control       1400   1424001   1425185   −   394   PncB   Nicotinic acid   COG1488   [H]                               phosphoribosyltransferase       1401   1425410   1425775   +   121       Predicted metal-binding protein       1402   1426225   1426971   −   248       Uncharacterized protein       1403   1426968   1428236   −   422       Predicted P-loop ATPase       1404   1428233   1429309   −   358       Translation elongation factor,   COG0050   [J]                               GTPase       1405   1429356   1435184   −   1942       Predicted protein of the CobN/Mg-   COG1429   [H]                               chelatase family       1406   1435198   1436574   −   458       Terpene cyclase/mutase family   COG1657   [I]                               protein       1407   1436627   1437628   −   333       Predicted permease   COG0701   [R]       1408   1437721   1438929   −   402       Predicted alternative 3-   COG1465   [E]                               dehydroquinate synthase       1409   1438936   1439748   −   270   FbaB   Fructose-1,6-bisphosphate aldolase   COG1830   [G]                               of the DhnA family       1410   1439755   1440072   −   105       Uncharacterized protein conserved   COG3388   [S]                               in archaea       1411   1440119   1441096   −   325       Predicted ornithine cyclodeaminase,   COG2423   [E]                               mu-crystallin homolog       1412   1441454   1442305   +   283   Kch_2   NAD-binding subunit of the Kef-type   COG1226 &amp;   [P][R]                               K+ transport systems,   COG1827       1413   1442302   1442811   −   169       Uncharacterized protein       1414   1442838   1444322   +   494   CobQ   Cobyric acid synthase   COG1492   [H]       1415   1444325   1444906   +   193       Predicted SAM-dependent   COG2519   [J]                               methyltransferase involved in tRNA-                               Met maturation       1416   1444991   1445791   −   266   NifH   Nitrogenase subunit NifH (ATPase)   COG1348   [P]       1417   1445815   1446627   +   270       Uncharacterized secreted protein   COG4086   [S]       1418   1446749   1447603   +   284   NadE   NAD synthase   COG0171   [H]       1419   1447622   1447993   +   123       Uncharacterized protein       1420   1447990   1448730   +   246       Uncharacterized protein       1421   1448743   1449780   +   345       Uncharacterized protein       1422   1449777   1450604   +   275   DapB   Dihydrodipicolinate reductase   COG0289   [E]       1423   1450639   1451508   +   289       Uncharacterized protein       1424   1452087   1454831   −   914   ValS   Valyl-tRNA synthetase   COG0525   [J]       1425   1454880   1455605   +   241       Predicted membrane protein   COG4089   [S]                               conserved in archaea       1426   1455566   1456741   +   391   HisC   Histidinol-phosphate/tyrosine   COG0079   [E]                               aminotransferase       1427   1456817   1457656   −   279       Fe—S oxidoreductase   COG0535   [R]       1428   1457683   1458321   +   212   CobL_2   Precorrin-6B methylase   COG2241   [H]       1429   1458332   1459861   +   509       Fe—S oxidoreductase   COG1032   [C]       1430   1459862   1460179   +   105   ModE   N-terminal domain of molybdenum-   COG2005   [R]                               binding protein       1431   1460163   1460975   −   270       Predicted calcineurin superfamily   COG1409   [R]                               phosphohydrolase       1432   1460972   1461496   −   174       Transcription factor homologous to   COG4008   [K]                               NACalpha-BTF3 fused to metal-                               binding domain       1433   1461502   1463100   −   532       ATPase subunit of an ABC-type   COG1123   [R]                               transport system, contain duplicated                               ATPase       1434   1463176   1463880   +   234   KptA   RNA:NAD 2′-phosphotransferase   COG1859   [J]       1435   1463867   1464556   +   229   Nfi   Deoxyinosine 3′endonuclease   COG1515   [L]                               (endonuclease V)       1436   1464534   1467488   +   984   Top5   Topoisomerase V       1437   1467491   1468675   −   394   CsdB   Selenocysteine lyase   COG0520   [E]       1438   1468781   