# Low-redundancy sequencing of the entire Lactococcus lactis IL1403 genome.

Alexander Bolotin, Stéphane Mauger, Karine Malarme, S. Dusko Ehrlich,

Alexei Sorokin

► To cite this version:

Alexander Bolotin, Stéphane Mauger, Karine Malarme, S. Dusko Ehrlich, Alexei Sorokin. Low-redundancy sequencing of the entire Lactococcus lactis IL1403 genome.. Antonie van Leeuwenhoek, 1999, 76 (1-4), pp.27-76. 10.1023/a:1002048720611. hal-04297789

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# Low-redundancy sequencing of the entire Lactococcus lactis

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## IL1403 genome

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Alexander Bolotin, Stéphane Mauger, Karine Malarme, S. Dusko Ehrlich & Alexei Sorokin Génétique

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Microbienne, INRA, Domaine de Vilvert, 78352 Jouy en Josas cedex, France.

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(Author for correspondence; E-mail: sorokine@biotec.jouy.inra.fr)

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## Abstract

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Lactococcus lactis is an AT-rich gram positive bacterium phylogenetically close to the genus

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Streptococcus. Various strains of L. lactis are used in dairy industry as starters for cheese making. L.

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lactis is also one of the well characterized laboratory microorganisms, widely used for studies on

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physiology of lactic acid bacteria. We describe here a low redundancy sequence of the genome of the

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strain L. lactis IL1403. The strategy which we followed to determine the sequence consists of two main

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steps. First, a limited number of plasmids and -phages that carryrandom segments of the genome were

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sequenced. Second, sequences of the inserts were used for production of novel sequencing templates by

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applying Multiplex Long Accurate PCR protocols. Using of these PCR product sallowed to determine

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the sequence of the entire 2.35 Mb genome with a very low redundancy, close to 2. The error rate of the

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sequence is estimated to be below 1%. The correctness of the sequence assembly was confirmed by PCR

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amplification of the entire L. lactis IL1403 genome, using a set of 266 oligonucleotides. Anotation of

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the sequence was undertaken by using automatic gene prediction computer tools. This allowed to

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identify 1495protein-encoding genes, to locate them on the genome map and to classify their functions

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on the basis of homology to known proteins. The function of about 700 genes expected to encode

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proteins that lack homologs in data bases cannot be reliably predicted in this way. The approach which

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we used eliminates high redundancy sequencing and mapping efforts, needed to obtain detailed and

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comprehensive genetic and physical maps of a bacterium.

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Availability of detailed genetic and physical maps of the L. lactis IL1403 genome provides many entries

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to study metabolism and physiology of bacteria from this group. The presence of 42 copies of five

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different IS elements in the IL1403 genome confirms the importance of these elements for genetic

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exchange in Lactococci. These include two previously unknown elements, present at seven and fifteen
copies and designated IS1077 and IS983, respectively. Five potential or rudimentary prophages were identified in the genome by detecting clusters of phage-related genes. The metabolic and regulatory potential of L. lactis was evaluated by inspecting gene sets classified into different functional categories. L. lactis has the genetic potential to synthesise 20 standard amino acids, purine and pyrimidine nucleotides and at least four cofactors. Some of these metabolites, which are usually present in chemically defined media, can probably be omitted. About twenty compounds can be used by L. lactis as a sole carbon source. Some 83 regulators were revealed, indicating a regulatory potential close to that of Haemophilus influenzae, a bacterium with a similar genome size. Unexpectedly, L. lactis has a complete set of late competence genes, which may have concerted transcriptional regulation and unleaded polycistronic mRNAs. These findings open new possibilities for developing genetic tools, useful for studies of gene regulation in AT-rich gram positive bacteria and for engineering of new strains for the diary industry.

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## 42 Introduction

Lactococcus lactis is probably the best characterised lactic acid bacterium, with highly developed knowledge on physiology and genetics. It is therefore an obvious target for genome sequencing, since the availability of the full sequence would greatly improve the efficiency of numerous studies that are currently being conducted with this organism, or are planned in the near future. We decided to undertake the L. lactis genome sequencing project in an academic setting, with resources of a single laboratory, which obviates the need to raise a rather large amount of funding which would be required for sequence determination by a private company, or by a consortium of academic laboratories. For this purpose, we developed an approach that allowed us to determine the genome sequence with a redundancy much lower than generally used, and at a commensurately lower cost. Due to the low redundancy, the sequence is of a so-called diagnostic quality, allowing to detect essentially all genes that have homologs in other organisms, but not the genes which may be present in the Lactococcus genome only.

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The approach most often used for sequencing of an entire bacterial genome is based on a high-throughput random clone sequencing (Fleischmann et al. 1995). This method is most efficient if the facilities to produce raw reading data are not limiting. However, the speed of accumulation of new sequencing data decreases exponentially with the linear increase of the number of randomly sequenced
58 templates (Lander &Waterman 1988). This becomes a limiting factor, in particular for relatively large
59 bacterial genomes. Furthermore, the assembly becomes exceedingly difficult if the genome contains
60 numerous repeated elements. The chromosome of L. lactis IL1403 was estimated to have a size of about
61 2.4 Mb (Le Bourgeois et al.1992). Application of the whole-genome random sequencing and assembly
62 method (Fleischmann et al.1995) would require producing of 30,000 random gel readings,
63 corresponding to six-fold coverage, and the sequence would be distributed in about 80 contigs. We
64 considered an alternative strategy that would consist in a much less massive random sequencing
65 followed by primer walking on templates generated by Long Range PCR (LR PCR, Cheng et al. 1994).
66 If sequence acquisition and assembly were carried out in parallel, template synthesis can be conducted
67 in such a way that the re-sequencing of the regions that were sequenced already is kept at a minimum.
68 We estimated that such approach may allow to sequence the whole L. lactis genome with a coverage of
69 only about two. Some 10,000 sequencing reactions instead of 30,000would therefore be required. We
70 report here the L.lactis genome sequence determined by this approach.
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72 Low-redundancy genome sequencing

73 The strategy of low-redundancy L. lactis genome sequencing is presented in Table 1. This strategy is a
74 compromise between completely random and directed approaches. Its objective was to reduce time and
75 effort or obtaining complete information about gene content and genome organisation. In the first stage,
76 a limited number of randomly chosen clones is sequenced, so that the speed of new sequence
77 accumulation keeps approximately constant. We estimated that this condition is fulfilled up to the
78 genome coverage of about one. A large number of small contigs, separated by sequencing gaps, is
79 present at the end of the first stage. In the second stage randomly chosen clones carrying large inserts
80 are sequenced by primer walking. This allows to close some sequencing gaps and extend the contigs, as
81 verified by sequence assembly, which is carried out in parallel with the acquisition of new sequence.
82 The redundancy is kept low by selecting the primers that correspond to the ends of the extended contigs
83 for the next round of primer walking. This stage is carried out until the rate of acquisition of the new
84 sequence is above about 1 new base for 3 sequenced bases. Finishing of the sequence is achieved by
85 applying another directed procedure, which was designated Multiplex Long Accurate PCR (MLA PCR)
86 and tested in the course of our participation in the Bacillus subtilis sequencing project (Sorokin et al.
1996; Bolotin et al. 1997; Lapidus et al. 1997). It involves mixing a large number of primers that correspond to the ends of contigs. A product will be obtained each time when the distance between two sites on the genome, corresponding to two contig ends, is less than the maximal size that can be synthesised by LR PCR. The probability of producing such products, as a function of the genome size and the number of primers present in LRPCR reaction is shown in Figure 1. For the genome of L. lactis size this probability is between 0.5 and 1 if some 20 primers are mixed (that is at least half of PCR reactions containing 20 randomly chosen primers will give an amplification product). It should be noted that the efficiency of gap closure is expected to increase with the progression of the sequencing project, since the number of contigs continuously decreases. This is in sharp contrast with the fully random approach, where the efficiency of gap closure decreases exponentially with sequence acquisition. We now believe that the long-insert library construction can be omitted.

Some statistical data of application of this strategy for the L. lactis sequencing are presented in Table 2. A library consisting of 2854 clones with insert sizes in the range from 1 to 2 kb, was constructed by using pBluescript II KS+ (Stratagene) or pSGMU2 (Errington1986) vectors. 2625 clones were sequenced by forward (M13-21) and 2168 by reverse (M13RP1) primers with successful sequencing rate of about 90%. After accumulating about 2100 kb of sequence 2357 oligonucleotides were synthesised to fill the gaps between the forward and reverse sequences. A total of about 3.3 Mb of sequence was thus acquired.

-FIXII vector (Stratagene) was used to construct along insert library. L. lactis chromosome was partially digested with Sau3A, fractionated by centrifugation in sucrose gradient, treated with Klenow polymerase in the presence of dGTP and dATP, and ligated with -FIXII arms cut by XhoI and treated with Klenow in the presence of dCTP and dTTP. 262 phages were chosen at random and the ends of inserts sequenced by the T7 primer (Stratagene). Of these, 122 phages which had a unique sequence obtained by the T7 primer, were sequenced by the T3 primer (Stratagene). These 122 clones appeared to constitute a nonredundant set and their inserts were sequenced by primer walking (see Table 2). Some 250 kb of sequence were obtained in this way.

MLA PCR was used to obtain new sequencing substrates. A critical step in the procedure is to identify in the mixture the two primers that give a product useful for sequencing. The previously developed protocol (Sorokin et al. 1996), where two steps were required for the identification, was modified here
so that only a single step is required. The principle of the modification is illustrated in Figure 2A. In this theoretical example each reaction contains 8 different primers. A total of 16 primers is used (labelled 1–16 on the left) and there are 16 reactions (labelled 1–16 on the top). To obtain a different primer combination in each reaction one primer is replaced at a time with a new primer (for instance, reaction 8 contains primers 1–8, reaction 9 contains primers 2–9, etc). The primer couples which give a useful product can be identified unambiguously, by simply identifying the reaction mixtures in which the product is synthesized, as illustrated in the three lower rows. For instance, if a product were found only in the reaction 8, primers 1 and 8 would be required for it, since only the reaction 8 contains these two primers together. Alternatively, if a product were found in reactions 4 to 10, primers 3 and 4 would be required. A general correlation between positive reactions and primer couples is given in the legend of Figure 2. An example of application of this protocol to the IL1403 genome, using 32 oligonucleotides in each reaction, is shown on Figure 2B (the analysis of 36 reactions out of a total of 96 that were routinely run together is displayed). There are 4 different products in the reaction mixtures, ranging between 1 and 10kb. The largest product appears in reactions 7 to 34, identifying that the primers 7 and 3 are required for its synthesis (see legend, Figure 2). The primers identified in this way were used to sequence the ends of the PCR products and thus confirm the identification and to extend the sequence.
In total 1641 such sequencing reactions on the products with sizes from 1 to 20 kb were performed and about 0.77 Mb of sequence was read (Table 2). This step allowed to finish the entire chromosome assembling, giving a contig of 2.34 Mb. The total redundancy was close to 2 (Table 2).
To test the correctness of the assembling we carried out LR PCR amplification of the entire genome using 266 oligonucleotides, predicted to be separated by distances 10–20 kb. The expected products were obtained (Figure 3), which indicates that the assembling is correct. The sequences of these 266 oligonucleotides are presented at http://spock.jouy.inra.fr.

The average redundancy of the L. lactis genome sequence is two. Such low redundancy does not allow to eliminate all errors by comparing multiple sequences corresponding to the same genome region. The error rate of this sequence is therefore determined by individual gel reading quality. We counted the number of ambiguities in the raw sequence data used for the assembling and found 46,954 ambiguities for a total of 4,687,630 bases. From this estimation the accuracy of the L. lactis diagnostic sequence is about 1% (one ambiguity/100 bases). However, assembling usually decreases the number of errors in
the final consensus sequence and the real error rate may be lower. We therefore carried out a different
quality test, aiming to detect the level of frame-shift errors in the open reading frames present in the
genome sequence. For this purpose we used the GENMARK programme (Borodovsky & Mc Ininch
1993), which predicts the genome regions statistically fit to encode proteins. Some 3544 protein coding
regions were thus detected. If the real density of genes in L. lactis were similar to that observed in other
bacterial genomes, we would expect only about 2300 such regions. There should therefore be over 1200
frame-shift errors in our sequence (the difference between 3544 regions detected and 2300 expected),
corresponding to about 1 error for two genes, or 2 kb. We suggest therefore that the overall error rate of
the diagnostic quality sequence after assembling, at a redundancy of 2, may be close to 1 in 1000.

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## Genome analysis

GC skew, replication origin and terminus. L. lactis IL1403 chromosome has the size of 2345 5 kb.
The average GC-content is 35.4%, its variation over the chromosome is shown on Figure 4. By analogy
with the analysis performed on the B. subtilis genome (Kunst et al. 1997), the deviation from the mean
GC content may indicate the presence of foreign insertion elements, such as transposons or prophages.
We did not detect, however, in the L. lactis genome, a correlation of GC-content with location of these
elements, determined by other approaches (see below). Several regions of highly elevated GC-content
were revealed (Figure 4). Six such peaks with GC-content higher than 46%, at positions 540, 1970,
2210, 2250, 2325 and 2340 (Figure 4, bottom) correspond to rRNA operons. Another GC rich region,
near position 2150 kb (Fig 4, bottom), corresponds to the cluster of ribosomal protein genes. We
conclude that the regions encoding ribosomes have a higher GC content than the other regions in L.
lactis. In two other AT-rich bacteria, B. subtilis and Rickettsia prowazekii, the regions encoding
ribosomal genes are not particularly GC-rich (Kunst et al. 1997; Andersson et al. 1998).

GC skew, replication origin and terminus. GC or AT skews are useful to predict positions of replication
origin and terminus (Lobry 1996a, b). The distributions of the values (C-G)/(C+G) and (A-T)/(A+T)
over the chromosomal region in the vicinity of dnaA gene is shown in Figure 5, top. A sharp transition
between positive and negative values is observed, and indicates the presence of the replication origin
(Figure 5A). This region contains four DnaA boxes (Figure 6), which also indicates the presence of the
replication origin. We choose the start point for the presentation of the circular L. lactis genome map at
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the middle of HindIII site near the replication origin and the map is oriented to be colinear with the
transcription direction of the dnaA and dnaN genes (see below, Figure 9).

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GC and AT skews may also indicate location of the replication terminus. This is seen for L. lactis
genome from Figure 5, bottom. The transition between positive and negative values occurs near the
position 1260 kb. These data correlate with the replication terminus location based on orientation of
transcription of potential genes and distribution of chi-sites over the genome (see below).

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IS-elements and prophages in L.lactis IL1403. Three different IS elements in the genome of L. lactis
IL1403 were known previously, designated IS981, IS982 and IS1076. Their number of copies (ten, one
and seven, respectively) and approximate locations were reported previously (Le Bourgeois et al. 1992,
1995; Polzin et al. 1993; Schouler et al. 1998). The element IS1076 was initially identified in the strain
L. lactis subsp. lactis CNRZ270 on the plasmid pUCL22 (Huang et al. 1991). Nucleotide sequence of
this element (Genbank accession X53013) shows complete identity to IS904, known from nisin-
producing lactococcus (Engelke et al. 1992). Our sequencing data confirmed that in all chromosome
locations where IS1076 was mapped, the nucleotide sequence identical to IS904 is present, and we
therefore keep the latter name on the map. We found, however, that another element, which we designate
IS1077, was also present in each of these seven sites. At two sites the IS1077 element is flanked by two
sequences identical to IS904. The orientation of IS904 relative to IS1077 is different in five cases out of
seven. A possible explanation for the fact that the two elements always occur together in this genome
would be that one of these elements carry a sequence essential for the transposition of the other. Since
IS904 can be found without IS1077 in other genomes, the essential sequence must be in IS904. By
searching Genbank we identified another copy of IS1077 in the plasmid pK214, (sequence accession
number is X92946). IS904 is also present on this plasmid.

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Fifteen copies of an element, which was not described earlier for lactococcus species and is designated
here IS983, were detected in the IL1403 genome. The closest relative from other species is IS1239 from
Streptococcus pyogenes (Ashbauch et al. 1998), and, from other lactic acid bacteria, it is IS1070,
discovered in the plasmid pNZ63 in Leuconostoc lactis NZ6009 (Vaughan & de Vos 1995).

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Chopin et al. (1989) detected in the chromosome of IL1403 two different prophages, bIL285 and
bIL286, which can be induced for lysogenic development by UV irradiation. Two more prophages,
bIL309 and bIL310, can also probably be induced if supplied in trans by some functions of the first two

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phages (Chopin & Perreira, pers. comm.). We tried to identify potential prophages in the chromosome by using homology search against a database containing known phage protein sequences. The database consisted of 1219 protein sequences, including the complete set of 50 putative proteins derived from the sequence of the r1t temperate phage of L. lactis (van Sinderen et al. 1996). A distribution of nonredundant homology hits over L. lactis genome is shown on Figure 7. This distribution indicates the presence of three regions, around 460, 1060 and 1410 kb, which may contain the pro-phages identified by Chopin et al. (1989). Two areas, around 40 and 2005 kb, may indicate a fourth and a fifth prophage. More detailed analysis of these areas will help to elucidate the correspondence between the prophages detected by sequencing and by induction of the lysogenic development.

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*Distribution of chi-sites over the chromosome.* Recent analyses suggested that so-called chi-sites, which in L. lactis have sequence 5'-GCGCGTG-3', protect DNA from exonuclease degradation (Biswas et al. 1995). The same sequence was reported to modulate the activities of RexAB exonuclease corresponding to RecBCD of E. coli and is thus involved in the regulation of homologous recombination (el Karoui et al. 1998). In E. coli and B. subtilis such sequences are over-represented and most of them are found to be co oriented with DNA replication (Burland et al. 1993; Chédin et al. 1998). The latter property was correlated either with the involvement of RecBCD in recombination, and therefore preferring the same DNA structures as the RecA protein (Tracy et al. 1998), or with a statistical bias of base distribution, due to codon usage (Biaudet et al. 1998). The chi sequence is presented in L. lactis on average once per 13.2 kb (178/2350 kb) and tends to be co-oriented with replication (Figure 8). Interestingly, the density of chi sequences increases up to one site per 9 kb (34/300 kb) in the region close to the replication origin. Also, chi-site density decreases in the regions near 460, 1060, 1410 and 2000 kb, where the putative prophages were detected (see above).

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*RNA genes.* Six rRNA operons were mapped on the L. lactis chromosome (Tulloch et al. 1991; Le Bourgeois et al. 1992) and one was sequenced (Beresford & Condon 1991; Chiaruttini & Milet 1993). We did not resequence all other operons since the diagnostic sequencing would not reveal reliably any difference. However, we confirmed map positions of these operons by PCR amplification of the corresponding genome regions.
232 tRNA genes were identified with the computer programme tRNA scan-SE (Lowe & Eddy 1997). We
233 detected 62 tRNA genes, corresponding to the 20 amino acids. Most of the tRNA genes were found to
234 be organised in four large operons, three of them transcribed as parts of rrnB, rrnE and rrnF rRNA
235 operons. The trnA operon, encoding seven tRNAs, was described earlier (Nilsson & Johansen 1994).
236 Twenty genes encoding tRNA were found to be isolated from other tRNA genes. RNA component of
237 RNAse P (rnpB gene) and 10S RNA (ssrA) were detected by homology at 1703 and 1458 kb,
238 respectively.

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240 Protein-coding genes. Prediction of protein-coding regions by methods based on statistical properties
241 of DNA is limited for the sequences of diagnostic quality, since potential frameshifts will hamper the
242 prediction of true stop codons. It is, however, possible to predict genes encoding proteins homologous
243 to proteins from other organisms. We used for the comparison 30757protein sequences, corresponding
244 to prokaryotic and phage genes, available from SwissProt (release of17.02.98). Several home-made Perl
245 5.0 or UNIX shell scripts had been used for automatic extraction of L.lactis protein sequences and other
246 parameters from the standard BLASTx or FASTx output files and organising them into clickable tables
247 or genome map drawings. The extracted protein set of L. lactis genome was then again used for
248 homology searches, to find all paralogous proteins encoded in the genome. The largest protein from the
249 FASTx comparison, or the one, having BLASTx homology hits to the same Swissprot entry, was
250 considered as really encoded by a particular area of the L. lactis genome. The final protein set consists
251 of 1495 proteins. If the true number of genes in the L. lactis genome were close to 2300 (a density of
252 one gene per kb), our analysis would have identified about two thirds of them. A version of the
253 automatically generated ORF map of L. lactis IL1403genome is shown on Figure 9. There is a strong
254 bias of gene orientations to be colinear with the direction of replication. The same phenomenon was
255 seen for another AT-rich Gram positive bacterium B. subtilis (Kunst et al. 1997), but not for the GC-
256 rich M. tuberculosis (Cole et al. 1998). It may be a characteristic of AT-rich gram positive
257 microorganisms.

258 Another automatic tool, based on the proposed functional classifications of genes in prokaryotic
259 genomes (Riley 1993; Fleischmann et al. 1995) and commentaries from SwissProt, has been used to
260 classify the genes. The programme uses list of functional categories and the relevant keywords with
assigned weights corresponding to each category for a given keyword. The advantages of such a classification method are: it is completely automatic, it can be applied to genes with hypothetical functions and needs the interaction with an expert only at the stage of construction of the keyword list.

After a keyword list was constructed and the programme had been educated y using several functionally annotated genomes, it provided satisfactory results, which can be used by experts as a draft for more precise functional annotation of the genome and classification of the genes. Any protein database can be automatically classified by using this approach and then used in turn to classify a set of new proteins.

Presumably, such method of automatic functional classification of protein databases can be further developed to give tools, which are completely independent from human expert and use different sources for functional description of proteins. Parameters of homology with several proteins, rather than with the best one, can be used to increase the performance of the approach for classification of hypothetical proteins. The functional classification of predicted genes is colour-encoded on Figure 9 and summarised in Figure 10 and in Table 3. A more detailed and systematically updated version of Table 3can be found at http://spock.jouy.inra.fr.

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276 Metabolic potential of L. lactis IL1403.

The automatic procedure for protein finding, function assignment and classification, described above, allows to estimate the potential of L. lactis as a free-living microorganism. Several of the detected systems were characterised experimentally earlier, by biochemical, genetic or gene cloning means.

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281 *Amino acid, vitamin and nucleotide biosynthesis*

Lactic acid bacteria are nutritionally fastidious. The presence of a gene for synthesis of a metabolite does not mean that a strain of L. lactis where the gene was found will not require this metabolite in the growth medium. The studies performed long ago (Anderson& Elliker 1953) and recently (Jensen& Hammer 1993; Cocaign-Bousquet et al. 1995) showed that synthetic medium for L. lactis should contain at least six amino acids (isoleucine, valine, leucine, histidine, methionine and glutamic acid) and seven vitamins (biotin, pyridoxal, folic acid, riboflavin, niacinamide, thiamine and pantothenic acid). Our analysis showed that L.lactis has a genetic potential to synthesise 20 standard amino acids and at least four cofactors (folic acid, menaquinone, riboflavin and thioredoxin). The genes for biosynthesis of
aromatic amino acids, threonine, branched chain amino acids and histidine were cloned and characterised earlier (Bardowski et al. 1992; Delorme et al. 1992; Godon et al. 1992; Griffin & Gasson 1995; Madsen et al. 1996). The regulation of transcription of the tryptophane operon was studied in detail (Raya et al. 1998; van de Guchte et al. 1998). The problem of fastidious nutritional requirements of L. lactis strains has recently been addressed by application of the single-omission technique (Cocaign-Bousquet et al. 1995; Novak et al. 1997) and genetic approaches (Lapujade et al. 1998). It was shown also that auxotrophy of IL1403, used as a dairy strain, for histidine and branched-chain amino acids is due to the recently acquired mutations (Delorme et al. 1993; Godon et al. 1993).

Biosynthesis and salvage of nucleotides and nucleosides in L. lactis were explored earlier and several pyrimidine and purine biosynthetic genes were cloned and sequenced (Martinussen et al. 1994; Andersen et al. 1996; Nilsson & Kilstrup 1998). It was demonstrated that milk does not contain sufficient purine compounds to support growth and therefore de novo biosynthesis is necessary (Dickely et al. 1995). Nucleoside compounds are not needed in the minimal synthetic medium to maintain exponential growth of L. lactis (Jensen & Hammer 1993). We detected 47 genes implicated in this metabolism. Most of the genes for biosynthesis of purines are clustered near the purDEK operon, which was recently characterised (Nilsson & Kilstrup 1998). A copy of IS983 is detected between the purDEK operon and other genes of purine biosynthesis.