1469572   −   263       Predicted RNA methylase   COG2263   [J]       1439   1469870   1472335   +   821       Uncharacterized membrane protein                               specific for M. kandleri, MK-13 family       1440   1472310   1473566   −   418   LeuC_1   3-isopropylmalate dehydratase large   COG0065   [E]                               subunit       1441   1473643   1474941   +   432       Replication factor A (ssDNA-binding   COG1599   [L]                               protein)       1442   1474919   1475872   +   317   RadA_2   RadA recombinase   COG0468   [L]       1443   1475944   1477071   +   375       Dehydrogenase (flavoprotein)   COG0644   [C]       1444   1477068   1477274   −   68   RPL24A   Ribosomal protein L24E   COG2075   [J]       1445   1477287   1477511   −   74   RPS28A   Ribosomal protein S28E/S33   COG2053   [J]       1446   1477629   1478021   +   130   RPS6A   Ribosomal protein S6E (S10)   COG2125   [J]       1447   1478058   1479296   +   412       Translation initiation factor 2, gamma   COG5257   [J]                               subunit (elF-2gamma; GTPase)       1448   1479303   1479695   +   130       Predicted RNA-binding protein   COG1412   [R]                               containing PIN domain       1449   1479700   1480290   +   196   MenG   Demethylmenaquinone   COG0684   [H]                               methyltransferase       1450   1480295   1480825   +   176   Ppa   Inorganic pyrophosphatase   COG0221   [C]       1451   1480832   1481383   +   183   RpoE1   DNA-directed RNA polymerase   COG1095   [K]                               subunit E′       1452   1481625   1481819   +   64   RpoE2   DNA-directed RNA polymerase   COG2093   [K]                               subunit E″       1453   1481816   1482391   +   191       Uncharacterized protein conserved   COG1909   [S]                               in archaea       1454   1482334   1482684   +   116   RPS24A   Ribosomal protein S24E   COG2004   [J]       1455   1482704   1482883   +   60   RPS31   Ribosomal protein S27AE   COG1998   [J]       1456   1482941   1483564   +   206       Mn2+-dependent serine/threonine   COG3642   [T]                               protein kinase       1457   1483561   1484421   −   286       Uncharacterized protein       1458   1484461   1485501   +   346   QRI7   O-sialoglycoprotein endopeptidase   COG0533   [O]       1459   1485851   1486678   +   275       Uncharacterized protein       1460   1486724   1488307   +   527   SerS   Seryl-tRNA synthetase   COG0172   [J]       1461   1488365   1489000   +   211   RPS1A   Ribosomal protein S3AE   COG1890   [J]       1462   1489038   1490084   +   348       Predicted RNA-binding protein,   COG1818   [R]                               contains THUMP domain       1463   1490418   1491233   +   271       Predicted TIM-barrel enzyme   COG0434   [R]       1464   1491224   1491904   +   226       Predicted nucleotidyltransferase of   COG2413   [R]                               the DNA polymerase beta                               superfamily       1465   1491877   1492431   −   184   UbiX   3-polyprenyl-4-hydroxybenzoate   COG0163   [H]                               decarboxylase       1466   1492501   1493112   −   203       Uncharacterized membrane protein       1467   1493235   1493510   +   91       Uncharacterized protein conserved   COG4009   [S]                               in archaea       1468   1493507   1494061   +   184       Uncharacterized protein conserved   COG4010   [S]                               in archaea       1469   1494113   1494733   +   206       Predicted phosphoesterases, related   COG2129   [R]                               to the lcc protein       1470   1494730   1495332   +   200       Predicted HD superfamily hydrolase   COG1418   [R]       1471   1495427   1495882   +   151   RpsM   Ribosomal protein S13   COG0099   [J]       1472   1495896   1496456   +   186   RpsD   Ribosomal protein related to S4   COG0522   [J]       1473   1496474   1496887   +   137   RpsK   Ribosomal protein S11   COG0100   [J]       1474   1496884   1497711   +   275   RpoA   DNA-directed RNA polymerase   COG0202   [K]                               alpha subunit       1475   1497708   1498091   +   127   RPL18A   Ribosomal protein L18E   COG1727   [J]       1476   1498106   1498585   +   159   RplM   Ribosomal protein L13   COG0102   [J]       1477   1498586   1498990   +   134   RpsI   Ribosomal protein S9   COG0103   [J]       1478   1499006   1499224   +   72   RPB10   DNA-directed RNA polymerase,   COG1644   [K]                               subunit N       1479   1499506   1500867   +   453       Uncharacterized protein specific for                               M. kandleri, MK-39 family       1480   1501160   1502089   +   309   PyrB   Aspartate carbamoyltransferase,   COG0540   [F]                               catalytic subunit       1481   1502086   1502556   +   156   PyrI   Aspartate carbamoyltransferase,   COG1781   [F]                               regulatory subunit       1482   1502646   1503560   +   304       Transcriptional regulator of the LysR   COG0583   [K]                               family       1483   1504035   1505579   −   514   FolP   Dihydropteroate synthase   COG0294   [H]       1484   1505554   1506294   −   246       Archaea-specific flavoprotein   COG1036   [C]       1485   1506320   1506547   −   75   MtrF   N5-methyl-   COG4218   [H]                               tetrahydromethanopterin:coenzyme                               M methyltransferase, subunit F       1486   1506670   1507077   −   135       Uncharacterized conserved protein   COG1786   [S]       1487   1507201   1507398   −   65   MrtA   Methyl coenzyme M reductase,   COG4058   [H]                               alpha subunit, fragment       1488   1507688   1508737   +   349       Fe—S oxidoreductase, related to   COG1625   [C]                               NifB/MoaA family       1489   1508860   1509792   +   310   CofD   2-phospho-L-lactate transferase   COG0391   [S]       1490   1509797   1510498   +   233   NfnB   Nitroreductase   COG0778   [C]       1491   1510584   1511174   +   196       Methylase of polypeptide chain   COG2890   [J]                               release factors       1492   1511252   1511560   +   102   CutA   Uncharacterized protein involved in   COG1324   [P]                               tolerance to divalent cations       1493   1511580   1512938   −   452   HypE_1   Hydrogenase maturation factor   COG1973   [O]       1494   1513509   1513742   +   77       Uncharacterized protein specific for                               M. kandleri, MK-20 family       1495   1513859   1514368   −   169   CysG_1   Siroheme synthase (precorrin-2   COG1648   [H]                               oxidase/ferrochelatase domain)       1496   1514479   1515249   −   256       Uncharacterized protein       1497   1515253   1516320   −   355       Uncharacterized protein conserved   COG4012   [S]                               in archaea       1498   1516295   1516912   −   205       Archaea-specific kinase related to   COG2054   [R]                               aspartokinase       1499   1517027   1517572   −   181   HyaD_1   Ni,Fe-hydrogenase maturation factor   COG0680   [C]       1500   1517569   1518687   −   372       Pyridoxal-phosphate-dependent   COG0076   [E]                               enzyme related to glutamate                               decarboxylase       1501   1518684   1519490   −   268       Predicted transcriptional regulator   COG1497   [K]                               containing a DNA-binding HTH                               domain       1502   1519494   1519919   −   141       Predicted transcriptional regulator   COG0864   [K]                               containing the CopG/Arc/MetJ DNA-                               binding domain and a 3H domain       1503   1519963   1520475   −   170       Uncharacterized conserved protein   COG1986   [S]       1504   1520450   1520923   −   157       Predicted nucleotidyltransferase of   COG1019   [R]                               the HIGH superfamily       1505   1520920   1521717   −   265       Predicted ATPase of the PP-loop   COG1365   [R]                               superfamily       1506   1521830   1522651   −   273       Uncharacterized conserved protein   COG1430   [S]       1507   1522677   1523396   +   239       Uncharacterized conserved protein   COG1624   [S]       1508   1523389   1524582   +   397       Archaeal S-adenosylmethionine   COG1812   [E]                               synthetase       1509   1524636   1526012   −   458   AnsB   L-asparaginase   COG0252   [EJ]       