### *Energy metabolism and transporters.*

The main feature of the energy metabolism in L. lactis is that fermented carbon sources are used mostly to maintain the energetic potential of the cells (Poolman 1993; Cocaign-Bousque et al. 1996). About 5% of the fermented sugar is used as the source of substrates for synthetic reactions (Novak et al. 1998). L.lactis does not have a functional citric acid cycle and gluconeogenesis enzymes and is unable to carry out many anaplerotic reactions. The exponential growth of this bacterium appears to be 'programmed' to happen only in sugar rich complex media, like milk. As mentioned above, many metabolites have to be added into the synthetic medium (Jensen & Hammer 1993), although the corresponding biosynthetic genes seem to be present.

It is interesting to compare the genetic potential of L. lactis to grow on different carbon sources with the available experimental data. The genetic potential can be estimated from the presence of the
319 biodegradation genes and the relevant transporters. IL1403 has genes which can be used to grow on
320 different carbon sources: glucose (glycolysis genes), fructose (positions 1519and 2230 kb), N-acetyl
321 glucosamine (1032 kb), xylose(1550 kb), ribose (1685 kb), mannose (777 kb), gluconate(606 and 2253
322 kb), maltose (692, 700 and 1526kb), lactose (2040 kb), galactose (2045 kb), mannitol(33 kb), different
323 -glucosides (186, 419, 830, 1490and 1520 kb). Glucuronate or galacturonate catabolic operon (1670
324 kb) can be used for utilisation of pectin degradation products as a supplementary source of energy and
325 carbon. Components of sugar-specific enzyme II of phosphoenol-pyruvate dependent transport systems
326 were found for mannitol (30 kb), sucrose or trehalose (435 kb), fructose (984 and 1747kb), mannose
327 (1748 kb) and -glucosides (175, 416, 830,1144 and 1489 kb). These findings are summarised in Table
328 4, along with references to experimental data on the growth of L. lactis on different carbon sources. The
329 ability to grow more efficiently in particular conditions can be acquired by L. lactis by means of plasmid
330 transfer. This is well illustrated by experimental studies of the system needed for efficient growth of L.
331 lactis in milk. To overgrow other bacteria in this niche L. lactis needs efficient systems for utilisation of
332 lactose and peptides. Such genes, which include PEP-dependent transporter for lactose and proteinase
333 for peptides, were found in the plasmidpLP712 isolated from Streptococcus lactis NCDO 712 (Gasson
334 1983; Maeda & Gasson 1986). The systemin coded by pLP712 contains a PEP-dependent transporter
335 for lactose. This allows efficient entry of lactose into glycolytic pathways through glucose, which is
336 phosphorylated by glucokinase, and galactose-6P, which is metabolised through the tagatose-6P
337 pathway, also encoded by pLP712. Sequence analysis of the IL1403 chromosome revealed that the genes
338 encoding the PTS-dependent pathway of lactose utilisation are absent in this strain. The chromosome
339 contains, however, another system for lactose utilisation, dependent on the transport by the product of
340 the lacS gene, encoding an HC symporter or galactose-lactose antiporter. This system was characterised
341 earlier for Streptococcus thermophilus. Special selection is needed for S. thermophilus strains to be able
342 to ferment galactose (Thomas & Craw, 1984; Hutkins et al. 1985). Strain IL1403 was isolated from
343 cheese starter culture and cured from plasmids for the purpose to be used as a general genetic engineering
344 host (Chopin et al. 1984; Simon et al. 1985). Probably one of the eliminated plasmids contained genes
345 for efficient utilisation of lactose, similar to the ones encoded by pLP712.

346 Chromosomal genes for galactose and lactose utilisation were cloned and characterised recently from
347 different L. lactis strains (Grossiord et al. 1998; Vaughan et al. 1998). It appeared that the strains can be
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divided in two groups by their possession or lack of the inducible -galactosidase gene. Since we found
the gene in IL1403, this strain belongs to the former group. It is different in this respect from another
model strain cured of plasmids, MG1363 (Gasson 1983), which does not have -galactosidase.

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Automatic analysis detected 14 genes involved in glycolysis, completing the description of this system
and revealed a second glyceraldehyde-phosphate dehydrogenase gene. It also confirmed the absence of
a complete citric acid cycle, revealing only the genes working around pyruvate, like citrate lyase (5
genes), malate oxidoreductase and pyruvate dehydrogenase (4 genes). Close analysis of the genes
automatically classified as relevant to glyconeogenesis confirmed that this process is not present in
L.lactis. No genes for fructose 1,6 bisphosphatase, phos71phoenolpyruvate carboxy kinase or
phosphoenolpyruvate synthetase were found.

352

353

354

355

356

357

358

It is interesting to mention that all genes of the pentose-phosphate pathway were detected, but not a
putative trans-aldolase. It is not yet clear which gene is encoding this function in B. subtilis. It seems
that the structure of the corresponding enzyme in AT-rich gram positive bacteria is different from that
in gram negative and GC-rich gram positive bacteria. The corresponding gene in AT-rich gram positive
bacteria still has to be identified.

359

360

361

362

363

364

Cell envelope

365

The cell surface structure has a large impact on the properties of lactic acid bacteria relevant for their
application in milk industry, such as resistance to stress, cell lysis, sensitivity to phages antimicrobial
agents and influence on the product texture. However, very few studies, mostly related to the potential
application of lactic acid bacteria as a live vehicle for vaccine delivery, were reported (Pouwels et al.
1998). Our analysis revealed 73 genes implicated in cell envelope function, including 29 membrane
proteins, 23 murein succulus and peptidoglycan biosynthesis genes and 21 surface polysaccharide
biosynthesis genes. Operons for the biosynthesis of extracellular polysaccharides were identified
recently in the chromosome of Streptococcus thermophilus (Stingele et al. 1996) and on a plasmid in L.
lactis (van Kranenburg et al. 1997). We did not find similar genes in the chromosome ofIL1403. This
may be another property of industrial interest which is encoded and propagated predominantly by
plasmids in L. lactis.

366

367

368

369

370

371

372

373

374

375

376
378 L. lactis is not known as a good secretor of proteins compared to, for example, Bacillus species.

379 Optimised gene constructions allow L. lactis to produce up to 20 mg of foreign protein per litre (Wells

380 et al. 1993; Le Loir et al. 1998), compared to 800 mg produced by B. subtilis (Hemila et al. 1992). The

381 reasons may be the lack of some components of the secretion machinery or the inefficiency of energy

382 metabolism. We did not detect components such as secDF genes, which are known to improve the

383 secretion efficiency in gram negative and gram positive bacteria (Pogliano & Beckwith 1994; Duong &

384 Wickner 1997; Bolhuis et al. 1998). Also, only one signal peptidase gene was found in IL1403, compared

385 to five detected in the B. subtilis genome (Kunst et al. 1997). Probably, the useful genes Figure 10.

386 Distribution of the detected genes by functional categories. Colours designating different categories are

387 defined in the legend of Figure 9. The number and the percentage of homology hits to SwissProt are

388 indicated for each category. Classification method is presented in the text. For protein secretion can be

389 acquired by lactococci from closely related species through plasmid transfer, if selective conditions for

390 this are created by industrial applications.

391 Natural competence for DNA-mediated transformation was not described for L. lactis species. However,

392 we found that the L. lactis genome contains four operons, comE, comF, comC and comG, which encode

393 nine genes that share strong similarity with the late competence genes from B. subtilis and S.

394 pneumoniae. Since L. lactis seems to possess a complete set of these genes and since no function other

395 than the involvement in DNA-mediated transformation is known for them, it is possible that L. lactis

396 can acquire natural competence. Sequence studies of late competence genes showed that they are quite

397 similar in different AT-rich gram positive bacteria, like B. subtilis or Streptococci (Dubnau 1997;

398 Campbell et al. 1998). It is apparent so that a big difference exists in the molecular mechanisms which

399 regulate the development of this process in Streptococci and Bacilli. In B. subtilis the regulator ComK

400 assembles the signals from earlier stages of competence development (van Sinderen et al. 1995; Hahn

401 et al. 1996). A functional counterpart of such a regulator was not yet discovered for Streptococci. A way

402 to discover the conditions for acquiring the competence may be the study of regulation of the late genes.

403 We analysed the regions preceding the first ORF in the four late competence operons. The corresponding

404 alignment is shown in Figure 11. It is apparent that a common feature exists for these regions, which

405 suggests that they may be recognised by a common transcription regulator. An interesting feature, which
seems to be unique for these genes, is the presence of a strictly conserved sequence AGTATG, in which ATG always corresponds to the start codon of the first gene in each operon. This is different from the usual ribosome binding site in AT-rich gram positive bacteria, which has a sequence (SD) homologous to the 30-end of 16S rRNA (Vollenoweth & Rabinowitz 1992). Several recent reports show that the efficiency of translation may be not much lower for mRNAs that start directly from ATG codon than for mRNAs with long leaders and strong SD-sequences (Resch et al. 1996; Moll et al. 1998; Van Etten & Janssen 1998), and that the ribosomal protein S1 is not needed for the translation of unleaded mRNA (Tedin et al. 1997). It appears that the absence of the leader region is a common feature of mRNAs of late competence genes in L. lactis.

Studies of the regulation of competence in Streptococci revealed the presence of a gene, encoding a small peptide, that stimulates the induction of expression of the whole competence regulon (Havarstein et al. 1995, 1997). In Streptococci the gene encoding competence-stimulating peptide (CSP) precursor was always found to be the first gene of an operon encoding a two-component regulatory system, which is involved in the induction of competence (Havarstein et al. 1996). Homology search over the L. lactis genome sequence did not reveal any two-component system which resembles the one regulating competence in Streptococci. However, we found an operon encoding proteins homologous to DprA or Smf protein, supposed to be required for chromosomal transformation in H. influenzae, and DNA topoisomerase I from B. subtilis. Interestingly, upstream of the dprA gene there is a sequence resembling that found in the putative com-promoters, described above (Figure 11B). A small ORF between this putative promoter and initiation codon of the dprA gene, may be a candidate for the gene of CSP precursor, since the C-terminal part of the encoded peptide resembles that of CSP from Streptococci. This potential CSP precursor does not have, however, a Gly-Gly pattern that is always found in the Streptococcal CSP precursors (Havarstein et al. 1997).

429

Regulatory functions

Regulation of gene expression in L. lactis was not yet thoroughly explored. A few examples of experimental study of chromosomal gene regulation are known (Bardowski et al. 1994; Kilstrup & Martinussen 1998; Luesink et al. 1998; Raya et al. 1998; van de Guchte et al. 1998; Vaughan et al. 1998; Wouters et al. 1998). Automatic analysis revealed 83 genes potentially involved in regulation, which is
about 6% of the total number of the identified ORFs. This figure is about two times higher than that for M. genitalium (Fraser et al. 1995), coincides with that found in H. influenzae (Fleischmann et al. 1995) and is about two-fold lower than that found in B. subtilis using the same classification criteria (Lapidus et al. 1997). These ratios support the hypothesis that the increase of genome size in bacteria results in the proportional increase of the number of different regulatory systems.

Seven two-component systems were detected. They are all organised in operons, consisting of a cognate sensor kinase and a response regulator. The genes of five two-component systems were cloned recently from the strain MG1363 by complementation of E.coli mutants (O'Connell-Motherway et al. 1997). All of them were identified in our sequence.

An interesting class of regulatory genes are the RAS-like GTP-binding proteins. Several such regulators were found in other bacteria, including the most intensively studied Era protein of E. coli, Obg of B.subtilis and several others, usually revealed by genome sequencing. Exact biological functions of most of these proteins are unknown, although they are sometimes essential and have pleiotropic functions. Interestingly, although all these proteins are homologous and can be considered as a family of paralogs. Each of the nine L. lactis proteins has its clear counterpart in B. subtilis or other bacteria. This suggests that each of these proteins may have a unique biological function in the cell and that revealing it in one microorganism will be directly applicable to the others. It would be interesting to test whether the counterparts of the B. subtilis genes from L. lactis can complement the corresponding mutations in B. subtilis and vice versa. A gene encoding the extra cytoplasmic function (ECF) -factor was detected in L. lactis. This finding can be interesting for studies of regulation of stress response in L. lactis. It is not clear if any of the 11 ECF factors from B. subtilis has the same biological function as the one detected in L. lactis. The most similar proteins are SigV, SigX and YlaC, but the biological function of none of them has yet been established in B. subtilis.

## Replication, transcription and translation

Seventy-seven, 30 and 134 genes were assigned to replication, transcription and translation functional categories, respectively. It is apparent that the replication system of L. lactis is very similar to that of B.subtilis. Counterparts of dnaB and dnaD genes, essential for DNA replication in B. subtilis and not present in gram negative bacteria were detected. Two DNA polymerase III -chain genes, one
corresponding to polC and another to dnaE of B. subtilis, were also detected in L. lactis. E. coli has only the latter gene. The transcription and translation machinery does not seem to have any remarkable difference compared to B. subtilis. Presumably B. subtilis with its well-developed genetic tools can be a convenient host organism to study gene regulation of L. lactis systems.

468

469 **Conclusions and perspectives**

We present here the data on a diagnostic sequencing study of the L. lactis IL1403 genome. The sequencing data with a low average redundancy (about 2) allowed to reveal 1495 proteins, encoded by the L. lactis genome, and to classify them by functions predicted on the basis of homology to known proteins. Some statistical properties of the L. lactis genome sequence were also calculated.

The data presented here allow to evaluate L. lactisas a model organism for studies of bacterial
metabolism, physiology and regulation. Compared to the well established models, like E. coli or B.
subtilis, L.lactis represents a simplified system and is, therefore, potentially more amenable for detailed
understanding. The absence of numerous genes, relative to E. coli orB. subtilis, should facilitate, in the
case of L. lactis, detecting of phenotypes associated with genes of unknownfunction. With regard to
even more simple microorganisms,such as Mycoplasma, the advantage of L. lactis is the ease of
manipulation and the absence of any pathogenicity for humans. These properties, withthe complete
genome information available, place L.lactis among the best model bacteria, to be used for fundamental
biological research.

483

484 Acknowledgements

We are grateful to the L. lactis community of this lab, and especially to the team leaders Marie-Christine and Alain Chopin, Emmanuelle Maguin, Pierre Renault and Alexandra Gruss for the interest to this work and stimulating discussions. Pierre Renault, Patrick Duwat, Meriem El Karoui, Isabelle Poquet, Catherine Schouler are gratefully acknowledged for the use of their unpublished sequence data in the early stages of this project. We thank Philippe Bessieres, Franck Samson, Véronique Biaudet-Brunaud and Nicole Vermeire (INRA, Jouy en Josas), and Gregory Kucherov74and Vladimir Grebinskii (INRIA, Nancy) for the discussions and advice on programming and computing.
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692 subtilis. Mol. Microbiol. 15(3): 455-462

693 Vaughan EE & de Vos WM (1995) Identification and characterization of the insertion element IS1070
694 from Leuconostoc lactis NZ6009. Gene 155 (1): 95-100

695 Vaughan EE, Pridmore RD & Mollet B (1998) Transcriptional regulation and evolution of lactose genes
696 in the galactose-lactose operon of Lactococcus lactis NCDO 2054. J. Bacteriol. 180(18):4893-4902

697 Vellanoweth RL & Rabinowitz JC (1992) The influence of ribosome-binding-site elements on
698 translational efficiency in Bacillus subtilis and Escherichia coli in vivo. Mol. Microbiol. 6(9):1105-
699 1114

700 Venter JC, Smith HO & Hood L (1996) A new strategy for genome sequencing. Nature 381: 364-
701 366Wells JM, Wilson PW, Norton PM & Le Page RW (1993) A model system for the investigation of
702 heterologous protein secretion pathways in Lactococcus lactis. Appl. Environ. Microbiol. 59(11): 3954-
703 3959

704 Wouters JA, Sanders JW, Kok J, de Vos WM, Kuipers OP & Abee T (1998) Clustered organization and
705 transcriptional analysis of a family of five csp genes of Lactococcus lactis MG1363. Microbiology 144
706 (10): 2885-2893

707

<figure><img src="image_2.png" /><figcaption>**Figure 1.** Probability of successful amplification in MLA PCR as a function of the number of oligonucleotides used in the same mixture. The calculation was done by generating the results of 10,000 independent random experiments and averaging these results. The longest distance between primers still allowing the amplification was supposed to be 20 kb. The genome sizes used for calculation are: 1 Mb (dashed line); 2.35 Mb (bold line); 4.2 Mb (thin line); 8 Mb (dotted line).</figcaption></figure>

708
A

<table><thead><tr><th></th><th>1</th><th>2</th><th>3</th><th>4</th><th>5</th><th>6</th><th>7</th><th>8</th><th>9</th><th>10</th><th>11</th><th>12</th><th>13</th><th>14</th><th>15</th><th>16</th></tr></thead><tbody><tr><td>1</td><td>+</td><td>+</td><td>+</td><td>+</td><td>+</td><td>+</td><td>+</td><td>+</td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr><td>2</td><td></td><td>+</td><td>+</td><td>+</td><td>+</td><td>+</td><td>+</td><td>+</td><td>+</td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr><td>3</td><td></td><td></td><td>+</td><td>+</td><td>+</td><td>+</td><td>+</td><td>+</td><td>+</td><td>+</td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr><td>4</td><td></td><td></td><td></td><td>+</td><td>+</td><td>+</td><td>+</td><td>+</td><td>+</td><td>+</td><td>+</td><td></td><td></td><td></td><td></td><td></td></tr><tr><td>5</td><td></td><td></td><td></td><td></td><td>+</td><td>+</td><td>+</td><td>+</td><td>+</td><td>+</td><td>+</td><td>+</td><td></td><td></td><td></td><td></td></tr><tr><td>6</td><td></td><td></td><td></td><td></td><td></td><td>+</td><td>+</td><td>+</td><td>+</td><td>+</td><td>+</td><td>+</td><td>+</td><td></td><td></td><td></td></tr><tr><td>7</td><td></td><td></td><td></td><td></td><td></td><td></td><td>+</td><td>+</td><td>+</td><td>+</td><td>+</td><td>+</td><td>+</td><td>+</td><td></td><td></td></tr><tr><td>8</td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td>+</td><td>+</td><td>+</td><td>+</td><td>+</td><td>+</td><td>+</td><td>+</td><td></td></tr><tr><td>9</td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td>+</td><td>+</td><td>+</td><td>+</td><td>+</td><td>+</td><td>+</td><td>+</td></tr><tr><td>10</td><td>+</td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td>+</td><td>+</td><td>+</td><td>+</td><td>+</td><td>+</td><td>+</td></tr><tr><td>11</td><td>+</td><td>+</td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td>+</td><td>+</td><td>+</td><td>+</td><td>+</td><td>+</td></tr><tr><td>12</td><td>+</td><td>+</td><td>+</td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td>+</td><td>+</td><td>+</td><td>+</td><td>+</td></tr><tr><td>13</td><td>+</td><td>+</td><td>+</td><td>+</td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td>+</td><td>+</td><td>+</td><td>+</td></tr><tr><td>14</td><td>+</td><td>+</td><td>+</td><td>+</td><td>+</td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td>+</td><td>+</td><td>+</td></tr><tr><td>15</td><td>+</td><td>+</td><td>+</td><td>+</td><td>+</td><td>+</td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td>+</td><td>+</td></tr><tr><td>16</td><td>+</td><td>+</td><td>+</td><td>+</td><td>+</td><td>+</td><td>+</td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td>+</td></tr><tr><td>Product 1x8</td><td>n</td><td>n</td><td>n</td><td>n</td><td>n</td><td>n</td><td>n</td><td>y</td><td>n</td><td>n</td><td>n</td><td>n</td><td>n</td><td>n</td><td>n</td><td>n</td></tr><tr><td>Product 3x4</td><td>n</td><td>n</td><td>n</td><td>y</td><td>y</td><td>y</td><td>y</td><td>y</td><td>y</td><td>y</td><td>y</td><td>n</td><td>n</td><td>n</td><td>n</td><td>n</td></tr><tr><td>Product 12x15</td><td>y</td><td>y</td><td>y</td><td>n</td><td>n</td><td>n</td><td>n</td><td>n</td><td>n</td><td>n</td><td>n</td><td>n</td><td>n</td><td>n</td><td>y</td><td>y</td></tr></tbody></table>

B

<figure><img src="image_3.png" /><figcaption>Figure 2. MLA PCR procedure. (A) The table illustrates a theoretical experiment with a total of 16 (M) primers, where each reaction mixture contains 8 (N) primers. The numbers at the top designate reaction mixtures, the numbers on the left designate individual primers, the '+' sign indicates presence of a given primer in a reaction mixture. The three last rows indicate the reaction mixtures in which amplification does (y) or does not (n) take place, if the primer couples 1 and 8, 3 and 4 or 12 and 15, respectively, give a product. To identify the primers which give a product from the analysis of the reactions the following rule is used: If N₁ and N₂ are the first and the last positive reaction, respectively, the primers giving the product will be: P₁=N₁; P₂=N₂ - N+1, if N₂>N₁ (the cases 1×8 and 3×4), or P₂=M+ N₂-N+1, if N₂<N₁ (the case 12×15). (B) Part of a real experiment with 96 primers, where each reaction contained 32 primers and *L. lactis* IL1403 chromosome as template. Sizes and positions of identified fragments are shown on the left. Numbers on the top designate the reaction mix. Arrows on the top indicate the reactions that are used to identify the primers which gave the 10 kb fragment. These primers are P₁=N₁=7, and P₂=N₂ - N+1=34-32+1=3.</figcaption></figure>
<figure><img src="image_4.png" /></figure>

**Figure 3.** Whole-genome PCR amplification of the *L. lactis* IL1403 chromosome. 266 oligonucleotides were used in 133 LR PCR reactions to amplify the entire genome. Correspondence of the sizes of amplified fragments and the physical map predicted from the sequence (Figure 9) indicates the correctness of sequence assembling. Left slot on each panel shows size marker (DNA of phage λ cut by HindIII). The PCR product designations correspond to the ones shown on Figure 9. The first panel from the top, left to the right: BA7, BA8, BB1, BB2, CC1, CC3, BB3, BB4, CC5, CC6, BB5, BB6, BB7, BA1, CB8, BB8, BC1, BC2, CL1, CL2, BC4, BA2, BC5, BC6, BC7, CB3, BC8, BD1, BD2; second panel: BD3, CB4, CC7, CC8, CD1, CD2, CD3, CG4, BD4, CD4, eg7, BD5, BD6, BD7, BD8, BE1, CH4, CE1, BE2, BE3, BE4, BE5, BE6, BE7, BE8, BF1, BF2, BF3, BF4; third panel: BF5, BA3, BF6, BF7, BF8, BG1, BG2, BG3, BG4, BG5, BG6, BG7, BG8, BH1, BH2, BH3, BH4, BA4, BH5, BH6, BH7, BH8, CB5, BI1, BI2, BI3, BI4, DA1, DA2; fourth panel: BI5, BI6, BI7, BI8, BJ1, BJ2, BJ3, BJ4, BJ5, BJ6, BJ7, BJ8, BK1, CB7, BK2, BK3, BK4, BA5, BK5, BK6, BK7, BK8, BL1, BL2, BL3, BL4, BL5, BL6, CE3; fifth panel: CE4, CK5, CK7, BA6, BL8, CE7, CE8, CA1, CA2, CA3, CA4, CA5, CA6, CA7, CA8, CB1, CF3. The sequences of the used oligonucleotides can be found at http://spock.jouy.inra.fr. Chromosome drawing, which is complementary to the one shown on Figure 9, approximately corresponds to the PCR fragments above it.
<figure><img src="image_5.png" /><figcaption>**Figure 4.** Distribution of the GC-content over the *L. lactis* chromosome. Zero point corresponds to the position of the origin of replication. Top panel: a sliding window of 20 kb and a step of 5 kb were used. Bottom panel: a sliding window of 5 kb and the step of 2 kb were used. The peaks near coordinates 540, 1970, 2210, 2250, 2325 and 2340 correspond to tRNA operons. A peak near 2150 kb corresponds to the cluster of ribosomal protein genes.</figcaption></figure>

<figure><img src="image_6.png" /><figcaption>**Figure 5.** GC and AT skew distribution over the *L. lactis* genome. Top panel: a sliding window of 10 kb and step of 1 kb were used. Inset: a sliding window of 1 kb and step of 0.1 kb, were used. In both cases a region near the *dnaA* gene was analysed. Change of the skew distribution sign indicates the position of replication origin. Bottom panel: a sliding window of 20 kb and a step of 5 kb were used. Zero coordinate is placed at the replication origin. The whole genome was analysed. Change of the skew distribution sign indicates the position of replication terminus.</figcaption></figure>

711

712

713

714
<figure><img src="image_7.png" /><figcaption>**Figure 6.** Sequence of the *L. lactis* chromosome near the origin of replication. The *Hind*III site shown in bold was chosen as a zero point to represent the genetic map of *L. lactis* IL1403. Putative *DnaA* boxes are shown in bold. The beginning of the *DnaA* gene and of the *rrnA* genes are shown. Numbering corresponds to that used in the map shown on Figure 9.</figcaption></figure>