1510   1526044   1526646   +   200   HisH   Glutamine amidotransferase   COG0118   [E]       1511   1526643   1527143   +   166       Predicted metabolic regulator   COG1719   [R]                               containing V4R domain       1512   1527145   1527771   +   208       Predicted serine protein kinase   COG1493   [T]                               homologous to HPr protein kinase,                               contains a Zn-ribbon       1513   1527775   1528134   +   119       Uncharacterized protein conserved                               in archaea       1514   1528140   1528403   +   87       Uncharacterized conserved protein   COG1873   [S]       1515   1528916   1529248   +   110       Predicted transcriptional regulator of   COG0640   [K]                               the ArsR family       1516   1529214   1530110   −   298   CbiB   Cobalamin biosynthesis protein   COG1270   [H]                               CobD/CbiB       1517   1530110   1531141   −   343   DPH2   Diphthamide synthase subunit DPH2   COG1736   [J]       1518   1531169   1531531   +   120   CbiG   Cobalamin biosynthesis protein CbiG   COG2073   [H]       1519   1531570   1532046   +   158       Uncharacterized protein conserved                               in archaea       1520   1532641   1533588   −   315   Dcm   Site-specific DNA methylase   COG0270   [L]       1521   1533710   1534465   +   251       ABC-type molybdate transport   COG0725   [P]                               system, periplasmic component       1522   1534462   1535247   +   261       ABC-type molybdate transport   COG0555   [O]                               systems, permease component       1523   1535234   1535920   +   228       ABC-type molibdate transport   COG3839   [G]                               systems, ATPase component       1524   1535907   1537154   +   415   MoeA   Molybdopterin biosynthesis enzyme   COG0303   [H]       1525   1537248   1537487   +   79   FwdG   Ferredoxin   COG1145   [C]       1526   1537502   1537897   +   131   FwdD   Formylmethanofuran dehydrogenase   COG1153   [C]                               subunit D       1527   1537981   1539282   +   433   FwdB_2   Formylmethanofuran dehydrogenase   COG1029   [C]                               subunit B, selenocysteine containing       1528   1539400   1539711   +   103       Zn-ribbon-containing protein       1529   1539750   1541495   +   581   FwdA   Formylmethanofuran dehydrogenase   COG1229   [C]                               subunit A       1530   1541523   1542326   +   267   FwdC   Formylmethanofuran dehydrogenase   COG2218   [C]                               subunit C       1531   1542396   1542695   +   99       Uncharacterized protein conserved   COG4013   [S]                               in archaea       1532   1542781   1544628   +   615       Predicted secreted protein       1533   1544563   1546239   −   558       Squalene cyclase   COG1657   [I]       1534   1546215   1551530   +   1771       Predicted protein of the CobN/Mg-   COG1429   [H]                               chelatase family       1535   1551496   1552785   −   429       Aspartokinase   COG0527   [E]       1536   1552958   1554892   −   644       P-loop ATPase of the PilT family   COG1855   [R]       1537   1554926   1555351   −   141   HisI_2   Phosphoribosyl-AMP cyclohydrolase   COG0139   [E]       1538   1555348   1556613   −   421   HisS   Histidyl-tRNA synthetase   COG0124   [J]       1539   1556613   1557965   −   450       tRNA/rRNA cytosine-C5-methylase   COG0144   [J]       1540   1557946   1558869   −   307   MoaA   Molybdenum cofactor biosynthesis   COG2896   [H]                               enzyme       1541   1558896   1559870   −   324       Uncharacterized protein conserved                               in archaea       1542   1560542   1561234   +   230       Predicted Zn-dependent hydrolase of   COG2220   [R]                               the beta-lactamase superfamily       1543   1561292   1562038   −   248       Uncharacterized membrane protein       1544   1562041   1563039   −   332   HypE_2   Hydrogenase maturation factor   COG0309   [O]       1545   1563101   1563502   +   133   RPS8A   Ribosomal protein S8E   COG2007   [J]       1546   1563499   1564155   −   218   HypB_2   Ni2+-binding GTPase involved in   COG0378   [OK]                               regulation of expression and                               maturation of hydrogenase       1547   1564142   1564570   −   142   HybF   Zn-finger-containing protein   COG0375   [R]                               HypA/HybF (possibly regulating                               hydrogenase expression)       1548   1564629   1565369   +   246   CysG_2   Uroporphyrinogen-III methylase   COG0007   [H]       1549   1565366   1566509   +   380   Kch_3   NAD-binding domain of the Kef-type   COG1226 &amp;   [P][R]                               K+ transport system fused to a   COG1827                               uncharacterized conserved domain       1550   1566513   1567199   −   228   HemD   Uroporphyrinogen-III synthase   COG1587   [H]       1551   1567196   1567507   −   103   SEC65   19 kDa subunit of the signal   COG1400   [U]                               recognition particle       1552   1567473   1568744   −   423       Uncharacterized protein specific for                               M. kandleri, MK-38 family       1553   1568769   1569284   +   171       Predicted allosteric regulator of   COG2061   [E]                               homoserine dehydrogenase                               containing an ACT domain       1554   1569260   1570273   +   337   ThrA   Homoserine dehydrogenase   COG0460   [E]       1555   1570324   1570851   −   175       Uncharacterized protein       1556   1570848   1571285   −   145       Uncharacterized membrane protein       1557   1571504   1571908   −   134       Predicted redox protein, regulator of   COG1765   [O]                               disulfide bond formation       1558   1571926   1572834   −   302       Selenophosphate synthetase-related   COG2144   [R]                               enzyme       1559   1572806   1573468   −   220       Uncharacterized protein       1560   1573487   1574383   +   298       Predicted permease   COG0679   [R]       1561   1574882   1575780   −   299   TrxB   Thioredoxin reductase   COG0492   [O]       1562   1575813   1576907   −   364       Predicted flavoprotein related to   COG2303   [E]                               choline dehydrogenase       1563   1576935   1577945   +   336       Uncharacterized protein       1564   1577960   1580194   +   744   InfB_1   Translation initiation factor 2,   COG0532   [J]                               GTPase       1565   1580201   1580878   +   225       Uncharacterized protein       1566   1580875   1581339   +   154   Dcd_2   Deoxycytidine deaminase   COG0717   [F]       1567   1581336   1581887   +   183       Zn-dependent hydrolase   COG0491   [R]       1568   1581884   1582210   −   108       Predicted metal-binding protein       1569   1582270   1583277   +   335       Permease of the major facilitator   COG0477   [GEPR]                               superfamily       1570   1583274   1584155   +   293   MMT1   Predicted Co/Zn/Cd cation   COG0053   [P]                               transporter       1571   1584185   1585000   −   271       Uncharacterized protein       1572   1584936   1585493   +   185       Uncharacterized protein       1573   1585777   1587114   +   445   CobB_1   Cobyrinic acid a,c-diamide synthase   COG1797   [H]       1574   1587128   1587742   +   204       Metal-dependent hydrolase of the   COG1237   [R]                               beta-lactamase superfamily       1575   1587924   1589219   −   431       tRNA/rRNA cytosine-C5-methylase   COG0144   [J]       1576   1589278   1590753   −   491       Amino acid transporter   COG0531   [E]       1577   1590858   1591445   −   195       Uncharacterized conserved protein   COG2411   [S]       1578   1591464   1592075   −   203   RpsB   Ribosomal protein S2   COG0052   [J]       1579   1592112   1592303   −   63       Ferredoxin   COG1146   [C]       1580   1592327   1592497   −   56   RpoZ   DNA-directed RNA polymerase   COG1758   [K]                               subunit K/omega       1581   1592624   1593769   −   381       Predicted deacylase   COG0624   [E]       1582   1593766   1594827   −   353       Uncharacterized conserved protein   COG3367   [S]       1583   1594854   1596443   −   529   HYS2   Archaeal DNA polymerase II small   COG1311   [L]                               subunit, predicted phosphatase       1584   1596507   1597112   +   201       Uncharacterized