715

<figure><img src="image_8.png" /><figcaption>**Figure 7.** Identification of putative prophages in the *L. lactis* IL1403 genome. The distribution shows the number of phage protein hits detected with a sliding window of 50 kb with a step of 10 kb, over the whole genome. Total number of hits on both strands is shown by bold line. Thin line shows difference of the numbers of hits detected separately on each strand and indicates the orientation of most of the phage genes.</figcaption></figure>

716

<figure><img src="image_9.png" /><figcaption>**Figure 8.** Distribution of chi-sites over the *L. lactis* genome. The distribution represents the number of chi sequences detected with a sliding window of 300 kb with a step of 10 kb, over the whole genome. Filled circles show total numbers of chi-sites in the window, open circles show the difference of the numbers of sites detected separately on each strand, refered to as D and R.</figcaption></figure>

717
<figure><img src="image_10.png" /></figure>
<figure><img src="image_11.png" /><figcaption>Figure 9.</figcaption></figure>
<figure><img src="image_12.png" /><figcaption>Figure 9.</figcaption></figure>
<figure><img src="image_13.png" /><figcaption>Figure 9.</figcaption></figure>
<figure><img src="image_14.png" /><figcaption>Figure 9.</figcaption></figure>
<figure><img src="image_15.png" /><figcaption>Figure 9.</figcaption></figure>
<figure><img src="image_16.png" /><figcaption>Figure 9.</figcaption></figure>
<figure><img src="image_17.png" /><figcaption>**Figure 10.** Distribution of the detected genes by functional categories. Colours designating different categories are defined in the legend of Figure 9. The number and the percentage of homology hits to SwissProt are indicated for each category. Classification method is presented in the text.</figcaption></figure>

<figure><img src="image_18.png" /><figcaption>**Figure 11.** Regulatory regions of the *L. lactis* competence genes. (A) Sequences of the regions upstream of the first gene in the four putative competence operons. Sequences corresponding to the recognition site of a hypothetical regulator are shown in bold capital letters. Start codons of the competence genes are italicised. Consensus sequence of the recognition site is shown at the bottom. (B) Sequence of the upstream region of the *dprA* gene. Putative recognition site of the hypothetical competence regulator is shown in bold capital letters. Conceptual translation of a small ORF upstream of the *dprA* gene is shown.</figcaption></figure>

<table><caption>**Table 1.** Low-redundancy whole-genome sequencing strategy</caption><thead><tr><td>Stage</td><td>Description</td></tr></thead><tbody><tr><td>Random small insert and large insert library construction</td><td>Shearing DNA randomly to 1–2 kb and 15–20 kb, respectively. Cloning in multicopy plasmids and λ-based FIXII vector.</td></tr><tr><td>Random sequencing of a limited number of plasmid inserts</td><td>Sequencing of plasmid inserts up to coverage of about one. Using forward (M13-21), reverse (M13RP1) and middle primers. The latter are chosen to sequence the middle of plasmid inserts, when necessary. Assembling is done in parallel with sequencing.</td></tr><tr><td>Random sequencing of a number of large inserts by primer walking.</td><td>Sequencing of large inserts by using synthetic oligonucleotides. Assembling is done in parallel with sequencing to avoid too high redundancy.</td></tr><tr><td>Synthesis of new sequencing substrates by MLA PCR approach.</td><td>Application of Multiplex Long Accurate PCR protocol for random generation of new sequencing substrates.</td></tr><tr><td>Sequencing of MLA PCR products.</td><td>Sequencing of MLA PCR products by primer walking. Assembling is done in parallel with sequencing.</td></tr><tr><td>Iteration</td><td>Iteration of the last two stages until the whole contiguous genome sequence is obtained.</td></tr><tr><td>Annotation</td><td>On-line annotation is done in parallel with the sequencing progress by using automatic computer tools based on BLASTx and FASTx algorithms.</td></tr></tbody></table>
<table><caption>Table 2. Summary of low-redundancy sequencing of the *L. lactis* IL1403 genome*</caption><tr><td>Small insert plasmids</td><td>2854</td></tr><tr><td>Average insert length (bp)</td><td>1520</td></tr><tr><td>Forward sequence reactions (M13-21 primer)</td><td>2625</td></tr><tr><td>Average useful sequence length (bp)</td><td>462</td></tr><tr><td>Reverse sequence reactions (M13RP1 primer)</td><td>2168</td></tr><tr><td>Average useful sequence length (bp)</td><td>422</td></tr><tr><td>Sequencing reactions in the middle of insert</td><td>2357</td></tr><tr><td>Average read length (bp)</td><td>494</td></tr><tr><td>Total characters from plasmid insert sequencing (bp)</td><td>3292004</td></tr><tr><td>Number of selected λ-clones</td><td>122</td></tr><tr><td>Average insert length (kb)</td><td>15.6</td></tr><tr><td>Number of gel readings from λ-inserts</td><td>622</td></tr><tr><td>Average read length (bp)</td><td>409</td></tr><tr><td>Total characters from λ-insert reads (bp)</td><td>254398</td></tr><tr><td>Number of gel readings from LR PCR products</td><td>1641</td></tr><tr><td>Average read length (bp)</td><td>470</td></tr><tr><td>Total characters read from LR PCR products (bp)</td><td>771270</td></tr><tr><td>Total oligonucleotides used</td><td>4620</td></tr><tr><td>Total gel readings</td><td>10235</td></tr><tr><td>Average read length (bp)</td><td>458</td></tr><tr><td>Total characters read (bp)</td><td>4687630</td></tr><tr><td>Size of final contig (bp)</td><td>2345160</td></tr><tr><td>Undefined letters in the final contig (bp)</td><td>3563</td></tr></table>

<footnote>*The figures were estimated by analysis of the assembling database and are therefore approximate (±5%).</footnote>
<table><caption>**Table 3.** Functional classification of the *L. lactis* genes. Genes are ordered by functional categories and their positions on the chromosome. Position on the chromosome (in kb) and the percentage of identity with the most homologous Swissprot entry is also shown</caption><thead><tr><th>BIO001.</th><th>AMINO-ACID BIOSYNTHESIS</th><th>95 genes</th></tr></thead><tbody><tr><td>BIO001.01 General</td><td></td><td>2 genes</td></tr><tr><td>DHSS_SYNP1</td><td>29%</td><td>485 SOLUBLE HYDROGENASE, SMALL SUBUNIT (EC 1.12.-.-)</td></tr><tr><td>PATB_BACSU</td><td>57%</td><td>1974 PUTATIVE AMINOTRANSFERASE B (EC 2.6.1.-)</td></tr><tr><td>BIO001.02 Aromatic amino-acid family</td><td></td><td>19 genes</td></tr><tr><td>AROF_ECOLI</td><td>41%</td><td>117 PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE, TYR-SENSITIVE (EC 4.1.2.15)</td></tr><tr><td>TRPE_HEMA</td><td>26%</td><td>736 ANTHRANILATE SYNTHASE COMPONENT I (EC 4.1.3.27)</td></tr><tr><td>AROG_HAEIN</td><td>40%</td><td>1278 PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE (EC 4.1.2.15)</td></tr><tr><td>TRPA_LACLA</td><td>100%</td><td>1492 TRYPTOPHAN SYNTHASE ALPHA CHAIN (EC 4.2.1.20)</td></tr><tr><td>TRPB_LACLA</td><td>100%</td><td>1493 TRYPTOPHAN SYNTHASE BETA CHAIN (EC 4.2.1.20)</td></tr><tr><td>TRPF_LACLA</td><td>99%</td><td>1495 N-(5'-PHOSPHORIBOSYL)ANTHRANILATE ISOMERASE (EC 5.3.1.24)</td></tr><tr><td>TRPC_LACLA</td><td>100%</td><td>1495 INDOLE-3-GLYCEROL PHOSPHATE SYNTHASE (EC 4.1.1.48)</td></tr><tr><td>TRPD_LACLA</td><td>100%</td><td>1496 ANTHRANILATE PHOSPHORIBOSYLTRANSFERASE (EC 2.4.2.18)</td></tr><tr><td>TRPG_LACLA</td><td>99%</td><td>1497 ANTHRANILATE SYNTHASE COMPONENT II (EC 4.1.3.27)</td></tr><tr><td>TRPE_LACLA</td><td>100%</td><td>1498 ANTHRANILATE SYNTHASE COMPONENT I (EC 4.1.3.27)</td></tr><tr><td>AROD_BACSU</td><td>37%</td><td>1686 3-DEHYDROQUINATE DEHYDRATASE (EC 4.2.1.10)</td></tr><tr><td>PHEA_LACLA</td><td>100%</td><td>1780 PREPHENATE DEHYDRATASE (EC 4.2.1.51)</td></tr><tr><td>AROK_LACLA</td><td>100%</td><td>1781 SHIKIMATE KINASE (EC 2.7.1.71)</td></tr><tr><td>AROA_LACLA</td><td>94%</td><td>1782 3-PHOSPHOSHIKIMATE 1-CARBOXYVINYLTRANSFERASE (EC 2.5.1.19)</td></tr><tr><td>TYRA_LACLA</td><td>90%</td><td>1783 PREPHENATE DEHYDROGENASE (EC 1.3.1.12)</td></tr><tr><td>AROC_BACSU</td><td>61%</td><td>1790 CHORISMATE SYNTHASE (EC 4.6.1.4)</td></tr><tr><td>AROB_HELPY</td><td>39%</td><td>1794 3-DEHYDROQUINATE SYNTHASE (EC 4.6.1.3)</td></tr><tr><td>YDIB_ECOLI</td><td>37%</td><td>1795 HYPOTHETICAL 31.2 KD PROTEIN IN LPP-AROD INTERGENIC REGION</td></tr><tr><td>AROG_BACSU</td><td>32%</td><td>2261 PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE (EC 4.1.2.15)</td></tr><tr><td>BIO001.03 Aspartate family</td><td></td><td>19 genes</td></tr><tr><td>AAT2_METJA</td><td>36%</td><td>57 PUTATIVE ASPARTATE AMINOTRANSFERASE 2 (EC 2.6.1.1)</td></tr><tr><td>ASSY_SYNY3</td><td>57%</td><td>125 ARGININOSUCCINATE SYNTHASE (EC 6.3.4.5)</td></tr><tr><td>AAT_BACSP</td><td>32%</td><td>161 ASPARTATE AMINOTRANSFERASE (EC 2.6.1.1)</td></tr><tr><td>ASNB_ECOLI</td><td>40%</td><td>354 ASPARAGINE SYNTHETASE B (GLUTAMINE-HYDROLYZING) (EC 6.3.5.4)</td></tr><tr><td>AK_METJA</td><td>30%</td><td>746 PROBABLE ASPARTOKINASE (EC 2.7.2.4)</td></tr><tr><td>METB_HELPY</td><td>65%</td><td>789 CYSTATHIONINE GAMMA-SYNTHASE (EC 4.2.99.9)</td></tr><tr><td>DHOM_LACLA</td><td>93%</td><td>1169 HOMOSERINE DEHYDROGENASE (EC 1.1.1.3)</td></tr><tr><td>KHSE_LACLA</td><td>88%</td><td>1170 HOMOSERINE KINASE (EC 2.7.1.39)</td></tr><tr><td>METF_HAEIN</td><td>32%</td><td>1279 5,10-METHYLENETETRAHYDROFOLATE REDUCTASE (EC 1.7.99.5)</td></tr><tr><td>METE_HAEIN</td><td>46%</td><td>1281 5-METHYL-TETRAHYDROPTEROYLTRIGLUTAMATE--HOMOCYSTEINE METHYLTRANSFERASE (EC 2.1.1.14)</td></tr><tr><td>DAPB_BACSU</td><td>50%</td><td>1600 DIHYDRODIPICOLINATE REDUCTASE (EC 1.3.1.26)</td></tr><tr><td>DAPA_BACSU</td><td>46%</td><td>1661 DIHYDRODIPICOLINATE SYNTHASE (EC 4.2.1.52)</td></tr><tr><td>DHAS_STRMU</td><td>75%</td><td>1663 ASPARTATE-SEMIALDEHYDE DEHYDROGENASE (EC 1.2.1.11)</td></tr><tr><td>AA1T_BACSU</td><td>50%</td><td>1877 ASPARTATE AMINOTRANSFERASE (EC 2.6.1.1)</td></tr><tr><td>METB_HELPY</td><td>41%</td><td>1976 CYSTATHIONINE GAMMA-SYNTHASE (EC 4.2.99.9)</td></tr><tr><td>META_ECOLI</td><td>46%</td><td>1977 HOMOSERINE O-SUCCINYLTRANSFERASE (EC 2.3.1.46)</td></tr><tr><td>PYRH_SYNY3</td><td>56%</td><td>2067 URIDYLATE KINASE (EC 2.7.4.-)</td></tr><tr><td>THRC_PSEAE</td><td>38%</td><td>2153 THREONINE SYNTHASE (EC 4.2.99.2)</td></tr><tr><td>ASNH_MYCTU</td><td>37%</td><td>2292 PUTATIVE ASPARAGINE SYNTHETASE (GLUTAMINE-HYDROLYZING) (EC 6.3.5.4)</td></tr><tr><td>BIO001.04 Branched chain family</td><td></td><td>11 genes</td></tr><tr><td>ILVX_BACSU</td><td>52%</td><td>1199 ACETOLACTATE SYNTHASE (EC 4.1.3.18)</td></tr><tr><td>LEU1_SYNY3</td><td>45%</td><td>1238 2-ISOPROPYLMALATE SYNTHASE (EC 4.1.3.12)</td></tr><tr><td>LEU3_LACLA</td><td>99%</td><td>1239 3-ISOPROPYLMALATE DEHYDROGENASE (EC 1.1.1.95)</td></tr><tr><td>LEU2_ACTTI</td><td>53%</td><td>1241 3-ISOPROPYLMALATE DEHYDRATASE (EC 4.2.1.33)</td></tr><tr><td>LEUD_LACLA</td><td>100%</td><td>1242 3-ISOPROPYLMALATE DEHYDRATASE SMALL SUBUNIT (EC 4.2.1.33)</td></tr><tr><td>ILVD_LACLA</td><td>98%</td><td>1244 DIHYDROXY-ACID DEHYDRATASE (EC 4.2.1.9)</td></tr><tr><td>ILVB_LACLA</td><td>82%</td><td>1246 ACETOLACTATE SYNTHASE LARGE SUBUNIT (EC 4.1.3.18)</td></tr><tr><td>ILVN_LACLA</td><td>100%</td><td>1247 ACETOLACTATE SYNTHASE SMALL SUBUNIT (EC 4.1.3.18)</td></tr><tr><td>ILVC_LACLA</td><td>97%</td><td>1247 KETOL-ACID REDUCTOISOMERASE (EC 1.1.1.86)</td></tr><tr><td>THDI_LACLA</td><td>99%</td><td>1249 THREONINE DEHYDRATASE BIOSYNTHETIC (EC 4.2.1.16)</td></tr></tbody></table>
<table><caption>Table 3.</caption><thead><tr><th>BIO002</th><th>Gene</th><th>Accession</th><th>Description</th></tr></thead><tbody><tr><td>BIO002.01</td><td>HEMK_HAEIN</td><td>46%</td><td>HEMK PROTEIN HOMOLOG</td></tr><tr><td>BPA1_STRAU</td><td>29%</td><td>832</td><td>NON-HAEIM BROMOPEROXIDASE RPO-A1 (EC 1.11.1.-)</td></tr><tr><td>HEMK_BACSU</td><td>46%</td><td>1151</td><td>PROBABLE OXYGEN-INDEPENDENT COPROPORPHYRINOGEN III OXIDASE (EC 1.-.-.-)</td></tr><tr><td>BCHE_RHOCA</td><td>26%</td><td>1179</td><td>MAGNESIUM-PROTOPORPHYRIN IX MONOMETHYL ESTER OXIDATIVE CYCLASE</td></tr><tr><td>66 KD SUBUNIT</td><td></td><td></td><td></td></tr><tr><td>HEMZ_YEREN</td><td>39%</td><td>1605</td><td>FERROCHELATASE (EC 4.99.1.1)</td></tr><tr><td>BIO002.04</td><td>Lipoate</td><td></td><td>0 genes</td></tr><tr><td>BIO002.05</td><td>Menaquinone and ubiquinone</td><td></td><td>4 genes</td></tr><tr><td>MENB_BACSU</td><td>73%</td><td>732</td><td>NAPHTHOATE SYNTHASE (EC 4.1.3.36)</td></tr><tr><td>MEND_BACSU</td><td>42%</td><td>735</td><td>2-SUCCINYL-6-HYDROXY-2,4-CYCLOHEXADIENE-1-CARBOXYLATE SYNTHASE (SHCHC SYNTHASE) / 2-OXOGLUTARATE DECARBOXYLASE (EC 4.1.1.71)</td></tr><tr><td>QUEA_HAEIN</td><td>44%</td><td>1613</td><td>S-ADENOSYLMETHIONINE:TRNA RIBOSYLTRANSFERASE-ISOMERASE (EC 5.-.-.-)</td></tr><tr><td>GRC2_LACLA</td><td>70%</td><td>1714</td><td>PROBABLE MENAQUINONE BIOSYNTHESIS METHLYTRANSFERASE (EC 2.1.1.-)</td></tr><tr><td>BIO002.06</td><td>Molybdopterin</td><td></td><td>0 genes</td></tr><tr><td>BIO002.07</td><td>Pantothenate</td><td></td><td>1 genes</td></tr><tr><td>COAA_HAEIN</td><td>43%</td><td>1464</td><td>PANTOTHENATE KINASE (EC 2.7.1.33)</td></tr><tr><td>BIO002.08</td><td>Pyridoxine</td><td></td><td>0 genes</td></tr><tr><td>BIO002.09</td><td>Riboflavin</td><td></td><td>5 genes</td></tr><tr><td>RIBD_ACTPL</td><td>51%</td><td>1020</td><td>RIBOFLAVIN-SPECIFIC DEAMINASE (EC 3.5.4.-)</td></tr><tr><td>RISA_ACTPL</td><td>54%</td><td>1021</td><td>RIBOFLAVIN SYNTHASE ALPHA CHAIN (EC 2.5.1.9)</td></tr><tr><td>GCH2_ACTPL</td><td>60%</td><td>1022</td><td>GTP CYCLOHYDROLASE II (EC 3.5.4.25) / 3,4-DIHYDROXY-2-BUTANONE 4- PHOSPHATE SYNTHASE</td></tr><tr><td>RISB_ACTPL</td><td>68%</td><td>1022</td><td>6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE (EC 2.5.1.9)</td></tr><tr><td>RIBF_CORAM</td><td>38%</td><td>1139</td><td>RIBOFLAVIN KINASE (EC 2.7.1.26)</td></tr><tr><td>BIO002.10</td><td>Thioredoxin, glutaredoxin, and glutathione</td><td></td><td>5 genes</td></tr><tr><td>GSHR_HAEIN</td><td>30%</td><td>861</td><td>GLUTATHIONE REDUCTASE (EC 1.6.4.2)</td></tr><tr><td>TRXB_CLOLI</td><td>47%</td><td>963</td><td>THIOREDOXIN REDUCTASE (EC 1.6.4.5)</td></tr><tr><td>BSAA_BACSU</td><td>56%</td><td>1400</td><td>GLUTATHIONE PEROXIDASE HOMOLOG RSAA</td></tr><tr><td>THIO_BACSU</td><td>54%</td><td>1687</td><td>THIOREDOXIN (TRX)</td></tr><tr><td>TRXB_MYCGE</td><td>36%</td><td>1691</td><td>THIOREDOXIN REDUCTASE (EC 1.6.4.5)</td></tr><tr><td>BIO002.11</td><td>Thiamine</td><td></td><td>10 genes</td></tr><tr><td>YZGD_BACSU</td><td>26%</td><td>165</td><td>HYPOTHETICAL 45.4 KD PROTEIN IN THIAMINASE I 5'REGION</td></tr><tr><td>THID_HAEIN</td><td>38%</td><td>483</td><td>PHOSPHOMETHYLPYRIMIDINE KINASE (EC 2.7.4.7)</td></tr><tr><td>YZGD_BACSU</td><td>42%</td><td>1092</td><td>HYPOTHETICAL 45.4 KD PROTEIN IN THIAMINASE I 5'REGION</td></tr><tr><td>THIE_BACSU</td><td>39%</td><td>1291</td><td>THIAMIN-PHOSPHATE PYROPHOSPHORYLASE (EC 2.5.1.3)</td></tr><tr><td>THID_HAEIN</td><td>48%</td><td>1292</td><td>PHOSPHOMETHYLPYRIMIDINE KINASE (EC 2.7.4.7)</td></tr><tr><td>THIM_HAEIN</td><td>34%</td><td>1293</td><td>HYDROXYETHYLTHIAZOLE KINASE (EC 2.7.1.50)</td></tr><tr><td>DCIP_ENTCL</td><td>41%</td><td>1337</td><td>INDOLE-3-FYRUVATE DECARBOXYLASE (EC 4.1.1.74)</td></tr><tr><td>YZGD_BACSU</td><td>31%</td><td>1662</td><td>HYPOTHETICAL 45.4 KD PROTEIN IN THIAMINASE I 5'REGION</td></tr><tr><td>POXB_LACPL</td><td>46%</td><td>2109</td><td>PYRUVATE OXIDASE (EC 1.2.3.3)</td></tr><tr><td>YZGD_BACSU</td><td>40%</td><td>2296</td><td>HYPOTHETICAL 45.4 KD PROTEIN IN THIAMINASE I 5'REGION</td></tr><tr><td>BIO002.12</td><td>Pyridine nucleotides</td><td></td><td>1 genes</td></tr><tr><td>NADE_ECOLI</td><td>65%</td><td>1107</td><td>NH(3)-DEPENDENT NAD</td></tr><tr><td>BIO003.</td><td>CELL ENVELOPE</td><td></td><td>73 genes</td></tr><tr><td>BIO003.01</td><td>Membranes, lipoproteins, and porins</td><td></td><td>29 genes</td></tr><tr><td>YQJG_BACSU</td><td>32%</td><td>129</td><td>HYPOTHETICAL 30.7 KD LIPOPROTEIN IN GLNQ-ANSR INTERGENIC REGION</td></tr><tr><td>PRECURSOR</td><td></td><td></td><td></td></tr><tr><td>MRP_STRSU</td><td>29%</td><td>147</td><td>MURAMIDASE-RELEASED PROTEIN PRECURSOR (136 KD SURFACE PROTEIN)</td></tr><tr><td>WAPA_STRMU</td><td>26%</td><td>149</td><td>WALL-ASSOCIATED PROTEIN PRECURSOR</td></tr><tr><td>TEE6_STRPY</td><td>39%</td><td>152</td><td>TRYPSIN-RESISTANT SURFACE T6 PROTEIN PRECURSOR</td></tr><tr><td>RFA1_KLEPN</td><td>29%</td><td>201</td><td>O-ANTIGEN EXPORT SYSTEM PERMEASE PROTEIN RPBA</td></tr><tr><td>PLPC_PASHA</td><td>42%</td><td>315</td><td>OUTER MEMBRANE LIPOPROTEIN 3 PRECURSOR (PLP3)</td></tr><tr><td>PLPA_PASHA</td><td>36%</td><td>316</td><td>OUTER MEMBRANE LIPOPROTEIN 1 PRECURSOR (PLP1)</td></tr><tr><td>HLPA_HAEIN</td><td>38%</td><td>317</td><td>28 KD OUTER MEMBRANE PROTEIN PRECURSOR</td></tr><tr><td>YAEC_ECOLI</td><td>37%</td><td>318</td><td>HYPOTHETICAL 29.4 KD LIPOPROTEIN IN RCSF-ABC INTERGENIC REGION</td></tr><tr><td>PRECURSOR</td><td></td><td></td><td></td></tr><tr><td>YOJL_ECOLI</td><td>27%</td><td>370</td><td>HYPOTHETICAL 38.5 KD LIPOPROTEIN IN ADA-OMPC INTERGENIC REGION</td></tr><tr><td>PRECURSOR</td><td></td><td></td><td></td></tr><tr><td>CSTA_MYCTU</td><td>51%</td><td>412</td><td>CARBON STARVATION PROTEIN A HOMOLOG</td></tr><tr><td>SPR_ECOLI</td><td>35%</td><td>480</td><td>LIPOPROTEIN SPR PRECURSOR</td></tr><tr><td>60IM_PSEPU</td><td>29%</td><td>562</td><td>60 KD INNER-MEMBRANE PROTEIN</td></tr><tr><td>CRTK_RHOCA</td><td>33%</td><td>571</td><td>CRTK PROTEIN</td></tr><tr><td>LGT_ECOLI</td><td>25%</td><td>604</td><td>PROLIOPROTEIN DIACYLGLYCERYL TRANSFERASE (EC 2.4.99.-)</td></tr></tbody></table>
<table><caption>Table 3.</caption><tr><td>WAPA_STRMU</td><td>26%</td><td>682</td><td>WALL-ASSOCIATED PROTEIN PRECURSOR</td></tr><tr><td>CAIC_ECOLI</td><td>26%</td><td>731</td><td>PROBABLE CROTONOBETAINE/CARNITINE-COA LIGASE (EC 6.3.2.-)</td></tr><tr><td>SPSE_BACSU</td><td>38%</td><td>906</td><td>STAGE V SPORULATION PROTEIN E</td></tr><tr><td>YD57_METJA</td><td>32%</td><td>935</td><td>PUTATIVE POTASSIUM CHANNEL PROTEIN MJ1357</td></tr><tr><td>MRP_STRSU</td><td>31%</td><td>1221</td><td>MURAMIDASE-RELEASED PROTEIN PRECURSOR (136 KD SURFACE PROTEIN)</td></tr><tr><td>CD59_HSVSA</td><td>32%</td><td>1299</td><td>SURFACE GLYCOPROTEIN CD59 HOMOLOG PRECURSOR</td></tr><tr><td>ADHS_STRPA</td><td>68%</td><td>1347</td><td>ADHESIN B PRECURSOR (SALIVA-BINDING PROTEIN)</td></tr><tr><td>P29K_STRGC</td><td>76%</td><td>1348</td><td>29 KD MEMBRANE PROTEIN IN PSAA 5' REGION (ORF1)</td></tr><tr><td>TMPC_TREPA</td><td>36%</td><td>1460</td><td>MEMBRANE LIPOPROTEIN TMPC PRECURSOR (MEMBRANE PROTEIN C)</td></tr><tr><td>LPLA_BACSU</td><td>27%</td><td>1526</td><td>LIPOPROTEIN LPLA PRECURSOR</td></tr><tr><td>YDEK_ECOLI</td><td>33%</td><td>1622</td><td>HYPOTHETICAL 136.5 KD LIPOPROTEIN IN HIPB-UXAB INTERGENIC</td></tr><tr><td>REGION PRECURSOR (ORFT)</td><td></td><td></td><td></td></tr><tr><td>CZCD_ALCEU</td><td>30%</td><td>1646</td><td>CATION EFFLUX SYSTEM PROTEIN CZCD</td></tr><tr><td>MRP_STRSU</td><td>37%</td><td>1729</td><td>MURAMIDASE-RELEASED PROTEIN PRECURSOR (136 KD SURFACE PROTEIN)</td></tr><tr><td>ADHS_STRSA</td><td>35%</td><td>2164</td><td>ADHESIN B PRECURSOR (SALIVA-BINDING PROTEIN)</td></tr></table>

<table><tr><td>BIO03.02 Murein sacculus and peptidoglycan</td><td>23 genes</td></tr><tr><td>MURA_BACSU</td><td>55%</td><td>311</td><td>PROBABLE UDP-N-ACETYLGUCOSAMINE 1-CARBOXYVINYLTRANSFERASE (EC 2.5.1.7)</td></tr><tr><td>PBP2_STRPN</td><td>46%</td><td>336</td><td>PENICILLIN-BINDING PROTEIN 2B</td></tr><tr><td>MURF_BACSU</td><td>39%</td><td>340</td><td>UDP-N-ACETYLMURAMOYLALANYL-D-GLUTAMYL-2,6-DIAMINOPIMELATE--D-ALANYL-D- ALANYL LIGASE (EC 6.3.2.15)</td></tr><tr><td>PBDP_BACSU</td><td>28%</td><td>390</td><td>PENICILLIN-BINDING PROTEIN 4 PRECURSOR (PBD 4)</td></tr><tr><td>PBPA_STROR</td><td>54%</td><td>528</td><td>PENICILLIN-BINDING PROTEIN 1A (PBP-1A)</td></tr><tr><td>MURA_ACICA</td><td>49%</td><td>532</td><td>UDP-N-ACETYLGUCOSAMINE 1-CARBOXYVINYLTRANSFERASE (EC 2.5.1.7)</td></tr><tr><td>RODA HELPY</td><td>32%</td><td>661</td><td>ROD SHAPE-DETERMINING PROTEIN RODA</td></tr><tr><td>PBPB_BACSU</td><td>27%</td><td>880</td><td>PENICILLIN-BINDING PROTEIN 2B (PBP-2B)</td></tr><tr><td>MRAY_BACSU</td><td>44%</td><td>889</td><td>PHOSPHO-N-ACETYLMURAMOYL-PENTAPEPTIDE-TRANSFERASE (EC 2.7.8.13)</td></tr><tr><td>RODA_ECOLI</td><td>28%</td><td>914</td><td>ROD SHAPE-DETERMINING PROTEIN RODA</td></tr><tr><td>MURB_BACSU</td><td>39%</td><td>1172</td><td>UDP-N-ACETYLENOLPYRUVOYLGLUCOSAMINE REDUCTASE (EC 1.1.1.158)</td></tr><tr><td>ALYS_ENTHR</td><td>39%</td><td>1400</td><td>AUTOLYSIN PRECURSOR (EC 3.5.1.28)</td></tr><tr><td>MURG_BACSU</td><td>45%</td><td>1629</td><td>UDP-N-ACETYLGUCOSAMINE--N-ACETYLMURAMYL-(PENTAPEPTIDE) PYROPHOSPHORYL-UNDECAPRENOL N-ACETYLGUCOSAMINE TRANSFERASE (EC 2.4.1.-)</td></tr><tr><td>MURD_BACSU</td><td>55%</td><td>1630</td><td>UDP-N-ACETYLMURAMOYLALANINE--D-GLUTAMATE LIGASE (EC 6.3.2.9)</td></tr><tr><td>MURE_BACSU</td><td>31%</td><td>1851</td><td>UDP-N-ACETYLMURAMOYLALANYL-D-GLUTAMATE--2,6-DIAMINOPIMELATE LIGASE (EC 6.3.2.13)</td></tr><tr><td>GCAD_BACSU</td><td>54%</td><td>1931</td><td>UDP-N-ACETYLGUCOSAMINE PYROPHOSPHORYLASE (EC 2.7.7.23)</td></tr><tr><td>ALYS_ENTHR</td><td>41%</td><td>1956</td><td>AUTOLYSIN PRECURSOR (EC 3.5.1.28)</td></tr><tr><td>DAC_STRSQ</td><td>25%</td><td>2111</td><td>D-ALANYL-D-ALANINE CARBOXYPEPTIDASE PRECURSOR (EC 3.4.16.4)</td></tr><tr><td>PBPF_BACSU</td><td>31%</td><td>2158</td><td>PENICILLIN-BINDING PROTEIN 1A (PBP-1A)</td></tr><tr><td>BACA_ECOLI</td><td>34%</td><td>2255</td><td>BACITRACIN RESISTANCE PROTEIN (PUTATIVE UNDECAPRENOL KINASE) (EC 2.7.1.66)</td></tr><tr><td>MRED_BACSU</td><td>22%</td><td>2294</td><td>ROD SHAPE-DETERMINING PROTEIN MRED</td></tr><tr><td>MREC_BACSU</td><td>30%</td><td>2295</td><td>ROD SHAPE-DETERMINING PROTEIN MREC</td></tr><tr><td>DACA_BACSU</td><td>35%</td><td>2336</td><td>D-ALANYL-D-ALANINE CARBOXYPEPTIDASE PRECURSOR (EC 3.4.16.4)</td></tr></table>

<table><tr><td>BIO03.03 Surface polysaccharides, lipopolysaccharides and antigens</td><td>21 genes</td></tr><tr><td>DLTE_BACSU</td><td>33%</td><td>142</td><td>DLTE PROTEIN</td></tr><tr><td>RFEC_SHIFL</td><td>35%</td><td>196</td><td>DTDP-4-DEHYDRORHAMNOSE 3,5-EPIMERASE (EC 5.1.3.13)</td></tr><tr><td>RBB2_ECOLI</td><td>46%</td><td>197</td><td>DTDP-GLUCOSE 4,6-DEHYDRATASE (EC 4.2.1.46)</td></tr><tr><td>RFBG_SHIFL</td><td>36%</td><td>200</td><td>DTDP-RHAMNOSYL TRANSFERASE RFBG (EC 2.-.-.-)</td></tr><tr><td>LICD_HAEIN</td><td>31%</td><td>213</td><td>LICD PROTEIN</td></tr><tr><td>TAGD_BACSU</td><td>55%</td><td>217</td><td>GLYCEROL-3-PHOSPHATE CYTIDYLYLTRANSFERASE (EC 2.7.7.39)</td></tr><tr><td>TAGH_BACSU</td><td>48%</td><td>935</td><td>TEICHOIC ACID TRANSLOCATION ATP-BINDING PROTEIN TAGH</td></tr><tr><td>TAGG_BACSU</td><td>29%</td><td>937</td><td>TEICHOIC ACID TRANSLOCATION PERMEASE PROTEIN TAGG</td></tr><tr><td>TAGB_BACSU</td><td>29%</td><td>941</td><td>TEICHOIC ACID BIOSYNTHESIS PROTEIN B PRECURSOR</td></tr><tr><td>TAGB_BACSU</td><td>27%</td><td>944</td><td>TEICHOIC ACID BIOSYNTHESIS PROTEIN B PRECURSOR</td></tr><tr><td>TAGD_BACSU</td><td>49%</td><td>948</td><td>GLYCEROL-3-PHOSPHATE CYTIDYLYLTRANSFERASE (EC 2.7.7.39)</td></tr><tr><td>TAGF_BACSU</td><td>38%</td><td>950</td><td>TEICHOIC ACID BIOSYNTHESIS PROTEIN F</td></tr><tr><td>TAGB_BACSU</td><td>30%</td><td>951</td><td>TEICHOIC ACID BIOSYNTHESIS PROTEIN B PRECURSOR</td></tr><tr><td>DLTD_BACSU</td><td>34%</td><td>1287</td><td>PROTEIN DLTD PRECURSOR</td></tr><tr><td>DLTC_LACCA</td><td>43%</td><td>1288</td><td>D-ALANYL CARRIER PROTEIN (DCP)</td></tr><tr><td>DLTB_BACSU</td><td>49%</td><td>1288</td><td>DLTB PROTEIN</td></tr><tr><td>TAGE_BACSU</td><td>25%</td><td>1475</td><td>PROBABLE POLY GLYCEROL-PHOSPHATE ALPHA-GLUCOSYLTRANSFERASE (EC 2.4.1.52)</td></tr><tr><td>TAGE_BACSU</td><td>23%</td><td>1477</td><td>PROBABLE POLY GLYCEROL-PHOSPHATE ALPHA-GLUCOSYLTRANSFERASE (EC 2.4.1.52)</td></tr><tr><td>RFBU_SALTY</td><td>25%</td><td>2186</td><td>RFBU PROTEIN</td></tr><tr><td>RFAK_SALTY</td><td>28%</td><td>2187</td><td>LIPOPOLYSACCHARIDE 1,2-N-ACETYLGUCOSAMINETRANSFERASE (EC 2.4.1.56)</td></tr><tr><td>KDTB_HAEIN</td><td>39%</td><td>2218</td><td>LIPOPOLYSACCHARIDE CORE BIOSYNTHESIS PROTEIN KDTB</td></tr></table>