protein       1585   1597109   1597681   +   190       Predicted epimerase related to   COG0235   [G]                               ribulose-5-phosphate 4-epimerase       1586   1597665   1598027   −   120       Uncharacterized protein conserved   COG1698   [S]                               in archaea       1587   1597981   1598511   +   176       Predicted transcriptional regulator   COG2771 &amp;   [K][S]                               containing DNA-binding HTH domain   COG1284       1588   1598508   1598981   +   157       Uncharacterized Zn-finger-containing   COG1645   [R]                               protein       1589   1598944   1600101   +   385       Predicted ATP-dependent   COG2232   [R]                               carboligase related to biotin                               carboxylase       1590   1600098   1601198   +   366   MurF   UDP-N-acetylmuramyl pentapeptide   COG0770   [M]                               synthase       1591   1601232   1601696   +   154   Ndk   Nucleoside diphosphate kinase   COG0105   [F]       1592   1601691   1603019   −   442   RecJ_1   Single-stranded-DNA-specific   COG0608   [L]                               exonuclease       1593   1603095   1603544   −   149   RpsO   Ribosomal protein S15P/S13E   COG0184   [J]       1594   1603551   1604117   −   188       Xanthosine triphosphate   COG0127   [F]                               pyrophosphatase       1595   1604190   1605986   +   598   InfB_2   Translation initiation factor 2,   COG0532   [J]                               GTPase       1596   1606043   1606858   −   271       Metal-dependent hydrolase of the   COG3608   [R]                               aminoacylase-2/carboxypeptidase Z                               family       1597   1606866   1607216   −   116       Uncharacterized conserved protein   COG1990   [S]       1598   1607390   1607761   +   123   RPL8A   Ribosomal protein HS6-type   COG1358   [J]                               (S12/L30/L7a)       1599   1608218   1608949   +   243       Uncharacterized protein conserved                               in archaea       1600   1608909   1610417   −   502   GuaB   IMP dehydrogenase   COG0516 &amp;   [F][R]                                   COG0517       1601   1610484   1611053   −   189       Uncharacterized membrane protein       1602   1611106   1611819   −   237       Uncharacterized protein conserved   COG1891   [S]                               in archaea       1603   1611915   1612466   +   183       Uncharacterized protein       1604   1612436   1614199   +   587   TopA   Topoisomerase IA   COG0550   [L]       1605   1614640   1615353   +   237       5-formyltetrahydrofolate cyclo-ligase   COG0212   [H]       1606   1615336   1616505   −   389   ArgD   Ornithine/acetylornithine   COG4992   [E]                               aminotransferase       1607   1616509   1617411   −   300   DapA   Dihydrodipicolinate synthase/N-   COG0329   [EM]                               acetylneuraminate lyase       1608   1617430   1617642   −   70   RPS17A   Ribosomal protein S17E   COG1383   [J]       1609   1617635   1617913   −   92   PheA   Chorismate mutase   COG1605   [E]       1610   1617867   1618727   −   286       Archaeal shikimate kinase   COG1685   [EH]       1611   1618931   1619194   −   87       Uncharacterized protein       1612   1619379   1620722   −   447   Ffh   Signal recognition particle GTPase   COG0541   [U]       1613   1620719   1621768   −   349   FtsY   Signal recognition particle GTPase   COG0552   [U]       1614   1621798   1622271   −   157   GIM5   Predicted prefoldin, molecular   COG1730   [O]                               chaperone implicated in de novo                               protein folding       1615   1622271   1622513   −   80   RPL20A   Ribosomal protein L20A (L18A)   COG2157   [J]       1616   1622531   1623196   −   221   TIF6   Translation initiation factor 6 (EIF6)   COG1976   [J]       1617   1623199   1623459   −   86   RPL31A   Ribosomal protein L31E   COG2097   [J]       1618   1623475   1623630   −   51   RPL39   Ribosomal protein L39E   COG2167   [J]       1619   1623644   1623997   −   117       DNA-binding protein   COG2118   [R]       1620   1624027   1624476   −   149   RPS19A   Ribosomal protein S19E (S16A)   COG2238   [J]       1621   1624522   1624839   −   105       