<table><tr><td>BIO03.04 Surface structures</td><td>0 genes</td></tr></table>

<table><tr><td>BIO04. CELLULAR PROCESSES</td><td>29 genes</td></tr></table>

<table><tr><td>BIO04.01 Cell division</td><td>8 genes</td></tr></table>
<table><caption>Table 3.</caption><thead><tr><th></th><th></th><th></th><th></th></tr></thead><tbody><tr><td>DIVC_BACSU</td><td>31%</td><td>22</td><td>CELL DIVISION PROTEIN DIVIC</td></tr><tr><td>FTSH_LACLA</td><td>98%</td><td>27</td><td>CELL DIVISION PROTEIN FTSH HOMOLOG (EC 3.4.24.-)</td></tr><tr><td>SFOJ_BACSU</td><td>44%</td><td>96</td><td>STAGE 0 SPORULATION PROTEIN J</td></tr><tr><td>FTSY_BACSU</td><td>58%</td><td>823</td><td>CELL DIVISION PROTEIN FTSY HOMOLOG</td></tr><tr><td>FTSE_ECOLI</td><td>40%</td><td>997</td><td>CELL DIVISION ATP-BINDING PROTEIN FTSE</td></tr><tr><td>SP3E_BACSU</td><td>49%</td><td>1701</td><td>STAGE III SPORULATION PROTEIN E</td></tr><tr><td>FTSZ_BACSU</td><td>61%</td><td>1918</td><td>CELL DIVISION PROTEIN FTSZ</td></tr><tr><td>FTSA_BACSU</td><td>37%</td><td>1919</td><td>CELL DIVISION PROTEIN FTSA</td></tr><tr><td colspan="4"><strong>BIO04.02 Cell killing</strong></td></tr><tr><td>HLY3_BACCE</td><td>44%</td><td>495</td><td>HEMOLYSIN III (HLY-III)</td></tr><tr><td>YQXC_BACSU</td><td>60%</td><td>879</td><td>HYPOTHETICAL 29.7 KD PROTEIN IN FOLD-AHRC INTERGENIC REGION</td></tr><tr><td>FRPA_NEIME</td><td>30%</td><td>1394</td><td>IRON-REGULATED PROTEIN FRPA</td></tr><tr><td colspan="4"><strong>BIO04.03 Chaperones</strong></td></tr><tr><td>SUGE_ECOLI</td><td>46%</td><td>122</td><td>SUGE PROTEIN</td></tr><tr><td>CH10_LACLA</td><td>100%</td><td>396</td><td>10 KD CHAPERONIN (PROTEIN CPN10)</td></tr><tr><td>CH60_LACLA</td><td>97%</td><td>397</td><td>60 KD CHAPERONIN (PROTEIN CPN60)</td></tr><tr><td>DNAK_LACLA</td><td>99%</td><td>977</td><td>DNAK PROTEIN (HEAT SHOCK PROTEIN 70)</td></tr><tr><td colspan="4"><strong>BIO04.04 Detoxification</strong></td></tr><tr><td>SODM_LACLA</td><td>100%</td><td>410</td><td>SUPEROXIDE DISMUTASE (MN) (EC 1.15.1.1)</td></tr><tr><td colspan="4"><strong>BIO04.05 Protein and peptide secretion</strong></td></tr><tr><td>SECA_STAAU</td><td>51%</td><td>115</td><td>PREPROTEIN TRANSLOCASE SECA SUBUNIT</td></tr><tr><td>TIG_BACSU</td><td>52%</td><td>534</td><td>TRIGGER FACTOR (TF)</td></tr><tr><td>LSPA_STAAU</td><td>43%</td><td>1023</td><td>LIPOPROTEIN SIGNAL PEPTIDASE (EC 3.4.23.36)</td></tr><tr><td>SECY_LACLA</td><td>98%</td><td>2138</td><td>PREPROTEIN TRANSLOCASE SECY SUBUNIT</td></tr><tr><td>LEPC_BACCL</td><td>41%</td><td>2330</td><td>SIGNAL PEPTIDASE I (EC 3.4.21.89)</td></tr><tr><td colspan="4"><strong>BIO04.06 Transformation</strong></td></tr><tr><td>CMA2_BACSU</td><td>46%</td><td>729</td><td>COMA OPERON PROTEIN 2</td></tr><tr><td>CMF3_BACSU</td><td>37%</td><td>1094</td><td>COMF OPERON PROTEIN 3</td></tr><tr><td>CMF1_BACSU</td><td>37%</td><td>1095</td><td>COMF OPERON PROTEIN 1</td></tr><tr><td>CME3_BACSU</td><td>28%</td><td>1811</td><td>COME OPERON PROTEIN 3</td></tr><tr><td>CME1_BACSU</td><td>39%</td><td>1812</td><td>COME OPERON PROTEIN 1</td></tr><tr><td>CMG3_BACSU</td><td>44%</td><td>2166</td><td>COMG OPERON PROTEIN 3 PRECURSOR</td></tr><tr><td>CMG2_BACSU</td><td>30%</td><td>2167</td><td>COMG OPERON PROTEIN 2</td></tr><tr><td>CMG1_BACSU</td><td>39%</td><td>2168</td><td>COMG OPERON PROTEIN 1</td></tr><tr><td colspan="4"><strong>BIO04.07 Other</strong></td></tr><tr><td colspan="4"><strong>BIO05. CENTRAL INTERMEDIARY METABOLISM</strong></td></tr><tr><td colspan="4"><strong>BIO05.01 General</strong></td></tr><tr><td>GRC3_BACSU</td><td>31%</td><td>184</td><td>PROBABLE HEPTAPRENYL DIPHOSPHATE SYNTHASE COMPONENT II (EC 2.5.1.30)</td></tr><tr><td>STRL_STRGR</td><td>42%</td><td>198</td><td>DTDP-4-DEHYDRORHAMNOSE REDUCTASE (EC 1.1.1.133)</td></tr><tr><td>ISPA_BACSU</td><td>47%</td><td>878</td><td>GERANYLTRANSTRANSFERASE (EC 2.5.1.10)</td></tr><tr><td>YWNE_BACSU</td><td>48%</td><td>985</td><td>HYPOTHETICAL 55.8 KD PROTEIN IN SPOIIQ-MTA INTERGENIC REGION</td></tr><tr><td>YWNE_BACSU</td><td>44%</td><td>1185</td><td>HYPOTHETICAL 55.8 KD PROTEIN IN SPOIIQ-MTA INTERGENIC REGION</td></tr><tr><td>GRC3_BACSU</td><td>35%</td><td>1378</td><td>PROBABLE HEPTAPRENYL DIPHOSPHATE SYNTHASE COMPONENT II (EC 2.5.1.30)</td></tr><tr><td>METK_STAAU</td><td>62%</td><td>1950</td><td>S-ADENOSYLmethIONINE SYNTHETASE (EC 2.5.1.6)</td></tr><tr><td colspan="4"><strong>BIO05.02 Amino sugars</strong></td></tr><tr><td>NYLA_PSES8</td><td>32%</td><td>167</td><td>6-AMINOHEXANOATE-CYCLIC-DIMER HYDROLASE (EC 3.5.2.12)</td></tr><tr><td>NODB_RHILV</td><td>37%</td><td>279</td><td>CHITOOLIGOSACCHARIDE DEACETYLASE (EC 3.5.1.-)</td></tr><tr><td>GLMS_MYCLE</td><td>36%</td><td>1032</td><td>PROBABLE GLUCOSAMINE--FRUCTOSE-6-PHOSPHATE AMINOTRANSFERASE (ISOMERIZING) (EC 2.6.1.16)</td></tr><tr><td>NAGD_ECOLI</td><td>28%</td><td>1154</td><td>NAGD PROTEIN</td></tr><tr><td>YYVH_BACSU</td><td>47%</td><td>1296</td><td>PUTATIVE UDP-N-ACETYLGLUCOSAMINE 2-EPIMERASE (EC 5.1.3.14)</td></tr><tr><td>NAGA_HAEIN</td><td>30%</td><td>1371</td><td>N-ACETYLGLUCOSAMINE-6-PHOSPHATE DEACETYLASE (EC 3.5.1.25)</td></tr><tr><td>HASC_STRPY</td><td>58%</td><td>1376</td><td>UTP--GLUCOSE-1-PHOSPHATE URIDYLYLTRANSFERASE (EC 2.7.7.9)</td></tr><tr><td>NAGB_HAEIN</td><td>32%</td><td>1611</td><td>GLUCOSAMINE-6-PHOSPHATE ISOMERASE (EC 5.3.1.10)</td></tr><tr><td colspan="4"><strong>BIO05.03 Degradation of polysaccharides</strong></td></tr><tr><td>NEPU_THEVU</td><td>30%</td><td>701</td><td>NEOPULLULANASE (EC 3.2.1.135)</td></tr><tr><td>AMY_BACST</td><td>44%</td><td>1275</td><td>ALPHA-AMYLASE PRECURSOR (EC 3.2.1.1)</td></tr><tr><td>O16G_BACTR</td><td>60%</td><td>1523</td><td>OLIGO-1,6-GLUCOSIDASE (EC 3.2.1.10)</td></tr><tr><td>CHIX_STROI</td><td>31%</td><td>2007</td><td>EXOCHITINASE 1 PRECURSOR (EC 3.2.1.14)</td></tr><tr><td>CH11_BACCI</td><td>34%</td><td>2007</td><td>CHITINASE A1 PRECURSOR (EC 3.2.1.14)</td></tr><tr><td colspan="4"><strong>BIO05.04 Phosphorus compounds</strong></td></tr><tr><td>DUT_HAEIN</td><td>40%</td><td>179</td><td>DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDHYDROLASE (EC 3.6.1.23)</td></tr><tr><td>DUT_HAEIN</td><td>38%</td><td>456</td><td>DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDHYDROLASE (EC 3.6.1.23)</td></tr><tr><td>SUHB_ECOLI</td><td>29%</td><td>531</td><td>EXTRAGENIC SUPPRESSOR PROTEIN SUHB</td></tr></tbody></table>
<table><caption>Table 3.</caption><thead><tr><th>Gene</th><th>Accession</th><th>Gene ID</th><th>Description</th></tr></thead><tbody><tr><td>APL_LACLA</td><td>96%</td><td>717</td><td>ALKALINE PHOSPHATASE LIKE PROTEIN</td></tr><tr><td>DUT_HAEIN</td><td>38%</td><td>1046</td><td>DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDHYDROLASE (EC 3.6.1.23)</td></tr><tr><td>DUT_HAEIN</td><td>37%</td><td>1441</td><td>DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDHYDROLASE (EC 3.6.1.23)</td></tr><tr><td>PPH_MYCPN</td><td>27%</td><td>1937</td><td>PUTATIVE PROTEIN PHOSPHATASE (EC 3.1.3.16)</td></tr><tr><td>FGPB_HAEIN</td><td>36%</td><td>2122</td><td>PHOSPHATIDYGLYCEROPHOSPHATASE B (EC 3.1.3.27)</td></tr><tr><td>Y328_SYNY3</td><td>35%</td><td>2264</td><td>PUTATIVE LOW MOLECULAR WEIGHT PROTEIN-TYROSINE-PHOSPHATASE (EC 3.1.3.48)</td></tr><tr><td colspan="4"><strong>BIO005.05 Polyamine biosynthesis</strong></td></tr><tr><td>ATDA_ECOLI</td><td>41%</td><td>1653</td><td>SPERMIDINE N1-ACETYLTRANSFERASE (EC 2.3.1.57)</td></tr><tr><td colspan="4"><strong>BIO005.06 Other</strong></td></tr><tr><td colspan="4"><strong>BIO006. ENERGY METABOLISM</strong></td></tr><tr><td colspan="4"><strong>BIO006.01 Aerobic</strong></td></tr><tr><td>MTLD_STRMU</td><td>61%</td><td>34</td><td>MANNITOL-1-PHOSPHATE 5-DEHYDROGENASE (EC 1.1.1.17)</td></tr><tr><td>OD02_MYCTU</td><td>34%</td><td>61</td><td>DIHYDROLIPOAMIDE SUCCINYLTRANSFERASE COMPONENT (E2) OF 2-OXOGLUTARATE DEHYDROGENASE COMPLEX (EC 2.3.1.61)</td></tr><tr><td>VDLC_HELPY</td><td>33%</td><td>78</td><td>PROBABLE SHORT-CHAIN TYPE DEHYDROGENASE/REDUCTASE VDLC (EC 1.-.-.-)</td></tr><tr><td>YOXD_BACSU</td><td>36%</td><td>141</td><td>HYPOTHETICAL OXIDOREDUCTASE IN RTP 5'REGION (EC 1.-.-.-)</td></tr><tr><td>NQOE_THETH</td><td>26%</td><td>159</td><td>NADH-UBIQUINONE OXIDOREDUCTASE CHAIN 14 (EC 1.6.5.3)</td></tr><tr><td>DHNA_BACSU</td><td>50%</td><td>334</td><td>NADH DEHYDROGENASE (EC 1.6.99.3)</td></tr><tr><td>LDH_BACSU</td><td>54%</td><td>377</td><td>L-LACTATE DEHYDROGENASE (EC 1.1.1.27)</td></tr><tr><td>NAOX_ENTFA</td><td>39%</td><td>395</td><td>NADH OXIDASE (EC 1.6.-.-)</td></tr><tr><td>LDH_LISMO</td><td>24%</td><td>488</td><td>L-LACTATE DEHYDROGENASE (EC 1.1.1.27)</td></tr><tr><td>YBBO_ECOLI</td><td>29%</td><td>617</td><td>HYPOTHETICAL OXIDOREDUCTASE IN USHA-TESA INTERGENIC REGION (EC 1.-.-.-)</td></tr><tr><td>NAOX_METJA</td><td>34%</td><td>792</td><td>PUTATIVE NADH OXIDASE (EC 1.6.-.-)</td></tr><tr><td>YWFD_BACSU</td><td>38%</td><td>799</td><td>HYPOTHETICAL OXIDOREDUCTASE IN ROCC-PTA INTERGENIC REGION (EC 1.-.-.-)</td></tr><tr><td>BUDC_KLETE</td><td>53%</td><td>916</td><td>ACETOIN(DIACETYL) REDUCTASE (EC 1.1.1.5)</td></tr><tr><td>PHBB_CHRVI</td><td>37%</td><td>916</td><td>ACETOACETYL-COA REDUCTASE (EC 1.1.1.36)</td></tr><tr><td>FRDA_SHEPU</td><td>45%</td><td>1136</td><td>FUMARATE REDUCTASE FLAVOPROTEIN SUBUNIT PRECURSOR (EC 1.3.99.1)</td></tr><tr><td>LDH_LACCA</td><td>37%</td><td>1140</td><td>L-LACTATE DEHYDROGENASE (EC 1.1.1.27)</td></tr><tr><td>GLPD_MYCLE</td><td>34%</td><td>1268</td><td>GLYCEROL-3-PHOSPHATE DEHYDROGENASE (EC 1.1.99.5)</td></tr><tr><td>LZM_MYCSM</td><td>40%</td><td>1277</td><td>LACTATE 2-MONOXYGENASE (EC 1.13.12.4)</td></tr><tr><td>VDLC_HELPY</td><td>36%</td><td>1341</td><td>PROBABLE SHORT-CHAIN TYPE DEHYDROGENASE/REDUCTASE VDLC (EC 1.-.-.-)</td></tr><tr><td>GPDA_ECOLI</td><td>25%</td><td>1355</td><td>GLYCEROL-3-PHOSPHATE DEHYDROGENASE (NAD+) (EC 1.1.1.8)</td></tr><tr><td>LDH_LACLA</td><td>100%</td><td>1367</td><td>L-LACTATE DEHYDROGENASE (EC 1.1.1.27)</td></tr><tr><td>GPDA_BACSU</td><td>34%</td><td>1375</td><td>GLYCEROL-3-PHOSPHATE DEHYDROGENASE (NAD)</td></tr><tr><td>YINL_LISMO</td><td>36%</td><td>1506</td><td>HYPOTHETICAL OXIDOREDUCTASE IN INLA 5'REGION (EC 1.-.-.-)</td></tr><tr><td>YQJQ_BACSU</td><td>38%</td><td>1569</td><td>HYPOTHETICAL OXIDOREDUCTASE IN GLNQ-ANSR INTERGENIC REGION (EC 1.-.-.-)</td></tr><tr><td>YINL_LISMO</td><td>72%</td><td>1576</td><td>HYPOTHETICAL OXIDOREDUCTASE IN INLA 5'REGION (EC 1.-.-.-)</td></tr><tr><td>MTLK_RHOSH</td><td>28%</td><td>1675</td><td>MANNITOL 2-DEHYDROGENASE (EC 1.1.1.67)</td></tr><tr><td>YQIG_BACSU</td><td>42%</td><td>1730</td><td>PROBABLE NADH-DEPENDENT FLAVIN OXIDOREDUCTASE YQIG (EC 1.-.-.-)</td></tr><tr><td>YPRA_CORGL</td><td>29%</td><td>2048</td><td>HYPOTHETICAL 33.0 KD PROTEIN IN PROB-PROA INTERGENIC REGION</td></tr><tr><td>YKGC_ECOLI</td><td>39%</td><td>2119</td><td>PROBABLE PYRIDINE NUCLEOTIDE-DISULFIDE OXIDOREDUCTASE IN EAHE-BETA INTERGENIC REGION</td></tr><tr><td>NAOX_ENTFA</td><td>35%</td><td>2175</td><td>NADH OXIDASE (EC 1.6.-.-)</td></tr><tr><td>YBBQ_ECOLI</td><td>33%</td><td>2278</td><td>HYPOTHETICAL 30.8 KD PROTEIN IN GIP-FDRA INTERGENIC REGION</td></tr><tr><td>OXIR_STRAT</td><td>40%</td><td>2318</td><td>PROBABLE OXIDOREDUCTASE (EC 1.-.-.-)</td></tr><tr><td colspan="4"><strong>BIO006.02 Amino acids and amines</strong></td></tr><tr><td>DHL2_LACCO</td><td>57%</td><td>488</td><td>L-2-HYDROXYISOCAPROATE DEHYDROGENASE (EC 1.1.1.-)</td></tr><tr><td>ASPG_BACLI</td><td>34%</td><td>741</td><td>L-ASPARAGINASE (EC 3.5.1.1)</td></tr><tr><td>OTCC_CLOPE</td><td>52%</td><td>806</td><td>ORNITHINE CARBAMOYLTRANSFERASE, CATABOLIC (EC 2.1.3.3)</td></tr><tr><td>DHCO_LACLA</td><td>86%</td><td>1262</td><td>N5-(CARBOXYETHYL)ORNITHINE SYNTHASE (EC 1.5.1.24)</td></tr><tr><td>OTCC_CLOPE</td><td>54%</td><td>2093</td><td>ORNITHINE CARBAMOYLTRANSFERASE, CATABOLIC (EC 2.1.3.3)</td></tr><tr><td colspan="4"><strong>BIO006.03 Anaerobic</strong></td></tr><tr><td>NRDD_ECOLI</td><td>52%</td><td>269</td><td>ANAEROBIC RIBONUCLEOSIDE-TRIPHOSPHATE REDUCTASE (EC 1.17.4.2)</td></tr><tr><td>NRDG_ECOLI</td><td>46%</td><td>270</td><td>ANAEROBIC RIBONUCLEOSIDE-TRIPHOSPHATE REDUCTASE ACTIVATING PROTEIN (EC 1.97.1.-)</td></tr><tr><td colspan="4"><strong>BIO006.04 ATP-proton motive force interconversion</strong></td></tr><tr><td>ATP6_MYCGE</td><td>28%</td><td>1087</td><td>ATP SYNTHASE A CHAIN (EC 3.6.1.34)</td></tr><tr><td>ATPE_STRMU</td><td>64%</td><td>1802</td><td>ATP SYNTHASE EPSILON CHAIN (EC 3.6.1.34)</td></tr><tr><td>ATPA_STRMU</td><td>79%</td><td>1804</td><td>ATP SYNTHASE ALPHA CHAIN (EC 3.6.1.34)</td></tr><tr><td>ATPA Synp1</td><td>65%</td><td>1806</td><td>ATP SYNTHASE ALPHA CHAIN (EC 3.6.1.34)</td></tr><tr><td>ATPF_STRMU</td><td>47%</td><td>1807</td><td>ATP SYNTHASE B CHAIN (EC 3.6.1.34)</td></tr><tr><td>ATP6_ENTFA</td><td>37%</td><td>1808</td><td>ATP SYNTHASE A CHAIN (EC 3.6.1.34)</td></tr><tr><td colspan="4"><strong>BIO006.05 Electron transport</strong></td></tr><tr><td colspan="4"><strong>BIO006.04 ATP-proton motive force interconversion</strong></td></tr><tr><td>ATP6_MYCGE</td><td>28%</td><td>1087</td><td>ATP SYNTHASE A CHAIN (EC 3.6.1.34)</td></tr><tr><td>ATPE_STRMU</td><td>64%</td><td>1802</td><td>ATP SYNTHASE EPSILON CHAIN (EC 3.6.1.34)</td></tr><tr><td>ATPA_STRMU</td><td>79%</td><td>1804</td><td>ATP SYNTHASE ALPHA CHAIN (EC 3.6.1.34)</td></tr><tr><td>ATPA Synp1</td><td>65%</td><td>1806</td><td>ATP SYNTHASE ALPHA CHAIN (EC 3.6.1.34)</td></tr><tr><td>ATPF_STRMU</td><td>47%</td><td>1807</td><td>ATP SYNTHASE B CHAIN (EC 3.6.1.34)</td></tr><tr><td>ATP6_ENTFA</td><td>37%</td><td>1808</td><td>ATP SYNTHASE A CHAIN (EC 3.6.1.34)</td></tr></tbody></table>
<table><caption>Table 3.</caption><thead><tr><th>Gene</th><th>Strand</th><th>Position</th><th>Gene</th><th>Strand</th><th>Position</th></tr></thead><tbody><tr><td>NIFJ_ANASP</td><td>44%</td><td>428</td><td>PYRUVATE-PLAVODOXIN OXIDOREDUCTASE (EC 1.-.-,-)</td><td></td><td></td></tr><tr><td>CYDA_BACSU</td><td>49%</td><td>706</td><td>CYTOCHROME D UBIQUINOL OXIDASE SUBUNIT I (EC 1.10.3.-)</td><td></td><td></td></tr><tr><td>CYDB_BACSU</td><td>43%</td><td>707</td><td>CYTOCHROME D UBIQUINOL OXIDASE SUBUNIT II (EC 1.10.3.-)</td><td></td><td></td></tr><tr><td>DHNA_HAEIN</td><td>28%</td><td>838</td><td>NADH DEHYDROGENASE (EC 1.6.99.3)</td><td></td><td></td></tr><tr><td>DHNA_HAEIN</td><td>32%</td><td>839</td><td>NADH DEHYDROGENASE (EC 1.6.99.3)</td><td></td><td></td></tr><tr><td>FIXC_ECOLI</td><td>37%</td><td>1193</td><td>FIXC PROTEIN</td><td></td><td></td></tr><tr><td colspan="6"><strong>BIO06.06 Entner-Doudoroff</strong></td></tr><tr><td>XDGK_BACSU</td><td>46%</td><td>1668</td><td>2-DEHYDRO-3-DEOXYGLUCONOKINASE (EC 2.7.1.45)</td><td></td><td></td></tr><tr><td colspan="6"><strong>BIO06.07 Fermentation</strong></td></tr><tr><td>QOR_PSEAE</td><td>32%</td><td>231</td><td>QUINONE OXIDOREDUCTASE (EC 1.6.5.5)</td><td></td><td></td></tr><tr><td>QOR_PSEAE</td><td>32%</td><td>721</td><td>QUINONE OXIDOREDUCTASE (EC 1.6.5.5)</td><td></td><td></td></tr><tr><td>DHSQ_BACSU</td><td>32%</td><td>915</td><td>SORBITOL DEHYDROGENASE (EC 1.1.1.14)</td><td></td><td></td></tr><tr><td>FADH_METMR</td><td>37%</td><td>1587</td><td>GLUTATHIONE-DEPENDENT FORMALDEHYDE DEHYDROGENASE (EC 1.2.1.1)</td><td></td><td></td></tr><tr><td>YBDH_ECOLI</td><td>31%</td><td>1595</td><td>HYPOTHETICAL OXIDOREDUCTASE IN CSTA-AHPC INTERGENIC REGION</td><td></td><td></td></tr><tr><td>ADH1_ZYMMO</td><td>60%</td><td>1852</td><td>ALCOHOL DEHYDROGENASE I (EC 1.1.1.1)</td><td></td><td></td></tr><tr><td>SUCD_CLOKL</td><td>40%</td><td>2210</td><td>SUCCINATE-SEMIALDEHYDE DEHYDROGENASE (NAD)</td><td></td><td></td></tr><tr><td>ADHE_ECOLI</td><td>44%</td><td>2211</td><td>ALCOHOL DEHYDROGENASE (EC 1.1.1.1)</td><td></td><td></td></tr><tr><td colspan="6"><strong>BIO06.08 Gluconeogenesis</strong></td></tr><tr><td>DCOA_KLEPN</td><td>40%</td><td>664</td><td>OXALOACETATE DECARBOXYLASE ALPHA CHAIN (EC 4.1.1.3)</td><td></td><td></td></tr><tr><td>SDHM_ECOLI</td><td>36%</td><td>842</td><td>L-SERINE DEHYDRATASE 2 (EC 4.2.1.13)</td><td></td><td></td></tr><tr><td>G6PB_BACST</td><td>39%</td><td>2224</td><td>GLUCOSE-6-PHOSPHATE ISOMERASE B (GPI B) (EC 5.3.1.9)</td><td></td><td></td></tr><tr><td colspan="6"><strong>BIO06.09 Glycolysis</strong></td></tr><tr><td>PGK_THEMA</td><td>57%</td><td>241</td><td>PHOSPHOGLYCERATE KINASE (EC 2.7.2.3)</td><td></td><td></td></tr><tr><td>ENO_MYCPN</td><td>52%</td><td>272</td><td>ENOLASE (EC 4.2.1.11)</td><td></td><td></td></tr><tr><td>PMGY_ZYMMO</td><td>62%</td><td>332</td><td>PHOSPHOGLYCERATE MUTASE (EC 5.4.2.1)</td><td></td><td></td></tr><tr><td>PGMB_LACLA</td><td>100%</td><td>440</td><td>BETA-PHOSPHOGLUCOMUTASE (EC 5.4.2.6)</td><td></td><td></td></tr><tr><td>G3P_LACLA</td><td>99%</td><td>552</td><td>GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE (EC 1.2.1.12)</td><td></td><td></td></tr><tr><td>ENO_BACSU</td><td>70%</td><td>631</td><td>ENOLASE (EC 4.2.1.11)</td><td></td><td></td></tr><tr><td>ENO_HAEIN</td><td>55%</td><td>649</td><td>ENOLASE (EC 4.2.1.11)</td><td></td><td></td></tr><tr><td>PGMB_LACLA</td><td>32%</td><td>748</td><td>BETA-PHOSPHOGLUCOMUTASE (EC 5.4.2.6)</td><td></td><td></td></tr><tr><td>TPIS_LACLA</td><td>99%</td><td>1146</td><td>TRIOSEPHOSPHATE ISOMERASE (EC 5.3.1.1)</td><td></td><td></td></tr><tr><td>KPYK_LACLA</td><td>54%</td><td>1368</td><td>PYRUVATE KINASE (EC 2.7.1.40)</td><td></td><td></td></tr><tr><td>K6PF_LACLA</td><td>99%</td><td>1370</td><td>6-PHOSPHOFRUCTOKINASE (EC 2.7.1.11)</td><td></td><td></td></tr><tr><td>PMG2_ECOLI</td><td>28%</td><td>1749</td><td>PROBABLE PHOSPHOGLYCERATE MUTASE 2 (EC 5.4.2.1)</td><td></td><td></td></tr><tr><td>ALF_MYCGE</td><td>46%</td><td>1959</td><td>FRUCTOSE-BISPHOSPHATE ALDOLASE (EC 4.1.2.13)</td><td></td><td></td></tr><tr><td>G3P_LACLA</td><td>81%</td><td>2313</td><td>GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE (EC 1.2.1.12)</td><td></td><td></td></tr><tr><td colspan="6"><strong>BIO06.10 Pentose phosphate pathway</strong></td></tr><tr><td>DXS_RHOCA</td><td>38%</td><td>1508</td><td>PROBABLE 1-DEOXYXYLULOSE-5-PHOSPHATE SYNTHASE (DXP SYNTHASE)</td><td></td><td></td></tr><tr><td>TKT_MYCLE</td><td>38%</td><td>1666</td><td>TRANSKETOLASE (EC 2.2.1.1)</td><td></td><td></td></tr><tr><td>DXS_BACSU</td><td>38%</td><td>1720</td><td>PROBABLE 1-DEOXYXYLULOSE-5-PHOSPHATE SYNTHASE (DXP SYNTHASE)</td><td></td><td></td></tr><tr><td>G6PD_BACSU</td><td>48%</td><td>2282</td><td>GLUCOSE-6-PHOSPHATE 1-DEHYDROGENASE (EC 1.1.1.49)</td><td></td><td></td></tr><tr><td>RPIA_ECOLI</td><td>39%</td><td>2297</td><td>RIBOSE 5-PHOSPHATE ISOMERASE A (EC 5.3.1.6)</td><td></td><td></td></tr><tr><td colspan="6"><strong>BIO06.11 Pyruvate dehydrogenase</strong></td></tr><tr><td>DDLD_BACST</td><td>55%</td><td>60</td><td>LIPOAMIDE DEHYDROGENASE COMPONENT (E3) OF PYRUVATE DEHYDROGENASE COMPLEX (EC 1.8.1.4)</td><td></td><td></td></tr><tr><td>CDPB_BACST</td><td>62%</td><td>63</td><td>PYRUVATE DEHYDROGENASE E1 COMPONENT, BETA SUBUNIT (EC 1.2.4.1)</td><td></td><td></td></tr><tr><td>ODPA_BACSU</td><td>51%</td><td>64</td><td>PYRUVATE DEHYDROGENASE E1 COMPONENT, ALPHA SUBUNIT (EC 1.2.4.1)</td><td></td><td></td></tr><tr><td>DLDH_ACHLA</td><td>26%</td><td>840</td><td>LIPOAMIDE DEHYDROGENASE COMPONENT (E3) OF PYRUVATE DEHYDROGENASE COMPLEX (EC 1.8.1.4)</td><td></td><td></td></tr><tr><td colspan="6"><strong>BIO06.12 Sugars</strong></td></tr><tr><td>GLGB_SYNY3</td><td>34%</td><td>144</td><td>1,4-ALPHA-GLUCAN BRANCHING ENZYME (EC 2.4.1.18)</td><td></td><td></td></tr><tr><td>BGL1_BACSU</td><td>24%</td><td>174</td><td>BETA-GLUCOSIDASE (EC 3.2.1.21)</td><td></td><td></td></tr><tr><td>BGLA_BACSU</td><td>41%</td><td>178</td><td>6-PHOSPHO-BETA-GLUCOSIDASE (EC 3.2.1.86)</td><td></td><td></td></tr><tr><td>RMLA_STRMU</td><td>88%</td><td>195</td><td>GLUCOSE-1-PHOSPHATE THYMYDYLYLTRANSFERASE (EC 2.7.7.24)</td><td></td><td></td></tr><tr><td>CAPI_STAAU</td><td>27%</td><td>210</td><td>CAPI PROTEIN</td><td></td><td></td></tr><tr><td>AHPC_BACSU</td><td>76%</td><td>333</td><td>ALKYL HYDROPEROXIDE REDUCTASE C22 PROTEIN (EC 1.6.4.-)</td><td></td><td></td></tr><tr><td>GUNM_CLOTM</td><td>31%</td><td>392</td><td>ENDOGLUCANASE M (EC 3.2.1.4)</td><td></td><td></td></tr><tr><td>CASB_KLEOX</td><td>51%</td><td>420</td><td>PHOSPHO-CELLOBIASE (EC 3.2.1.-)</td><td></td><td></td></tr><tr><td>XYNB_BUTFI</td><td>29%</td><td>440</td><td>ENDO-1,4-BETA-XYLANASE B (EC 3.2.1.8)</td><td></td><td></td></tr><tr><td>6PGD_SALTY</td><td>68%</td><td>606</td><td>6-PHOSPHOGLUCONATE DEHYDROGENASE, DECARBOXYLATING (EC 1.1.1.44)</td><td></td><td></td></tr><tr><td>GAL7_LACHE</td><td>36%</td><td>614</td><td>GALACTOSE-1-PHOSPHATE URIDYLYLTRANSFERASE (EC 2.7.7.10)</td><td></td><td></td></tr><tr><td>PFL_STRMU</td><td>83%</td><td>656</td><td>FORMATE ACETYLTRANSFERASE (EC 2.3.1.54)</td><td></td><td></td></tr><tr><td>MALQ_ECOLI</td><td>29%</td><td>692</td><td>4-ALPHA-GLUCANOTRANSFERASE (EC 2.4.1.25)</td><td></td><td></td></tr><tr><td>GLGC_BACST</td><td>57%</td><td>694</td><td>GLUCOSE-1-PHOSPHATE ADENYLYLTRANSFERASE (EC 2.7.7.27)</td><td></td><td></td></tr><tr><td>GLGD_BACST</td><td>31%</td><td>695</td><td>GLYCOGEN BIOSYNTHESIS PROTEIN GLGD</td><td></td><td></td></tr><tr><td>GLGA_BACSU</td><td>46%</td><td>697</td><td>GLYCOGEN SYNTHASE (EC 2.4.1.21)</td><td></td><td></td></tr><tr><td>PHSG_BACSU</td><td>44%</td><td>699</td><td>GLYCOGEN PHOSPHORYLASE (EC 2.4.1.1)</td><td></td><td></td></tr><tr><td>BGLA_BACSU</td><td>54%</td><td>831</td><td>6-PHOSPHO-BETA-GLUCOSIDASE (EC 3.2.1.86)</td><td></td><td></td></tr><tr><td>GAL7_STRLI</td><td>24%</td><td>849</td><td>GALACTOSE-1-PHOSPHATE URIDYLYLTRANSFERASE (EC 2.7.7.10)</td><td></td><td></td></tr><tr><td>UDP_HAEIN</td><td>39%</td><td>853</td><td>URIDINE PHOSPHORYLASE (EC 2.4.2.3)</td><td></td><td></td></tr></tbody></table>
<table><caption>Table 3.</caption><thead><tr><th>Gene</th><th>Accession</th><th>Gene ID</th><th>Description</th></tr></thead><tbody><tr><td>WCAL_SALTY</td><td>35%</td><td>947</td><td>PUTATIVE COLANIC ACID BIOSYNTHESIS GLYCOSYL TRANSFERASE WCAL</td></tr><tr><td>DEOD_STRTR</td><td>72%</td><td>954</td><td>PURINE NUCLEOSIDE PHOSPHORYLASE (EC 2.4.2.1)</td></tr><tr><td>LACC_STRMU</td><td>33%</td><td>982</td><td>TAGATOSE-6-PHOSPHATE KINASE (EC 2.7.1.-)</td></tr><tr><td>JMGHA_HAEIN</td><td>37%</td><td>1134</td><td>DNA-3-METHYLADENINE GLYCOSIDASE (EC 3.2.2.20)</td></tr><tr><td>GLPK_BACSU</td><td>61%</td><td>1270</td><td>GLYCEROL KINASE (EC 2.7.1.30)</td></tr><tr><td>THGA_ECOLI</td><td>40%</td><td>1319</td><td>GALACTOSIDE ACETYLTRANSFERASE (EC 2.3.1.18)</td></tr><tr><td>GIDB_BACSU</td><td>60%</td><td>1378</td><td>GLUCOSE INHIBITED DIVISION PROTEIN B</td></tr><tr><td>DEOC_BACSU</td><td>60%</td><td>1461</td><td>DEOXYRIBOSE-PHOSPHATE ALDOLASE (EC 4.1.2.4)</td></tr><tr><td>BGL1_BACSU</td><td>56%</td><td>1488</td><td>BETA-GLUCOSIDASE (EC 3.2.1.21)</td></tr><tr><td>GLK_BACSU</td><td>34%</td><td>1517</td><td>GLUCOKINASE (EC 2.7.1.2)</td></tr><tr><td>BGLA_THEMA</td><td>33%</td><td>1518</td><td>BETA-GLUCOSIDASE A (EC 3.2.1.21)</td></tr><tr><td>STRH_STRPN</td><td>29%</td><td>1524</td><td>BETA-N-ACETYLHEXOSAMINIDASE PRECURSOR (EC 3.2.1.52)</td></tr><tr><td>XYNB_BACPU</td><td>48%</td><td>1540</td><td>BETA-XYLOSIDASE (EC 3.2.1.37)</td></tr><tr><td>CALM_ACICA</td><td>29%</td><td>1543</td><td>ALDOSE 1-EPIMERASE PRECURSOR (EC 5.1.3.3)</td></tr><tr><td>XYLB_BACSU</td><td>49%</td><td>1544</td><td>XYLULOSE KINASE (EC 2.7.1.17)</td></tr><tr><td>XYLA_THETU</td><td>50%</td><td>1545</td><td>XYULOSE ISOMERASE (EC 5.3.1.5)</td></tr><tr><td>XYNX_CLOTM</td><td>28%</td><td>1618</td><td>EXOGLUCANASE XYNX PRECURSOR (EC 3.2.1.91)</td></tr><tr><td>ALKH_BACSU</td><td>35%</td><td>1668</td><td>4-HYDROXY-2-OXOGLUTARATE ALDOLASE (EC 4.1.3.16)</td></tr><tr><td>UXAC_ECOLI</td><td>44%</td><td>1669</td><td>URONATE ISOMERASE (EC 5.3.1.12)</td></tr><tr><td>UXUA_THENE</td><td>57%</td><td>1673</td><td>MANNONATE DEHYDRATASE (EC 4.2.1.8)</td></tr><tr><td>RBSK_BACSU</td><td>47%</td><td>1683</td><td>RIBOKINASE (EC 2.7.1.15)</td></tr><tr><td>ASCB_ECOLI</td><td>53%</td><td>1718</td><td>6-PHOSPHO-BETA-GLUCOSIDASE ASCB (EC 3.2.1.86)</td></tr><tr><td>GIDA_BACSU</td><td>61%</td><td>1895</td><td>GLUCOSE INHIBITED DIVISION PROTEIN A</td></tr><tr><td>RPE_SYNY3</td><td>47%</td><td>1983</td><td>RIBULOSE-PHOSPHATE 3-EPIMERASE (EC 5.1.3.1)</td></tr><tr><td>GALE_STRMU</td><td>60%</td><td>2034</td><td>UDP-GLUCOSE 4-EPIMERASE (EC 5.1.3.2)</td></tr><tr><td>BGA2_ECOLI</td><td>34%</td><td>2036</td><td>EVOLVED BETA-GALACTOSIDASE ALPHA-SUBUNIT (EC 3.2.1.23)</td></tr><tr><td>THGA_LACLA</td><td>100%</td><td>2038</td><td>GALACTOSIDE O-ACETYLTRANSFERASE (EC 2.3.1.18)</td></tr><tr><td>GAL7_STRMU</td><td>52%</td><td>2039</td><td>GALACTOSE-1-PHOSPHATE URYDILYLTRANSFERASE (EC 2.7.7.10)</td></tr><tr><td>GAL1_STRMU</td><td>58%</td><td>2041</td><td>GALACTOKINASE (EC 2.7.1.6)</td></tr><tr><td>GALM_HAEIN</td><td>36%</td><td>2042</td><td>ALDOSE 1-EPIMERASE (EC 5.1.3.3)</td></tr><tr><td>GLK_BACSU</td><td>47%</td><td>2081</td><td>GLUCOKINASE (EC 2.7.1.2)</td></tr><tr><td>GNTK_BACSU</td><td>49%</td><td>2249</td><td>GLUCONOXINASE (EC 2.7.1.12)</td></tr><tr><td>YQEC_BACSU</td><td>53%</td><td>2250</td><td>HYPOTHETICAL 32.8 KD PROTEIN IN NUCB-AROD INTERGENIC REGION</td></tr><tr><td colspan="4"><strong>BIO06.13 TCA cycle</strong></td></tr><tr><td>CISY_THIFE</td><td>29%</td><td>665</td><td>CITRATE SYNTHASE (EC 4.1.3.7)</td></tr><tr><td>ACON_BRAJA</td><td>51%</td><td>667</td><td>ACONITATE HYDRATASE (EC 4.2.1.3)</td></tr><tr><td>IDH_STRMU</td><td>60%</td><td>669</td><td>ISOCITRATE DEHYDROGENASE (NADP) (EC 1.1.1.42)</td></tr><tr><td>MLES_LACLA</td><td>98%</td><td>920</td><td>MALOLACTIC ENZYME (EC 1.--.--)</td></tr><tr><td>MAOX_BACST</td><td>49%</td><td>1201</td><td>MALATE OXIDOREDUCTASE (NAD) (EC 1.1.1.38)</td></tr><tr><td>CITC_ECOLI</td><td>37%</td><td>1205</td><td>[CITRATE (PRO-3S)-LYASE] LIGASE (EC 6.2.1.22)</td></tr><tr><td>CILG_HAEIN</td><td>52%</td><td>1205</td><td>CITRATE LYASE ACYL CARRIER PROTEIN (CITRATE LYASE GAMMA CHAIN)</td></tr><tr><td>CITB_KLEPN</td><td>52%</td><td>1206</td><td>CITRATE LYASE BETA CHAIN (EC 4.1.3.6)</td></tr><tr><td>CILB_ECOLI</td><td>56%</td><td>1207</td><td>CITRATE LYASE ALPHA CHAIN (EC 4.1.3.6)</td></tr><tr><td colspan="4"><strong>BIO07. FATTY ACID AND PHOSPHOLIPID METABOLISM</strong></td></tr><tr><td colspan="4"><strong>BIO07.01 General</strong></td></tr><tr><td>LPLA1_MYCPN</td><td>36%</td><td>65</td><td>PROBABLE LIPOATE-PROTEIN LIGASE A (EC 6.--.--)</td></tr><tr><td>PLSX_BACSU</td><td>47%</td><td>71</td><td>FATTY ACID/PHOSPHOLIPID SYNTHESIS PROTEIN PLSX HOMOLOG</td></tr><tr><td>GLPQ_BACSU</td><td>33%</td><td>217</td><td>GLYCEROPHOSPHORYL DIESTER PHOSPHODIESTERASE (EC 3.1.4.46)</td></tr><tr><td>PABZ_ECOLI</td><td>42%</td><td>558</td><td>(3R)-HYDROXYMYRISTOYL-[ACYL CARRIER PROTEIN] DEHYDRATASE (EC 4.2.1.-)</td></tr><tr><td>PAB1_HAEIN</td><td>42%</td><td>559</td><td>ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE (NADH) (EC 1.3.1.9)</td></tr><tr><td>DLTA_LACCA</td><td>24%</td><td>653</td><td>D-ALANINE-ACTIVATING ENZYME (EC 6.3.2.-)</td></tr><tr><td>ACCC_METJA</td><td>48%</td><td>662</td><td>BIOTIN CARBOXYLASE (EC 6.3.4.14)</td></tr><tr><td>PABD_BACSU</td><td>45%</td><td>781</td><td>MALONYL COA-ACYL CARRIER PROTEIN TRANSACYLASE (EC 2.3.1.39)</td></tr><tr><td>FABG_BACSU</td><td>46%</td><td>782</td><td>3-OXOACYL-[ACYL-CARRIER PROTEIN] REDUCTASE (EC 1.1.1.100)</td></tr><tr><td>FABF_VIBHA</td><td>42%</td><td>783</td><td>3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE II (EC 2.3.1.41)</td></tr><tr><td>BCCP_ANASP</td><td>51%</td><td>784</td><td>BIOTIN CARBOXYL CARRIER PROTEIN OF ACETYL-COA CARBOXYLASE (EC 6.4.1.2)</td></tr><tr><td>PABZ_HAEIN</td><td>50%</td><td>784</td><td>(3R)-HYDROXYMYRISTOYL-[ACYL CARRIER PROTEIN] DEHYDRATASE (EC 4.2.1.-)</td></tr><tr><td>ACCC_BACSU</td><td>59%</td><td>786</td><td>BIOTIN CARBOXYLASE (EC 6.3.4.14)</td></tr><tr><td>ACCA_HAEIN</td><td>49%</td><td>788</td><td>ACETYL-COENZYME A CARBOXYLASE CARBOXYL TRANSFERASE SUBUNIT</td></tr><tr><td colspan="4"><strong>BIO08. PURINES, PYRIMIDINES, NUCLEOSIDES AND NUCLEOTIDES</strong></td></tr><tr><td>ALPHA (EC 6.4.1.2)</td><td></td><td></td><td></td></tr><tr><td>KDGL_STRMU</td><td>68%</td><td>1093</td><td>DIACYLGLYCEROL KINASE (EC 2.7.1.107)</td></tr><tr><td>ATOB_HAEIN</td><td>44%</td><td>1608</td><td>ACETYL-COA ACETYLTRANSFERASE (EC 2.3.1.9)</td></tr><tr><td>FABG_BACSU</td><td>39%</td><td>1824</td><td>3-OXOACYL-[ACYL-CARRIER PROTEIN] REDUCTASE (EC 1.1.1.100)</td></tr><tr><td>PAC_BACSH</td><td>45%</td><td>1883</td><td>PENICILLIN ACYLASE (EC 3.5.1.11)</td></tr><tr><td>FGSA_BACSU</td><td>43%</td><td>2026</td><td>CDP-DIACYLGLYCEROL--GLYCEROL-3-PHOSPHATE 3-PHOSPHATIDYLTRANSFERASE (EC 2.7.8.5)</td></tr><tr><td>CDSA_PSEAE</td><td>32%</td><td>2179</td><td>PHOSPHATIDATE CYTIDILYLTRANSFERASE (EC 2.7.7.41)</td></tr><tr><td colspan="4"><strong>BIO08.1 PURINES, PYRIMIDINES, NUCLEOSIDES AND NUCLEOTIDES</strong></td></tr><tr><td colspan="4"><strong>BIO08.01 2'-deoxyribonucleotide metabolism</strong></td></tr></tbody></table>
<table><caption>Table 3.</caption><thead><tr><th colspan="4">BIO08.02 Nucleotide and nucleoside interconversions</th><th>4 genes</th></tr></thead><tbody><tr><td>DGK2_LACAC</td><td>62%</td><td>491</td><td>DEOXYGUANOSINE KINASE (EC 2.7.1.113)</td><td>/ DEOXYADENOSINE KINASE (EC 2.7.1.76) SUBUNIT 2</td></tr><tr><td>KITH_STRGC</td><td>79%</td><td>583</td><td>THYMIDINE KINASE (EC 2.7.1.21)</td><td></td></tr><tr><td>DGK2_LACAC</td><td>55%</td><td>1168</td><td>DEOXYGUANOSINE KINASE (EC 2.7.1.113)</td><td>/ DEOXYADENOSINE KINASE (EC 2.7.1.76) SUBUNIT 2</td></tr><tr><td>KCY_BACSU</td><td>49%</td><td>1740</td><td>PROBABLE CYTIDYLATE KINASE (EC 2.7.4.14)</td><td></td></tr><tr><th colspan="4">BIO08.03 Purine ribonucleotide biosynthesis</th><th>22 genes</th></tr><tr><td>IMDH_STRPY</td><td>82%</td><td>219</td><td>INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE (EC 1.1.1.205)</td><td></td></tr><tr><td>ADD_ECOLI</td><td>33%</td><td>285</td><td>ADENOSINE DEAMINASE (EC 3.5.4.4)</td><td></td></tr><tr><td>POLD_STRTR</td><td>65%</td><td>874</td><td>METHYLENETETRAHYDROFOLATE DEHYDROGENASE (EC 1.5.1.5) / METHENYLTETRAHYDROFOLATE CYCLOHYDROLASE (EC 3.5.4.9)</td><td></td></tr><tr><td>PTH5_STRMU</td><td>65%</td><td>958</td><td>FORMATE--TETRAHYDROFOLATE LIGASE (EC 6.3.4.3)</td><td></td></tr><tr><td>IMDH_HELPY</td><td>37%</td><td>1156</td><td>INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE (EC 1.1.1.205)</td><td></td></tr><tr><td>GUA8_BACSU</td><td>67%</td><td>1514</td><td>GMP SYNTHASE (GLUTAMINE-HYDROLYZING) (EC 6.3.5.2)</td><td></td></tr><tr><td>PURK_SYNY3</td><td>33%</td><td>1548</td><td>PHOSPHORIBOSYLAMINOIMIDAZOLE CARBOXYLASE ATPASE SUBUNIT (EC 4.1.1.21)</td><td></td></tr><tr><td>PUR6_HAEIN</td><td>59%</td><td>1549</td><td>PHOSPHORIBOSYLAMINOIMIDAZOLE CARBOXYLASE CATALYTIC SUBUNIT (EC 4.1.1.21)</td><td></td></tr><tr><td>PUR2_BACSU</td><td>55%</td><td>1550</td><td>PHOSPHORIBOSYLAMINE-GLYCINE LIGASE (EC 6.3.4.13)</td><td></td></tr><tr><td>PUR9_BACSU</td><td>55%</td><td>1555</td><td>PHOSPHORIBOSYLAMINOIMIDAZOLECARBOXAMIDE FORMYLTRANSFERASE (EC 2.1.2.3)</td><td></td></tr><tr><td>PUR3_BACSU</td><td>45%</td><td>1561</td><td>PHOSPHORIBOSYLGLYCINAMIDE FORMYLTRANSFERASE (EC 2.1.2.2)</td><td></td></tr><tr><td>PUR5_BACSU</td><td>60%</td><td>1562</td><td>PHOSPHORIBOSYLFORMYLGLYCINAMIDINE CYCLO-LIGASE (EC 6.3.3.1)</td><td></td></tr><tr><td>PUR1_BACSU</td><td>61%</td><td>1568</td><td>AMIDOPHOSPHORIBOSYLTRANSFERASE PRECURSOR (EC 2.4.2.14)</td><td></td></tr><tr><td>PURL_BACSU</td><td>58%</td><td>1571</td><td>PHOSPHORIBOSYLFORMYLGLYCINAMIDINE SYNTHASE II (EC 6.3.5.3)</td><td></td></tr><tr><td>PURQ_BACSU</td><td>61%</td><td>1573</td><td>PHOSPHORIBOSYLFORMYLGLYCINAMIDINE SYNTHASE I (EC 6.3.5.3)</td><td></td></tr><tr><td>PUR7_STRPN</td><td>66%</td><td>1574</td><td>PHOSPHORIBOSYLAMINOIMIDAZOLE-SUCCINOCARBOXAMIDE SYNTHASE (EC 6.3.2.6)</td><td></td></tr><tr><td>PUR8_BACSU</td><td>76%</td><td>1685</td><td>ADENYLOSUCCINATE LYASE (EC 4.3.2.2)</td><td></td></tr><tr><td>PUR8_STRMU</td><td>81%</td><td>1685</td><td>ADENYLOSUCCINATE LYASE (EC 4.3.2.2)</td><td></td></tr><tr><td>KGUA_SYNY3</td><td>48%</td><td>1946</td><td>GUANYLATE KINASE (EC 2.7.4.8)</td><td></td></tr><tr><td>PURA_BACSU</td><td>59%</td><td>2009</td><td>ADENYLOSUCCINATE SYNTHETASE (EC 6.3.4.4)</td><td></td></tr><tr><td>PURQ_BACSU</td><td>31%</td><td>2107</td><td>PHOSPHORIBOSYLFORMYLGLYCINAMIDINE SYNTHASE I (EC 6.3.5.3)</td><td></td></tr><tr><td>KAD_LACLA</td><td>98%</td><td>2137</td><td>ADENYLATE KINASE (EC 2.7.4.3)</td><td></td></tr><tr><th colspan="4">BIO08.04 Pyrimidine ribonucleotide biosynthesis</th><th>10 genes</th></tr><tr><td>PYRG_BACSU</td><td>64%</td><td>486</td><td>CTP SYNTHASE (EC 6.3.4.2)</td><td></td></tr><tr><td>PYRE_BACSU</td><td>57%</td><td>1078</td><td>OROTATE PHOSPHORIBOSYLTRANSFERASE (EC 2.4.2.10)</td><td></td></tr><tr><td>PYRC_LACLE</td><td>42%</td><td>1079</td><td>DIHYDROOROTASE (EC 3.5.2.3)</td><td></td></tr><tr><td>DCOP_LACLC</td><td>97%</td><td>1380</td><td>DIROTDINE 5'-PHOSPHATE DECARBOXYLASE (EC 4.1.1.23)</td><td></td></tr><tr><td>PYDB_LACLC</td><td>93%</td><td>1381</td><td>DIHYDROOROTATE DEHYDROGENASE B (EC 1.3.3.1)</td><td></td></tr><tr><td>CDD_BACSU</td><td>54%</td><td>1461</td><td>CYTIDINE DEAMINASE (EC 3.5.4.5)</td><td></td></tr><tr><td>TYSY_LACLA</td><td>98%</td><td>1579</td><td>THYMIDYLATE SYNTHASE (EC 2.1.1.45)</td><td></td></tr><tr><td>PYDA_LACLC</td><td>98%</td><td>1589</td><td>DIHYDROOROTATE DEHYDROGENASE A (EC 1.3.3.1)</td><td></td></tr><tr><td>CARA_BACSU</td><td>56%</td><td>1640</td><td>CARBAMOYL-PHOSPHATE SYNTHASE, PYRIMIDINE-SPECIFIC, SMALL CHAIN (EC 6.3.5.5)</td><td></td></tr><tr><td>PYRB_SYNY3</td><td>42%</td><td>1641</td><td>ASPARTATE CARBAMOYLTRANSFERASE (EC 2.1.3.2)</td><td></td></tr><tr><th colspan="4">BIO08.05 Salvage of nucleosides and nucleotides</th><th>11 genes</th></tr><tr><td>HPRT_LACLA</td><td>99%</td><td>25</td><td>HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE (EC 2.4.2.8)</td><td></td></tr><tr><td>XTHY_BACSU</td><td>48%</td><td>401</td><td>THYMIDYLATE KINASE (EC 2.7.4.9)</td><td></td></tr><tr><td>APT_ECOLI</td><td>54%</td><td>621</td><td>ADENINE PHOSPHORIBOSYLTRANSFERASE (EC 2.4.2.7)</td><td></td></tr><tr><td>KPRS_BACSU</td><td>66%</td><td>824</td><td>RIBOSE-PHOSPHATE PYROPHOSPHOKINASE (EC 2.7.6.1)</td><td></td></tr><tr><td>DEOB_BACSU</td><td>55%</td><td>953</td><td>PHOSPHOPENTOMUTASE (EC 5.4.2.7)</td><td></td></tr><tr><td>XPT_BACSU</td><td>52%</td><td>1157</td><td>XANTHINE PHOSPHORIBOSYLTRANSFERASE (EC 2.4.2.-)</td><td></td></tr><tr><td>HPRT_BACSU</td><td>56%</td><td>1557</td><td>HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE (EC 2.4.2.8)</td><td></td></tr><tr><td>URK_HAEIN</td><td>52%</td><td>1705</td><td>URIDINE KINASE (EC 2.7.1.48)</td><td></td></tr><tr><td>KPRS_BACCL</td><td>26%</td><td>1906</td><td>RIBOSE-PHOSPHATE PYROPHOSPHOKINASE (EC 2.7.6.1)</td><td></td></tr><tr><td>UPP_LACLA</td><td>97%</td><td>1972</td><td>URACIL PHOSPHORIBOSYLTRANSFERASE (EC 2.4.2.9)</td><td></td></tr><tr><td>PURR_BACSU</td><td>50%</td><td>2331</td><td>PUR OPERON REPRESSOR</td><td></td></tr><tr><th colspan="4">BIO08.06 Sugar-nucleotide biosynthesis and interconversions</th><th>0 genes</th></tr><tr><th colspan="4">BIO09. REGULATORY FUNCTIONS</th><th>94 genes</th></tr><tr><th colspan="4">BIO09.01 General</th><th>41 genes</th></tr><tr><td>YQAE_BACSU</td><td>35%</td><td>11</td><td>HYPOTHETICAL TRANSCRIPTIONAL REGULATOR IN SPOIIIC-CWLA INTERGENIC REGION (ORF7)</td><td></td></tr><tr><td>XRE_BACSU</td><td>50%</td><td>44</td><td>PUTATIVE PBSX REPRESSOR</td><td></td></tr><tr><td>RELA_STREQ</td><td>66%</td><td>106</td><td>PUTATIVE GTP PYROPHOSPHOKINASE (EC 2.7.6.5)</td><td></td></tr><tr><td>TER8_PASPI</td><td>29%</td><td>128</td><td>TETRACYCLINE REPRESSOR PROTEIN CLASS H</td><td></td></tr><tr><td>YQAE_BACSU</td><td>34%</td><td>133</td><td>HYPOTHETICAL TRANSCRIPTIONAL REGULATOR IN SPOIIIC-CWLA INTERGENIC REGION (ORF7)</td><td></td></tr><tr><td>TER2_ECOLI</td><td>38%</td><td>143</td><td>TETRACYCLINE REPRESSOR PROTEIN CLASS B (TRANSPOSON TN10)</td><td></td></tr></tbody></table>
<table><caption>Table 3.</caption><thead><tr><th>Gene</th><th>Transcriptional Regulator</th><th>Transcriptional Region</th><th>Transcriptional Effect</th></tr></thead><tbody><tr><td>CODY_BACSU</td><td>49%</td><td>162</td><td>CODY PROTEIN (VEGETATIVE PROTEIN 286B)</td></tr><tr><td>MECB_BACSU</td><td>51%</td><td>549</td><td>NEGATIVE REGULATOR OF GENETIC COMPETENCE MECB</td></tr><tr><td>CTSR_BACSU</td><td>45%</td><td>627</td><td>TRANSCRIPTIONAL REGULATOR CTSR</td></tr><tr><td>MECB_BACSU</td><td>50%</td><td>629</td><td>NEGATIVE REGULATOR OF GENETIC COMPETENCE MECB</td></tr><tr><td>YP20_BACLI</td><td>34%</td><td>737</td><td>HYPOTHETICAL P20 PROTEIN</td></tr><tr><td>SLYA_SALTY</td><td>26%</td><td>747</td><td>TRANSCRIPTIONAL REGULATOR SLYA (SALMOLYSIN)</td></tr><tr><td>YP20_BACLI</td><td>33%</td><td>795</td><td>HYPOTHETICAL P20 PROTEIN</td></tr><tr><td>BLAI_BACLI</td><td>31%</td><td>843</td><td>PENICILLINASE REPRESSOR (REGULATORY PROTEIN BLAI)</td></tr><tr><td>DEGU_BACSU</td><td>39%</td><td>910</td><td>TRANSCRIPTIONAL REGULATORY PROTEIN DEGU (PROTEASE PRODUCTION ENHANCER PROTEIN)</td></tr><tr><td>HRCA_LACLA</td><td>99%</td><td>975</td><td>HEAT-INDUCIBLE TRANSCRIPTION REPRESSOR HRCA</td></tr><tr><td>SORC_KLEPN</td><td>21%</td><td>1204</td><td>SORBITOL (SOR) OPERON REGULATOR</td></tr><tr><td>XRE_BACSU</td><td>42%</td><td>1220</td><td>PUTATIVE PBSX REPRESSOR</td></tr><tr><td>YQAE_BACSU</td><td>35%</td><td>1300</td><td>HYPOTHETICAL TRANSCRIPTIONAL REGULATOR IN SPOIIIC-CWLA INTERGENIC REGION (ORF7)</td></tr><tr><td>Y186_HAEIN</td><td>39%</td><td>1506</td><td>HYPOTHETICAL TRANSCRIPTIONAL REGULATOR HI0186</td></tr><tr><td>TER2_ECOLI</td><td>29%</td><td>1551</td><td>TETRACYCLINE REPRESSOR PROTEIN CLASS B (TRANSPOSON TN10)</td></tr><tr><td>TFDT_ALCEU</td><td>40%</td><td>1594</td><td>TRANSCRIPTIONAL REGULATORY PROTEIN TFDT</td></tr><tr><td>GLNB_PREDI</td><td>56%</td><td>1631</td><td>NITROGEN REGULATORY PROTEIN P-II (PII SIGNAL TRANSDUCING PROTEIN)</td></tr><tr><td>PYRR_BACCL</td><td>60%</td><td>1644</td><td>PYRIMIDINE OPERON REGULATORY PROTEIN PYRR</td></tr><tr><td>SMTB_SYNY3</td><td>34%</td><td>1645</td><td>TRANSCRIPTIONAL REPRESSOR SMTB HOMOLOG</td></tr><tr><td>ARR2_ECOLI</td><td>31%</td><td>1730</td><td>ARSENICAL RESISTANCE OPERON REPRESSOR</td></tr><tr><td>GERE_BACSU</td><td>41%</td><td>1737</td><td>GERMINATION PROTEIN GERE</td></tr><tr><td>PHOU_ECOLI</td><td>36%</td><td>1750</td><td>PHOSPHATE TRANSPORT SYSTEM REGULATORY PROTEIN</td></tr><tr><td>TENA_BACSU</td><td>41%</td><td>1818</td><td>TRANSCRIPTIONAL ACTIVATOR TENA</td></tr><tr><td>BIRA_BACSU</td><td>34%</td><td>1820</td><td>BIRA BIFUNCTIONAL PROTEIN (BIOTIN OPERON REPRESSOR)</td></tr><tr><td>Y186_HAEIN</td><td>31%</td><td>1927</td><td>HYPOTHETICAL TRANSCRIPTIONAL REGULATOR HI0186</td></tr><tr><td>BIRA_BACSU</td><td>33%</td><td>1953</td><td>BIRA BIFUNCTIONAL PROTEIN (BIOTIN OPERON REPRESSOR)</td></tr><tr><td>RPC2_BPP22</td><td>30%</td><td>2003</td><td>REPRESSOR PROTEIN C2</td></tr><tr><td>Y186_HAEIN</td><td>34%</td><td>2032</td><td>HYPOTHETICAL TRANSCRIPTIONAL REGULATOR HI0186</td></tr><tr><td>NADR_ECOLI</td><td>30%</td><td>2047</td><td>TRANSCRIPTIONAL REGULATOR NADR</td></tr><tr><td>FLP_LACCA</td><td>41%</td><td>2062</td><td>PROBABLE TRANSCRIPTIONAL REGULATOR FLP</td></tr><tr><td>ACKA_BACSU</td><td>54%</td><td>2069</td><td>ACETATE KINASE (EC 2.7.2.1)</td></tr><tr><td>GLNR_BACSU</td><td>50%</td><td>2264</td><td>REGULATORY PROTEIN GLNR</td></tr><tr><td>YQAE_BACSU</td><td>41%</td><td>2276</td><td>HYPOTHETICAL TRANSCRIPTIONAL REGULATOR IN SPOIIIC-CWLA INTERGENIC REGION (ORF7)</td></tr><tr><td>FNR_BACSU</td><td>28%</td><td>2298</td><td>ANAEROBIC REGULATORY PROTEIN</td></tr><tr><td>ACRR_ECOLI</td><td>32%</td><td>2317</td><td>POTENTIAL ACRAB OPERON REPRESSOR</td></tr><tr><td colspan="4"><strong>BIO09.02 Two-component systems 13 genes</strong></td></tr><tr><td>RESE_BACSU</td><td>33%</td><td>400</td><td>SENSOR PROTEIN RESE (EC 2.7.3.-)</td></tr><tr><td>YYCF_BACSU</td><td>69%</td><td>401</td><td>HYPOTHETICAL 27.2 KD SENSORY TRANSDUCTION PROTEIN IN ROCR-PURA INTERGENIC REGION</td></tr><tr><td>DEGS_BACBR</td><td>40%</td><td>909</td><td>SENSOR PROTEIN DEGS (EC 2.7.3.-)</td></tr><tr><td>CZCR_ALCEU</td><td>39%</td><td>1028</td><td>TRANSCRIPTIONAL ACTIVATOR PROTEIN CZCR</td></tr><tr><td>YEDV_ECOLI</td><td>28%</td><td>1030</td><td>PROBABLE SENSOR PROTEIN YEDV (EC 2.7.3.-)</td></tr><tr><td>PHOP_BACSU</td><td>40%</td><td>1456</td><td>ALKALINE PHOSPHATASE SYNTHESIS TRANSCRIPTIONAL REGULATOR</td></tr><tr><td colspan="4"><strong>BIO09.03 LacI-family regulators 6 genes</strong></td></tr><tr><td>CYTR_ECOLI</td><td>28%</td><td>728</td><td>TRANSCRIPTIONAL REPRESSOR CYTR</td></tr><tr><td>RBSR_BACSU</td><td>31%</td><td>1533</td><td>RIBOSE OPERON REPRESSOR</td></tr><tr><td>RBSR_BACSU</td><td>42%</td><td>1684</td><td>RIBOSE OPERON REPRESSOR</td></tr><tr><td>CCPA_STAXY</td><td>47%</td><td>1692</td><td>PROBABLE CATABOLITE CONTROL PROTEIN A</td></tr><tr><td>PURR_HAEIN</td><td>34%</td><td>1724</td><td>PURINE NUCLEOTIDE SYNTHESIS REPRESSOR</td></tr><tr><td>YYAG_BACSU</td><td>36%</td><td>2196</td><td>HYPOTHETICAL TRANSCRIPTIONAL REGULATOR IN TETB-EXOA INTERGENIC REGION</td></tr><tr><td colspan="4"><strong>BIO09.04 LysR-family regulators 4 genes</strong></td></tr><tr><td>YWFK_BACSU</td><td>25%</td><td>375</td><td>HYPOTHETICAL TRANSCRIPTIONAL REGULATOR IN PTA 3' REGION</td></tr><tr><td>MLER_LACLA</td><td>100%</td><td>893</td><td>MALOLACTIC FERMENTATION SYSTEM TRANSCRIPTIONAL ACTIVATOR</td></tr><tr><td>YWBI_BACSU</td><td>29%</td><td>1261</td><td>HYPOTHETICAL TRANSCRIPTIONAL REGULATOR IN EPR-GALK INTERGENIC REGION</td></tr><tr><td>YWBI_BACSU</td><td>30%</td><td>1926</td><td>HYPOTHETICAL TRANSCRIPTIONAL REGULATOR IN EPR-GALK INTERGENIC REGION</td></tr><tr><td colspan="4"><strong>BIO09.05 AraC-family regulators 4 genes</strong></td></tr></tbody></table>
<table><caption>Table 3.</caption><thead><tr><th>Gene</th><th>30%</th><th>480</th><th>Description</th></tr></thead><tbody><tr><td>SLAP_LACBR</td><td>30%</td><td>480</td><td>S-LAYER PROTEIN PRECURSOR (SURFACE LAYER PROTEIN)</td></tr><tr><td>ADAA_BACSU</td><td>44%</td><td>517</td><td>METHYLPHOSPHOTRIESTER-DNA ALKYLTRANSFERASE</td></tr><tr><td>LUMQ_PHOLE</td><td>32%</td><td>1547</td><td>PROBABLE TRANSCRIPTIONAL REGULATOR LUMQ</td></tr><tr><td>TOXA_CLODI</td><td>30%</td><td>2284</td><td>TOXIN A</td></tr><tr><td colspan="4"><strong>BIO09.06 GntR-family regulators</strong></td></tr><tr><td>YHHX_ECOLI (F345)</td><td>44%</td><td>261</td><td>HYPOTHETICAL 38.8 KD PROTEIN IN GNTR-GGT INTERGENIC REGION</td></tr><tr><td>TREER_BACSU</td><td>44%</td><td>434</td><td>TREHALOSE OPERON TRANSCRIPTIONAL REPRESSOR</td></tr><tr><td>PARR_ECOLI</td><td>30%</td><td>1459</td><td>FATTY ACYL RESPONSIVE REGULATOR (P30 PROTEIN)</td></tr><tr><td>YIN1_STRAM (ORF 1)</td><td>30%</td><td>1676</td><td>HYPOTHETICAL TRANSCRIPTIONAL REGULATOR IN INSTABLE DNA LOCUS</td></tr><tr><td>YXAM_BACSU</td><td>24%</td><td>2215</td><td>HYPOTHETICAL 44.7 KD PROTEIN IN GNTR-HTPG INTERGENIC REGION</td></tr><tr><td>YXAT_BACSU</td><td>18%</td><td>2305</td><td>HYPOTHETICAL 44.3 KD PROTEIN IN GNTR-HTPG INTERGENIC REGION</td></tr><tr><td colspan="4"><strong>BIO09.07 DeoR-family regulators</strong></td></tr><tr><td>YXEP_BACSU</td><td>33%</td><td>278</td><td>HYPOTHETICAL 41.6 KD PROTEIN IN IDH-DEOR INTERGENIC REGION</td></tr><tr><td>YXEB_BACSU</td><td>35%</td><td>327</td><td>PROBABLE ABC TRANSPORTER BINDING PROTEIN IN IDH-DEOR INTERGENIC REGION PRECURSOR</td></tr><tr><td>YXEA_BACSU</td><td>37%</td><td>575</td><td>HYPOTHETICAL 13.0 KD PROTEIN IN IDH-DEOR INTERGENIC REGION PRECURSOR</td></tr><tr><td>GATR_ECOLI</td><td>31%</td><td>794</td><td>GALACTITOL UTILIZATION OPERON REPRESSOR</td></tr><tr><td>YXEP_BACSU</td><td>43%</td><td>980</td><td>HYPOTHETICAL 41.6 KD PROTEIN IN IDH-DEOR INTERGENIC REGION</td></tr><tr><td>YRJG_ECOLI</td><td>32%</td><td>1031</td><td>HYPOTHETICAL 22.4 KD PROTEIN IN DEOR-CMR INTERGENIC REGION</td></tr><tr><td>GLPR_HAEIN</td><td>33%</td><td>1330</td><td>GLYCEROL-3-PHOSPHATE REGULON REPRESSOR</td></tr><tr><td>YXEA_BACSU</td><td>39%</td><td>1504</td><td>HYPOTHETICAL 13.0 KD PROTEIN IN IDH-DEOR INTERGENIC REGION PRECURSOR</td></tr><tr><td colspan="4"><strong>BIO09.08 MarR-family regulators</strong></td></tr><tr><td>YDEA_ECOLI</td><td>32%</td><td>329</td><td>HYPOTHETICAL 42.5 KD PROTEIN IN UXAB-MARR INTERGENIC REGION</td></tr><tr><td>PETP_RHOCA</td><td>34%</td><td>1338</td><td>PETP PROTEIN</td></tr><tr><td colspan="4"><strong>BIO09.09 BglG-family regulators</strong></td></tr><tr><td>LICT_BACSU</td><td>41%</td><td>1491</td><td>TRANSCRIPTION ANTITERMINATOR LICT</td></tr><tr><td colspan="4"><strong>BIO09.10 GTP-binding proteins</strong></td></tr><tr><td>YYAF_BACSU</td><td>68%</td><td>12</td><td>HYPOTHETICAL 40.1 KD GTP-BINDING PROTEIN IN RPSF-SPOOJ INTERGENIC REGION</td></tr><tr><td>HPLX_ECOLI</td><td>44%</td><td>222</td><td>GTP-BINDING PROTEIN HPLX</td></tr><tr><td>EPA_STRMU</td><td>75%</td><td>353</td><td>GTP-BINDING PROTEIN ERA HOMOLOG</td></tr><tr><td>YPHC_BACSU</td><td>62%</td><td>760</td><td>HYPOTHETICAL 48.8 KD GTP-BINDING PROTEIN IN CMK-GPSA INTERGENIC REGION</td></tr><tr><td>LEPA_BACSU</td><td>77%</td><td>1116</td><td>GTP-BINDING PROTEIN LEPA</td></tr><tr><td>YSKC_BACSU (ORFX)</td><td>66%</td><td>1163</td><td>HYPOTHETICAL GTP-BINDING PROTEIN IN LONA-HEMA INTERGENIC REGION</td></tr><tr><td>OBO_BACSU</td><td>64%</td><td>1626</td><td>SPOOB-ASSOCIATED GTP-BINDING PROTEIN</td></tr><tr><td>SR54_SYNY3</td><td>51%</td><td>1654</td><td>SIGNAL RECOGNITION PARTICLE PROTEIN (FIPTY-FOUR HOMOLOG)</td></tr><tr><td>THDF_BACSU</td><td>60%</td><td>2308</td><td>POSSIBLE THIOPHENE AND FURAN OXIDATION PROTEIN THDF</td></tr><tr><td colspan="4"><strong>BIO10. REPLICATION</strong></td></tr><tr><td colspan="4"><strong>BIO10.01 Degradation of DNA</strong></td></tr><tr><td>ADDB_BACSU</td><td>28%</td><td>5</td><td>ATP-DEPENDENT NUCLEASE SUBUNIT B</td></tr><tr><td>ADDA_BACSU</td><td>32%</td><td>7</td><td>ATP-DEPENDENT NUCLEASE SUBUNIT A</td></tr><tr><td>ADDA_BACSU</td><td>33%</td><td>9</td><td>ATP-DEPENDENT NUCLEASE SUBUNIT A</td></tr><tr><td>UVRB_HAEIN</td><td>40%</td><td>555</td><td>EXCINUCLEASE ABC SUBUNIT B</td></tr><tr><td>RECU_ERWCH</td><td>36%</td><td>619</td><td>SINGLE-STRANDED-DNA-SPECIFIC EXONUCLEASE RECJ (EC 3.1.1.-)</td></tr><tr><td>EXOA_BACSU</td><td>40%</td><td>796</td><td>EXODEXYRIBONUCLEASE (EC 3.1.11.2)</td></tr><tr><td>UVRC_BACSU</td><td>54%</td><td>855</td><td>EXCINUCLEASE ABC SUBUNIT C</td></tr><tr><td>EX7L_BACSU</td><td>43%</td><td>876</td><td>PUTATIVE EXODEXYRIBONUCLEASE LARGE SUBUNIT (EC 3.1.11.6)</td></tr><tr><td>END3_BACSU</td><td>50%</td><td>1081</td><td>PROBABLE ENDONUCLEASE III (EC 4.2.99.18)</td></tr><tr><td>EX5A_ECOLI</td><td>27%</td><td>1777</td><td>EXODEXYRIBONUCLEASE V 67 KD POLYPEPTIDE (EC 3.1.11.5)</td></tr><tr><td>EX5A_ECOLI</td><td>32%</td><td>1778</td><td>EXODEXYRIBONUCLEASE V 67 KD POLYPEPTIDE (EC 3.1.11.5)</td></tr><tr><td colspan="4"><strong>BIO10.02 DNA replication, restriction, modification, recombination, and repair genes</strong></td></tr><tr><td>DNAA_STAAU</td><td>45%</td><td>1</td><td>CHROMOSOMAL REPLICATION INITIATOR PROTEIN DNA</td></tr><tr><td>DP3B_STAAU</td><td>41%</td><td>2</td><td>DNA POLYMERASE III, BETA CHAIN (EC 2.7.7.7)</td></tr><tr><td>MFD_BACSU</td><td>50%</td><td>19</td><td>TRANSCRIPTION-REPAIR COUPLING FACTOR (TRCP)</td></tr><tr><td>PRIM_BPP4</td><td>21%</td><td>38</td><td>PUTATIVE P4-SPECIFIC DNA PRIMASE (EC 2.7.7.-)</td></tr><tr><td>YQXN_BACSU (ORF3)</td><td>31%</td><td>58</td><td>HYPOTHETICAL 29.3 KD PROTEIN IN BEX-DNAG/DNAE INTERGENIC REGION</td></tr><tr><td>YQEU_BACSU</td><td>44%</td><td>103</td><td>HYPOTHETICAL 28.8 KD PROTEIN IN DNAJ-RPSU INTERGENIC REGION</td></tr><tr><td>YAAK_BACSU</td><td>44%</td><td>120</td><td>HYPOTHETICAL 11.8 KD PROTEIN IN DNAZ-RECR INTERGENIC REGION</td></tr><tr><td>T3RE_BACCE 3.1.21.5)</td><td>29%</td><td>151</td><td>TYPE III RESTRICTION-MODIFICATION SYSTEM ENZYME RES (EC 3.2.2.-)</td></tr><tr><td>UNG_STRPN</td><td>53%</td><td>230</td><td>URACIL-DNA GLYCOSYLASE (EC 3.2.2.-)</td></tr></tbody></table>