Predicted RNA-binding protein   COG1534   [J]                               containing KH domain, possibly                               ribosomal protein       1622   1624826   1625212   −   128   RPR2   RNAse P subunit RPR2   COG2023   [J]       1623   1625166   1626401   +   411       Uncharacterized protein specific for                               M. kandleri, MK-39 family       1624   1626335   1626904   +   189   HyaD_2   Ni,Fe-hydrogenase maturation factor   COG0680   [C]       1625   1626880   1627365   −   161       Ferredoxin fused to cHTH-type DNA-   COG1145   [C]                               binding domain       1626   1627362   1628921   −   519       Membrane protein implicated in   COG2244   [R]                               protein export       1627   1628934   1629821   −   295   IlvE   Branched-chain amino acid   COG0115   [EH]                               aminotransferase       1628   1630003   1631064   +   353       Uncharacterized protein       1629   1631048   1631341   +   97       Uncharacterized protein       1630   1631363   1632712   −   448       tRNA/rRNA cytosine-C5-methylase   COG0144   [J]       1631   1632739   1633479   +   246   ArgB   Acetylglutamate kinase   COG0548   [E]       1632   1633413   1633727   +   104       Uncharacterized protein conserved   COG1849   [S]                               in archaea       1633   1633814   1634437   +   207       Uncharacterized protein       1634   1634606   1635241   −   211       Zn-dependent hydrolase   COG0491   [R]       1635   1635284   1636138   +   284       N6-adenine-specific DNA methylase       1636   1636477   1637091   −   204       Uncharacterized protein specific for                               M. kandleri, MK-1 family       1637   1637295   1637957   −   220       Orphan DOD family homing   COG1372   [L]                               endonuclease       1638   1637857   1638960   −   367       Orphan DOD family homing   COG1372   [L]                               endonuclease       1639   1639406   1640485   +   359       Uncharacterized conserved protein   COG1679   [S]       1640   1640674   1641513   −   279       Uncharacterized protein       1641   1641667   1642548   +   293   FtsJ   23S rRNA methylase   COG0293   [J]       1642   1642496   1642894   −   132   CpsB_2   Mannose-6-phosphate isomerase   COG0662   [G]       1643   1642891   1644282   −   463   CobB_2   Cobyrinic acid a,c-diamide synthase   COG1797   [H]       1644   1644369   1644533   +   54       Uncharacterized protein       1645   1644717   1645973   −   418       Predicted dehydrogenase   COG0644   [C]                               (flavoprotein)       1646   1646079   1647389   −   436       Predicted pseudouridylate synthase   COG1258   [J]       1647   1647793   1649076   +   427   Eno   Enolase   COG0148   [G]       1648   1649073   1650479   −   468       Uncharacterized membrane protein       1649   1650476   1651831   −   451   PurF   Glutamine   COG0034   [F]                               phosphoribosylpyrophosphate                               amidotransferase       1650   1652250   1655972   −   1240       Archaeal DNA polymerase II, large   COG1933   [L]                               subunit       1651   1656406   1657362   −   318   SplB   DNA photolyase   COG1533   [L]       1652   1657359   1658759   −   466   LldP   L-lactate permease   COG1620   [C]       1653   1658795   1659637   +   280       Uncharacterized protein       1654   1659793   1660500   −   235       ATPase subunit of a ABC-type   COG1136   [V]                               transport system involved in                               lipoprotein release       1655   1660512   1661624   −   370       Permease subunit of a ABC-type   COG0577   [V]                               transport system involved in                               lipoprotein release       1656   1661638   1662354   −   238       Archaea-specific Zn-finger-   COG1326   [R]                               containing protein       1657   1662382   1662804   +   140       Uncharacterized protein conserved   COG2090   [S]                               in archaea       1658   1662954   1663568   −   204       Predicted RNA-binding protein   COG1491   [J]       1659   1663572   1663961   −   129       Uncharacterized protein conserved   COG1460   [S]                               in archaea       1660   1663977   1664285   −   102   RPL21A   Ribosomal protein L21E   COG2139   [J]       1661   1664287   1664700   −   137       RecB-family nuclease   COG4080   [L]       1662   1664704   1665924   −   406   Pgk   3-phosphoglycerate kinase   COG0126   [G]       1663   1665945   1666487   −   180       Predicted sugar phosphate   COG0794   [M]                               isomerase involved in capsule                               formation       1664   1666501   1667181   −   226   TpiA   Triosephosphate isomerase   COG0149   [G]       1665   1667190   1667828   −   212   RpiA   Ribose 5-phosphate isomerase   COG0120   [G]       1666   1667891   1669519   +   542   CarB_3   Carbamoylphosphate synthase large   COG0458   [EF]                               subunit       1667   1669535   1670410   +   291   PrsA   Phosphoribosylpyrophosphate   COG0462   [FE]                               synthetase       1668   1670607   1670876   +   89       Uncharacterized protein conserved   COG4014   [S]                               in archaea       1669   1670877   1671116   −   79       Uncharacterized conserved protein   COG1873   [S]       1670   1671113   1671736   −   207       GTP: adenosylcobinamide-phosphate   COG2266   [H]                               guanylyltransferase       1671   1671733   1672458   −   241   CobS   Cobalamin-5-phosphate synthase   COG0368   [H]       1672   1672455   1673528   −   357   PgpA   Predicted   COG1865 &amp;   [S][I]                               phosphatidlglycerophosphatase A   COG1267                               fused to a uncharacterized                               conserved domain       1673   1673554   1676526   +   990   NtpB   Archaeal/vacuolar-type H+-ATPase   COG1156 &amp;   [C][L]                               subunit B, contains an intein   COG1372       1674   1676578   1677276   +   232   NtpD   Archaeal/vacuolar-type H+-ATPase   COG1394   [C]                               subunit D       1675   1677295   1677675   +   126       Uncharacterized conserved protein   COG1417   [S]       1676   1677675   1678118   +   147       Uncharacterized protein conserved   COG2083   [S]                               in archaea       1677   1678361   1678825   +   154   HHT1_3   Histone H3/H4   COG2036   [L]       1678   1678882   1681107   −   741   MPH1/   ERCC4-like helicase-nuclease   COG1111 &amp;   [L][L]                           MUS81       COG1948       1679   1681086   1681853   −   255       Predicted nucletide kinase   COG4088   [F]       1680   1681881   1682882   +   333   ArsA   Predicted ATPase involved in   COG0003   [D]                               chromosome partitioning       1681   1682894   1683577   +   227       Predicted phosphatase of the PHP   COG1387   [ER]                               family       1682   1683574   1686540   −   988   RtcB   Uncharacterized conserved protein,   COG1690 &amp;   [S][L]                               contains a DOD family homing   COG1372                               endonuclease insertion       1683   1686554   1687210   −   218       Uncharacterized conserved protein   COG3382   [S]       1684   1687182   1687805   −   207       SAM-dependent methyltransferase   COG0500   [QR]       1685   1687856   1688686   +   276       Uncharacterized protein       1686   1688751   1689122   +   123       Uncharacterized conserved protein   COG1504   [S]       1687   1689119   1689883   −   254   PstB   ABC-type phosphate transport   COG1117   [P]                               system, ATPase component       1688   1689888   1691672   −   288   PstA   ABC-type phosphate transport   COG0581 &amp;   [P][P]                               system, permease component   COG0573       1690   1691739   1692728   −   329   PstS   ABC-type phosphate transport   COG0226   [P]                               system, periplasmic component       1691   1692804   1693688   +   294       Predicted ATPase of the PP-loop   COG0037   [D]                               superfamily implicated in cell cycle                               control       1692   1693706   1694500   +   264       Predicted ATPase of the PP-loop   COG0037   [D]                               superfamily implicated in cell cycle                               control                  
 
         [0205]