66
<table><caption>Table 3.</caption><thead><tr><th>RECR_STRTR</th><th>76%</th><th>338</th><th>RECOMBINATION PROTEIN RECR</th></tr></thead><tbody><tr><td>FPG_LACLC</td><td>90%</td><td>356</td><td>FORMAMIDOPYRIMIDINE-DNA GLYCOSYLASE (EC 3.2.2.23)</td></tr><tr><td>RECA_LACLA</td><td>94%</td><td>357</td><td>RECA PROTEIN</td></tr><tr><td>SSB_BACSU</td><td>44%</td><td>395</td><td>SINGLE-STRAND BINDING PROTEIN (SSB)</td></tr><tr><td>HOLB_BACSU</td><td>35%</td><td>402</td><td>DNA POLYMERASE III, DELTA' SUBUNIT (EC 2.7.7.7)</td></tr><tr><td>DNLJ_HROMR</td><td>43%</td><td>423</td><td>DNA LIGASE (EC 6.5.1.2)</td></tr><tr><td>DNAC_ECOLI</td><td>27%</td><td>454</td><td>DNA REPLICATION PROTEIN DNAC</td></tr><tr><td>DP3A_HELPY</td><td>26%</td><td>494</td><td>DNA POLYMERASE III, ALPHA CHAIN (EC 2.7.7.7)</td></tr><tr><td>PRIM_LACLA</td><td>100%</td><td>542</td><td>DNA PRIMASE (EC 2.7.7.-)</td></tr><tr><td>DFP_ECOLI</td><td>30%</td><td>565</td><td>DNA/PANTOTHENATE METABOLISM FLAVOPROTEIN</td></tr><tr><td>T1R1_ECOLI</td><td>32%</td><td>640</td><td>TYPE I RESTRICTION ENZYME ECOR124II R PROTEIN (EC 3.1.21.3)</td></tr><tr><td>YC18_MYTJA</td><td>27%</td><td>644</td><td>HYPOTHETICAL PROTEIN MJ1218</td></tr><tr><td>YABF_BACSU</td><td>47%</td><td>687</td><td>HYPOTHETICAL 20.7 KD PROTEIN IN METS-KSGA INTERGENIC REGION</td></tr><tr><td>YAAJ_BACSU</td><td>51%</td><td>725</td><td>HYPOTHETICAL 17.8 KD PROTEIN IN SERS-DNAH INTERGENIC REGION</td></tr><tr><td>DNAC_BACSU</td><td>56%</td><td>752</td><td>REPLICATIVE DNA HELICASE (EC 3.6.1.-)</td></tr><tr><td>DNAB_BACSU</td><td>27%</td><td>756</td><td>REPLICATION INITIATION AND MEMBRANE ATTACHMENT PROTEIN</td></tr><tr><td>DNAI_BACSU</td><td>38%</td><td>757</td><td>PRIMOSOMAL PROTEIN DNAI</td></tr><tr><td>LEP3_NPVAC</td><td>26%</td><td>833</td><td>LATE EXPRESSION FACTOR 3</td></tr><tr><td>MUTY_ECOLI</td><td>43%</td><td>857</td><td>A/G-SPECIFIC ADENINE GLYCOSYLASE (EC 3.2.2.-)</td></tr><tr><td>RECN_BACSU</td><td>44%</td><td>881</td><td>DNA REPAIR PROTEIN RECN (RECOMBINATION PROTEIN N)</td></tr><tr><td>GYRB_STRPN</td><td>82%</td><td>926</td><td>DNA GYrase SUBUNIT B (EC 5.99.1.3)</td></tr><tr><td>GRPE_LACLA</td><td>99%</td><td>975</td><td>GRPE PROTEIN</td></tr><tr><td>RIR2_MYCTU</td><td>48%</td><td>999</td><td>RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE BETA CHAIN (EC 1.17.4.1)</td></tr><tr><td>RIR1_MYCTU</td><td>50%</td><td>1001</td><td>RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE ALPHA CHAIN (EC 1.17.4.1)</td></tr><tr><td>PARE_STAAU</td><td>70%</td><td>1005</td><td>TOPOISOMERASE IV SUBUNIT B (EC 5.99.1.-)</td></tr><tr><td>DING_BACSU</td><td>38%</td><td>1007</td><td>PROBABLE ATP-DEPENDENT HELICASE DING HOMOLOG</td></tr><tr><td>PARC_STAAU</td><td>53%</td><td>1009</td><td>TOPOISOMERASE IV SUBUNIT A (EC 5.99.1.-)</td></tr><tr><td>RADC_BACSU</td><td>41%</td><td>1033</td><td>DNA REPAIR PROTEIN RADC HOMOLOG (ORFB)</td></tr><tr><td>SSB_BACSU</td><td>61%</td><td>1041</td><td>SINGLE-STRAND BINDING PROTEIN (SSB)</td></tr><tr><td>DNAD_BACSU</td><td>37%</td><td>1081</td><td>DNA REPLICATION PROTEIN DNAD</td></tr><tr><td>GYRA_STAAU</td><td>23%</td><td>1120</td><td>DNA GYrase SUBUNIT A (EC 5.99.1.3)</td></tr><tr><td>PCRA_BACST</td><td>49%</td><td>1132</td><td>ATP-DEPENDENT HELICASE PCRA (EC 3.6.1.-)</td></tr><tr><td>MUTX_STRPN</td><td>34%</td><td>1134</td><td>MUTATOR MUTT PROTEIN (7,8-DIHYDRO-8-OXOGUANINE-TRIPHOSPHATASE)</td></tr><tr><td>DYR_LACLA</td><td>87%</td><td>1161</td><td>DIHYDROFOLATE REDUCTASE (EC 1.5.1.3)</td></tr><tr><td>DPRA_HAEIN</td><td>43%</td><td>1251</td><td>DNA PROCESSING CHAIN A</td></tr><tr><td>TOP1_BACSU</td><td>64%</td><td>1253</td><td>DNA TOPOISOMERASE I (EC 5.99.1.2)</td></tr><tr><td>DNAC_ECOLI</td><td>27%</td><td>1446</td><td>DNA REPLICATION PROTEIN DNAC</td></tr><tr><td>SSB_BACSU</td><td>68%</td><td>1447</td><td>SINGLE-STRAND BINDING PROTEIN (SSB)</td></tr><tr><td>MUTS_AQUFY</td><td>34%</td><td>1689</td><td>DNA MISMATCH REPAIR PROTEIN</td></tr><tr><td>RECQ_ECOLI</td><td>35%</td><td>1854</td><td>ATP-DEPENDENT DNA HELICASE RECQ (EC 3.6.1.-)</td></tr><tr><td>DING_BACSU</td><td>34%</td><td>1878</td><td>PROBABLE ATP-DEPENDENT HELICASE DING HOMOLOG</td></tr><tr><td>DING_BACSU</td><td>28%</td><td>1880</td><td>PROBABLE ATP-DEPENDENT HELICASE DING HOMOLOG</td></tr><tr><td>PRIA_BACSU</td><td>58%</td><td>1944</td><td>PRIMOSOMAL PROTEIN N' (REPLICATION FACTOR Y)</td></tr><tr><td>YAAA_BACSU</td><td>49%</td><td>2030</td><td>HYPOTHETICAL 7.9 KD PROTEIN IN DNAN-RECF INTERGENIC REGION</td></tr><tr><td>RECF_LACLC</td><td>99%</td><td>2031</td><td>REFC PROTEIN</td></tr><tr><td>DINF_ECOLI</td><td>42%</td><td>2085</td><td>DNA-DAMAGE-INDUCIBLE PROTEIN P</td></tr><tr><td>RADA_BACSU</td><td>60%</td><td>2129</td><td>DNA REPAIR PROTEIN RADA HOMOLOG (DNA REPAIR PROTEIN SMS HOMOLOG)</td></tr><tr><td>DP3A_BACSU</td><td>42%</td><td>2171</td><td>DNA POLYMERASE III, ALPHA CHAIN (EC 2.7.7.7)</td></tr><tr><td>DP01_STRPN</td><td>68%</td><td>2192</td><td>DNA POLYMERASE I (EC 2.7.7.7)</td></tr><tr><td>SSB_BACSU</td><td>60%</td><td>2254</td><td>SINGLE-STRAND BINDING PROTEIN (SSB)</td></tr><tr><td>DP3X_BACSU</td><td>43%</td><td>2259</td><td>DNA POLYMERASE III SUBUNITS GAMMA AND TAU (EC 2.7.7.7)</td></tr><tr><td>RUVB_PSEAE</td><td>59%</td><td>2269</td><td>HOLLIDAY JUNCTION DNA HELICASE RUVB</td></tr><tr><td>RUVA_HAEIN</td><td>40%</td><td>2269</td><td>HOLLIDAY JUNCTION DNA HELICASE RUVA</td></tr><tr><td>HEXB_STRPN</td><td>57%</td><td>2271</td><td>DNA MISMATCH REPAIR PROTEIN HEXB</td></tr><tr><td>HEXA_STRPN</td><td>79%</td><td>2274</td><td>DNA MISMATCH REPAIR PROTEIN HEXA</td></tr><tr><td>DNAJ_LACLA</td><td>99%</td><td>2287</td><td>DNAJ PROTEIN</td></tr><tr><td>RECG_ECOLI</td><td>36%</td><td>2311</td><td>ATP-DEPENDENT DNA HELICASE RECG (EC 3.6.1.-)</td></tr></tbody></table>

## BIO11. TRANSCRIPTION

27 genes

### BIO11.01 Degradation of RNA

### 18 genes

<table><tbody><tr><td>TRU_AECOLI</td><td>34%</td><td>482</td><td>PSEUDOURIDYLATE SYNTHASE I (EC 4.2.1.70)</td></tr><tr><td>YACO_BACSU</td><td>26%</td><td>595</td><td>HYPOTHETICAL RNA METHYLASE IN CYSS 3' REGION</td></tr><tr><td>MIAA_MYCLE</td><td>32%</td><td>613</td><td>PROBABLE TRNA DELTA(2)-ISOPENTENYLPYROPHOSPHATE TRANSFERASE (EC 2.5.1.8)</td></tr><tr><td>RNC_BACSU</td><td>44%</td><td>807</td><td>RIBONUCLEASE III (EC 3.1.26.3)</td></tr><tr><td>VACB_HAEIN</td><td>37%</td><td>965</td><td>VACB PROTEIN HOMOLOG</td></tr><tr><td>ALDC_BACBR</td><td>31%</td><td>1114</td><td>ALPHA-ACETOLACTATE DECARBOXYLASE PRECURSOR (EC 4.1.1.5)</td></tr><tr><td>TRUB_SYNY3</td><td>39%</td><td>1138</td><td>TRNA PSEUDOURIDINE 55 SYNTHASE (PSI5 SYNTHASE)</td></tr><tr><td>YGL3_BACST</td><td>57%</td><td>1160</td><td>HYPOTHETICAL 18.2 KD PROTEIN IN GLDA 3' REGION (ORF3)</td></tr><tr><td>ALDC_BACSU</td><td>35%</td><td>1250</td><td>ALPHA-ACETOLACTATE DECARBOXYLASE (EC 4.1.1.5)</td></tr><tr><td>RNH2_ECOLI</td><td>47%</td><td>1326</td><td>RIBONUCLEASE HII (EC 3.1.26.4)</td></tr><tr><td>SBCD_BACSU</td><td>32%</td><td>1354</td><td>EXONUCLEASE SBCD HOMOLOG (FRAGMENT)</td></tr><tr><td>PAPS_BACSU</td><td>39%</td><td>1598</td><td>POLY(A) POLYMERASE (EC 2.7.7.19)</td></tr><tr><td>RIMM_HAEIN</td><td>26%</td><td>1603</td><td>16S rRNA PROCESSING PROTEIN RIMM</td></tr><tr><td>PNPA_BACSU</td><td>58%</td><td>1903</td><td>POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE (EC 2.7.7.8)</td></tr></tbody></table>
<table><caption>Table 3.</caption><thead><tr><th>Gene</th><th>Strand</th><th>Position</th><th>Gene</th><th>Strand</th><th>Position</th></tr></thead><tbody><tr><td>YACO_BACSU</td><td>47%</td><td>1921</td><td>HYPOTHETICAL RNA METHYLASE IN CYSS 3' REGION</td><td></td><td></td></tr><tr><td>SPLR_NPVAC</td><td>30%</td><td>2008</td><td>SPHEROIDIN-LIKE PROTEIN PRECURSOR (SPINDOLIN-LIKE PROTEIN)</td><td></td><td></td></tr><tr><td>SAGE_STRPY</td><td>47%</td><td>2094</td><td>STREPTOCOCCAL ACID GLYCOPROTEIN</td><td></td><td></td></tr><tr><td>NUSG_STRGR</td><td>43%</td><td>2154</td><td>TRANSCRIPTION ANTITERMINATION PROTEIN NUSG</td><td></td><td></td></tr><tr><td colspan="6"><strong>BIO11.02 RNA synthesis, modification, and DNA transcription</strong></td></tr><tr><td>RPSD_NEIGO</td><td>24%</td><td>466</td><td>RNA POLYMERASE SIGMA FACTOR RPOD (SIGMA-70)</td><td></td><td></td></tr><tr><td>RPSD_LACLA</td><td>100%</td><td>544</td><td>RNA POLYMERASE SIGMA FACTOR RPOD</td><td></td><td></td></tr><tr><td>RPOE_BACSU</td><td>33%</td><td>621</td><td>DNA-DIRECTED RNA POLYMERASE DELTA SUBUNIT (EC 2.7.7.6)</td><td></td><td></td></tr><tr><td>GREA_RICPR</td><td>47%</td><td>624</td><td>TRANSCRIPTION ELONGATION FACTOR GREA (TRANSCRIPT CLEAVAGE FACTOR GREA)</td><td></td><td></td></tr><tr><td>RPOC_MYCGE</td><td>46%</td><td>1838</td><td>DNA-DIRECTED RNA POLYMERASE BETA CHAIN (EC 2.7.7.6)</td><td></td><td></td></tr><tr><td>RPOB_SPICI</td><td>31%</td><td>1842</td><td>DNA-DIRECTED RNA POLYMERASE BETA CHAIN (EC 2.7.7.6)</td><td></td><td></td></tr><tr><td>RPOA_BACSU</td><td>57%</td><td>2132</td><td>DNA-DIRECTED RNA POLYMERASE ALPHA CHAIN (EC 2.7.7.6)</td><td></td><td></td></tr><tr><td>SIGV_BACSU</td><td>23%</td><td>2222</td><td>RNA POLYMERASE SIGMA FACTOR SIGV</td><td></td><td></td></tr><tr><td colspan="6"><strong>BIO11.03 RNA processing</strong></td></tr><tr><td>YQFR_BACSU</td><td>48%</td><td>414</td><td>PROBABLE RNA HELICASE IN CCCA-SODA INTERGENIC REGION</td><td></td><td></td></tr><tr><td colspan="6"><strong>BIO12. TRANSLATION</strong></td></tr><tr><td colspan="6"><strong>BIO12.01 Aminoacyl tRNA synthetases</strong></td></tr><tr><td>SYW_CLOLO</td><td>63%</td><td>68</td><td>TRYPTOPHANYL-TRNA SYNTHETASE (EC 6.1.1.2)</td><td></td><td></td></tr><tr><td>TGT_HAEIN</td><td>54%</td><td>153</td><td>QUEUINE TRNA-RIBOSYL/TRANSFERASE (EC 2.4.2.29)</td><td></td><td></td></tr><tr><td>SYK_BACSU</td><td>58%</td><td>374</td><td>LYSYL-TRNA SYNTHETASE (EC 6.1.1.6)</td><td></td><td></td></tr><tr><td>SYY1_BACSU</td><td>55%</td><td>388</td><td>TYROSYL-TRNA SYNTHETASE 1 (EC 6.1.1.1)</td><td></td><td></td></tr><tr><td>Y449_MYCPN</td><td>34%</td><td>393</td><td>HYPOTHETICAL PROTEIN MG449 HOMOLOG</td><td></td><td></td></tr><tr><td>SYM_BACSU</td><td>62%</td><td>798</td><td>METHIONYL-TRNA SYNTHETASE (EC 6.1.1.10)</td><td></td><td></td></tr><tr><td>SYL_MYCTU</td><td>43%</td><td>826</td><td>LEUCYL-TRNA SYNTHETASE (EC 6.1.1.4)</td><td></td><td></td></tr><tr><td>SYGB_BACSU</td><td>41%</td><td>1101</td><td>GLYCYL-TRNA SYNTHETASE BETA CHAIN (EC 6.1.1.14)</td><td></td><td></td></tr><tr><td>SYK_BACSU</td><td>32%</td><td>1129</td><td>LYSYL-TRNA SYNTHETASE (EC 6.1.1.6)</td><td></td><td></td></tr><tr><td>YH13_LACLA</td><td>97%</td><td>1228</td><td>HYPOTHETICAL 38.0 KD PROTEIN IN HISC-HISG INTERGENIC REGION (ORF3)</td><td></td><td></td></tr><tr><td>SYS_BACSU</td><td>57%</td><td>1747</td><td>SERYL-TRNA SYNTHETASE (EC 6.1.1.11)</td><td></td><td></td></tr><tr><td>SYA_THETH</td><td>41%</td><td>1759</td><td>ALANYL-TRNA SYNTHETASE (EC 6.1.1.7)</td><td></td><td></td></tr><tr><td>SYN_BACSU</td><td>59%</td><td>1875</td><td>ASPARAGINYL-TRNA SYNTHETASE (EC 6.1.1.22)</td><td></td><td></td></tr><tr><td>CYCHELPY</td><td>43%</td><td>1898</td><td>CYSTEINYL-TRNA SYNTHETASE (EC 6.1.1.16)</td><td></td><td></td></tr><tr><td>SYI_STAAU</td><td>28%</td><td>1911</td><td>ISOLEUCYL-TRNA SYNTHETASE (EC 6.1.1.5)</td><td></td><td></td></tr><tr><td>SYI CAMJE</td><td>43%</td><td>1912</td><td>ISOLEUCYL-TRNA SYNTHETASE (EC 6.1.1.5)</td><td></td><td></td></tr><tr><td>SYT_MYCLE</td><td>42%</td><td>1968</td><td>THREONYL-TRNA SYNTHETASE (EC 6.1.1.3)</td><td></td><td></td></tr><tr><td>SYFB_BACSU</td><td>45%</td><td>1987</td><td>PHENYLALANYL-TRNA SYNTHETASE BETA CHAIN (EC 6.1.1.20)</td><td></td><td></td></tr><tr><td>SYFA_BACSU</td><td>62%</td><td>1989</td><td>PHENYLALANYL-TRNA SYNTHETASE ALPHA CHAIN (EC 6.1.1.20)</td><td></td><td></td></tr><tr><td>SYD_SYNY3</td><td>51%</td><td>2021</td><td>ASPARTYL-TRNA SYNTHETASE (EC 6.1.1.12)</td><td></td><td></td></tr><tr><td>SYH_STREQ</td><td>63%</td><td>2023</td><td>HISTIDYL-TRNA SYNTHETASE (EC 6.1.1.21)</td><td></td><td></td></tr><tr><td>SYR_SYNY3</td><td>36%</td><td>2096</td><td>ARGINYL-TRNA SYNTHETASE (EC 6.1.1.19)</td><td></td><td></td></tr><tr><td>SYE HelpY</td><td>45%</td><td>2120</td><td>GLUTAMYL-TRNA SYNTHETASE (EC 6.1.1.17)</td><td></td><td></td></tr><tr><td>SYP_HAEIN</td><td>45%</td><td>2177</td><td>PROLYL-TRNA SYNTHETASE (EC 6.1.1.15)</td><td></td><td></td></tr><tr><td>SYV_THETH</td><td>43%</td><td>2229</td><td>VALYL-TRNA SYNTHETASE (EC 6.1.1.9)</td><td></td><td></td></tr><tr><td>SYFB_MYCGE</td><td>29%</td><td>2233</td><td>PHENYLALANYL-TRNA SYNTHETASE BETA CHAIN (EC 6.1.1.20)</td><td></td><td></td></tr><tr><td colspan="6"><strong>BIO12.02 Degradation of proteins, peptides, and glycopeptides</strong></td></tr><tr><td>GCP_HAEIN</td><td>41%</td><td>291</td><td>PROBABLE O-SIALOGLYCOPYROTEIN ENDOPEPTIDASE (EC 3.4.24.57)</td><td></td><td></td></tr><tr><td>AMPN_LACLC</td><td>98%</td><td>301</td><td>AMINOPEPTIDASE N (EC 3.4.11.2)</td><td></td><td></td></tr><tr><td>AMP1_SYNY3</td><td>45%</td><td>599</td><td>PUTATIVE METHIONINE AMINOPEPTIDASE A (EC 3.4.11.18)</td><td></td><td></td></tr><tr><td>CLPP_SYRSL</td><td>87%</td><td>670</td><td>ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT (EC 3.4.21.92)</td><td></td><td></td></tr><tr><td>YQHT_BACSU</td><td>41%</td><td>688</td><td>PUTATIVE PEPTIDASE IN GCVT-SPOIIIAA INTERGENIC REGION (EC 3.4.-)</td><td></td><td></td></tr><tr><td>PEPV_LACDL</td><td>47%</td><td>858</td><td>XAA-HIS DIPEPTIDASE (EC 3.4.13.3)</td><td></td><td></td></tr><tr><td>P54_ENTFC</td><td>40%</td><td>959</td><td>P54 PROTEIN PRECURSOR</td><td></td><td></td></tr><tr><td>CLPX_BACSU</td><td>67%</td><td>1162</td><td>ATP-DEPENDENT CLP PROTEASE ATP-BINDING SUBUNIT CLPX</td><td></td><td></td></tr><tr><td>CLPP_SYNP7</td><td>29%</td><td>1433</td><td>ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT (EC 3.4.21.92)</td><td></td><td></td></tr><tr><td>CLPB_HAEIN</td><td>56%</td><td>1564</td><td>CLPB PROTEIN</td><td></td><td></td></tr><tr><td>PEPQ_LACDL</td><td>50%</td><td>1693</td><td>XAA-PRO DIPEPTIDASE (EC 3.4.13.9)</td><td></td><td></td></tr><tr><td>PRTM_LACPA</td><td>32%</td><td>1761</td><td>PROTEASE MATURATION PROTEIN PRECURSOR</td><td></td><td></td></tr><tr><td>PEPF_LACLA</td><td>97%</td><td>1763</td><td>OLIGOENDOPEPTIDASE F (EC 3.4.24.-)</td><td></td><td></td></tr><tr><td>PEPO_LACLC</td><td>99%</td><td>1847</td><td>NEUTRAL ENDOPEPTIDASE (EC 3.4.24.-)</td><td></td><td></td></tr><tr><td>PEPC_LACLC</td><td>98%</td><td>1927</td><td>AMINOPEPTIDASE C (EC 3.4.22.-)</td><td></td><td></td></tr><tr><td>PTR_ECOLI</td><td>22%</td><td>2028</td><td>PROTEASE III PRECURSOR (EC 3.4.24.55)</td><td></td><td></td></tr><tr><td>YMXG_BACSU</td><td>23%</td><td>2029</td><td>HYPOTHETICAL PROCESSING PROTEASE (EC 3.4.-.-)</td><td></td><td></td></tr><tr><td>YEGQ_ECOLI</td><td>37%</td><td>2049</td><td>PUTATIVE PROTEASE IN BAER-OGRK INTERGENIC REGION (EC 3.4.-.-)</td><td></td><td></td></tr><tr><td>LEP3_BACSU</td><td>34%</td><td>2084</td><td>TYPE 4 PREPILIN-LIKE PROTEIN SPECIFIC LEADER PEPTIDASE (EC 3.4.99.-)</td><td></td><td></td></tr><tr><td>PEPX_LACLC</td><td>79%</td><td>2115</td><td>XAA-PRO DIPEPTIDYL-PEPTIDASE (EC 3.4.14.11)</td><td></td><td></td></tr><tr><td>YYXA_BACSU</td><td>47%</td><td>2185</td><td>HYPOTHETICAL PROTEASE IN ROCR-PURA INTERGENIC REGION (EC 3.4.21.-)</td><td></td><td></td></tr><tr><td>HTOA_HAEIN</td><td>33%</td><td>2218</td><td>PROBABLE PERIPLASMIC SERINE PROTEASE DO/HKOA-LIKE PRECURSOR</td><td></td><td></td></tr></tbody></table>
<table><caption>Table 3.</caption><thead><tr><th colspan="3">BIO12.03 Nucleoproteins</th><th colspan="2">2 genes</th></tr></thead><tbody><tr><td>DBH_BACST</td><td>67%</td><td>500</td><td>DNA-BINDING PROTEIN II (HB)</td><td></td></tr><tr><td>DBH_VIBPR</td><td>37%</td><td>900</td><td>DNA-BINDING PROTEIN HU</td><td></td></tr></tbody><thead><tr><th colspan="3">BIO12.04 Protein modification</th><th colspan="2">2 genes</th></tr></thead><tbody><tr><td>CYPH_MYCTU</td><td>31%</td><td>366</td><td>PROBABLE PEPTIDYL-PROLYL CIS-TRANS ISOMERASE (EC 5.2.1.8)</td><td></td></tr><tr><td>CYPH_MYCTU</td><td>37%</td><td>912</td><td>PROBABLE PEPTIDYL-PROLYL CIS-TRANS ISOMERASE (EC 5.2.1.8)</td><td></td></tr></tbody><thead><tr><th colspan="3">BIO12.05 Ribosomal proteins: synthesis and modification</th><th colspan="2">55 genes</th></tr></thead><tbody><tr><td>PRMA_BACSU</td><td>43%</td><td>102</td><td>PROBABLE METHYLTRANSFERASE (EC 2.1.1.-)</td><td></td></tr><tr><td>RL34_COXBU</td><td>70%</td><td>131</td><td>50S RIBOSOMAL PROTEIN L34</td><td></td></tr><tr><td>RL28_BACSU</td><td>56%</td><td>193</td><td>50S RIBOSOMAL PROTEIN L28</td><td></td></tr><tr><td>RS21_BACSU</td><td>87%</td><td>235</td><td>30S RIBOSOMAL PROTEIN S21 (BS-B)</td><td></td></tr><tr><td>RS4_BACSU</td><td>62%</td><td>281</td><td>30S RIBOSOMAL PROTEIN S4 (BS4)</td><td></td></tr><tr><td>R14H_BACSH</td><td>35%</td><td>306</td><td>30S RIBOSOMAL PROTEIN S14 HOMOLOG</td><td></td></tr><tr><td>DEAD_KLEPN</td><td>45%</td><td>351</td><td>ATP-DEPENDENT RNA HELICASE DEAD</td><td></td></tr><tr><td>YYVD_BACSU</td><td>51%</td><td>630</td><td>HYPOTHETICAL 22.0 KD PROTEIN IN FLIT-SECA INTERGENIC REGION</td><td></td></tr><tr><td>RL33_LACLA</td><td>100%</td><td>659</td><td>50S RIBOSOMAL PROTEIN L33</td><td></td></tr><tr><td>RL9_BACST</td><td>52%</td><td>751</td><td>50S RIBOSOMAL PROTEIN L9 (BL17)</td><td></td></tr><tr><td>YLXQ_ENTFC</td><td>48%</td><td>773</td><td>PROBABLE RIBOSOMAL PROTEIN IN INPB 5' REGION</td><td></td></tr><tr><td>RS1_BUCAP</td><td>32%</td><td>852</td><td>30S RIBOSOMAL PROTEIN S1</td><td></td></tr><tr><td>RL19_BACST</td><td>73%</td><td>895</td><td>50S RIBOSOMAL PROTEIN L19</td><td></td></tr><tr><td>RS14_SYNY3</td><td>41%</td><td>908</td><td>30S RIBOSOMAL PROTEIN S14</td><td></td></tr><tr><td>RL21_BACSU</td><td>67%</td><td>1088</td><td>50S RIBOSOMAL PROTEIN L21 (BL20)</td><td></td></tr><tr><td>RL27_BACSU</td><td>74%</td><td>1089</td><td>50S RIBOSOMAL PROTEIN L27 (BL30)</td><td></td></tr><tr><td>RL7_BACSU</td><td>61%</td><td>1298</td><td>50S RIBOSOMAL PROTEIN L7/L12 (BL9)</td><td></td></tr><tr><td>RL7_STRPN</td><td>76%</td><td>1299</td><td>50S RIBOSOMAL PROTEIN L7/L12 (FRAGMENT)</td><td></td></tr><tr><td>RL10_BACSU</td><td>63%</td><td>1299</td><td>50S RIBOSOMAL PROTEIN L10 (BL5)</td><td></td></tr><tr><td>RS16_BACSU</td><td>59%</td><td>1606</td><td>30S RIBOSOMAL PROTEIN S16 (BS17)</td><td></td></tr><tr><td>YKGM_ECOLI</td><td>45%</td><td>1636</td><td>HYPOTHETICAL 9.9 KD PROTEIN IN INTF-KAEH INTERGENIC REGION</td><td></td></tr><tr><td>RL20_BACSU</td><td>69%</td><td>1891</td><td>50S RIBOSOMAL PROTEIN L20</td><td></td></tr><tr><td>RS15_BACSU</td><td>62%</td><td>1934</td><td>30S RIBOSOMAL PROTEIN S15 (BS18)</td><td></td></tr><tr><td>RL11_BACSU</td><td>67%</td><td>2058</td><td>50S RIBOSOMAL PROTEIN L11 (BL1)</td><td></td></tr><tr><td>RL11_STACA</td><td>80%</td><td>2059</td><td>50S RIBOSOMAL PROTEIN L11</td><td></td></tr><tr><td>R14H_BACSH</td><td>30%</td><td>2125</td><td>30S RIBOSOMAL PROTEIN S14 HOMOLOG</td><td></td></tr><tr><td>RL17_BACSU</td><td>72%</td><td>2131</td><td>50S RIBOSOMAL PROTEIN L17 (BL15)</td><td></td></tr><tr><td>RS11_BACSU</td><td>82%</td><td>2133</td><td>30S RIBOSOMAL PROTEIN S11 (BS11)</td><td></td></tr><tr><td>RS13_BACSU</td><td>70%</td><td>2133</td><td>30S RIBOSOMAL PROTEIN S13 (BS14)</td><td></td></tr><tr><td>RL15_STAU</td><td>67%</td><td>2139</td><td>50S RIBOSOMAL PROTEIN L15</td><td></td></tr><tr><td>RS5_BACSU</td><td>77%</td><td>2140</td><td>30S RIBOSOMAL PROTEIN S5 (BS5)</td><td></td></tr><tr><td>RL6_BACST</td><td>63%</td><td>2141</td><td>50S RIBOSOMAL PROTEIN L6 (BL10)</td><td></td></tr><tr><td>RS8_BACSU</td><td>72%</td><td>2142</td><td>30S RIBOSOMAL PROTEIN S8 (BS8)</td><td></td></tr><tr><td>RL5_BACST</td><td>80%</td><td>2144</td><td>50S RIBOSOMAL PROTEIN L5</td><td></td></tr><tr><td>RL24_BACST</td><td>62%</td><td>2144</td><td>50S RIBOSOMAL PROTEIN L24</td><td></td></tr><tr><td>RL14_BACSU</td><td>80%</td><td>2144</td><td>50S RIBOSOMAL PROTEIN L14</td><td></td></tr><tr><td>RS17_BACSU</td><td>77%</td><td>2145</td><td>30S RIBOSOMAL PROTEIN S17 (BS16)</td><td></td></tr><tr><td>RL16_BACSU</td><td>76%</td><td>2145</td><td>50S RIBOSOMAL PROTEIN L16</td><td></td></tr><tr><td>RS3_BACSU</td><td>73%</td><td>2146</td><td>30S RIBOSOMAL PROTEIN S3 (BS3)</td><td></td></tr><tr><td>RL22_BACSU</td><td>62%</td><td>2146</td><td>50S RIBOSOMAL PROTEIN L22</td><td></td></tr><tr><td>RS19_BACST</td><td>77%</td><td>2147</td><td>30S RIBOSOMAL PROTEIN S19 (BS19)</td><td></td></tr><tr><td>RL2_BACSU</td><td>76%</td><td>2147</td><td>50S RIBOSOMAL PROTEIN L2 (BL2)</td><td></td></tr><tr><td>RL4_BACSU</td><td>60%</td><td>2149</td><td>50S RIBOSOMAL PROTEIN L4</td><td></td></tr><tr><td>RL3_BACSU</td><td>69%</td><td>2149</td><td>50S RIBOSOMAL PROTEIN L3 (BL3)</td><td></td></tr><tr><td>RS10_STRMU</td><td>81%</td><td>2150</td><td>30S RIBOSOMAL PROTEIN S10</td><td></td></tr><tr><td>RL33_MYCCA</td><td>57%</td><td>2155</td><td>50S RIBOSOMAL PROTEIN L33</td><td></td></tr><tr><td>RS2 PEDAC</td><td>71%</td><td>2207</td><td>30S RIBOSOMAL PROTEIN S2</td><td></td></tr><tr><td>RS2_BACSU</td><td>100%</td><td>2208</td><td>30S RIBOSOMAL PROTEIN S2 (BS1)</td><td></td></tr><tr><td>RS18_BACST</td><td>63%</td><td>2254</td><td>30S RIBOSOMAL PROTEIN S18 (BS21)</td><td></td></tr><tr><td>RS6_BACSU</td><td>58%</td><td>2254</td><td>30S RIBOSOMAL PROTEIN S6 (BS9)</td><td></td></tr><tr><td>RS9_BACSU</td><td>65%</td><td>2326</td><td>30S RIBOSOMAL PROTEIN S9 (BS10)</td><td></td></tr><tr><td>RL13_STACA</td><td>63%</td><td>2327</td><td>50S RIBOSOMAL PROTEIN L13</td><td></td></tr><tr><td>RS7_ECOLI</td><td>64%</td><td>2334</td><td>30S RIBOSOMAL PROTEIN S7</td><td></td></tr><tr><td>RS7_BACSU</td><td>71%</td><td>2334</td><td>30S RIBOSOMAL PROTEIN S7 (BS7)</td><td></td></tr><tr><td>RS12_SYNY3</td><td>67%</td><td>2335</td><td>30S RIBOSOMAL PROTEIN S12</td><td></td></tr></tbody><thead><tr><th colspan="3">BIO12.06 tRNA modification</th><th colspan="2">8 genes</th></tr></thead><tbody><tr><td>SP5C_BACSU</td><td>55%</td><td>17</td><td>PROBABLE PEPTIDYL-TRNA HYDROLASE (EC 3.1.1.29)</td><td></td></tr><tr><td>RNPA_BACSU</td><td>47%</td><td>129</td><td>RIBONUCLEASE P PROTEIN COMPONENT (EC 3.1.26.5)</td><td></td></tr><tr><td>KSGA_BACSU</td><td>52%</td><td>687</td><td>DIMETHYLADENOSINE TRANSFERASE (EC 2.1.1.-)</td><td></td></tr><tr><td>YGCA_HAEIN</td><td>30%</td><td>1192</td><td>HYPOTHETICAL RNA METHYLTRANSFERASE HI0333 (EC 2.1.1.-)</td><td></td></tr><tr><td>TRMD_HAEIN</td><td>50%</td><td>1603</td><td>TRNA (GUANINE-N1)-METHYLTRANSFERASE (EC 2.1.1.31)</td><td></td></tr><tr><td>MDMC_STRMY</td><td>31%</td><td>1762</td><td>O-METHYLTRANSFERASE (EC 2.1.1.-)</td><td></td></tr><tr><td>FMT_BACSU</td><td>46%</td><td>1941</td><td>METHIONYL-TRNA FORMYLTRANSFERASE (EC 2.1.2.9)</td><td></td></tr><tr><td>YGCA_HAEIN</td><td>27%</td><td>2235</td><td>HYPOTHETICAL RNA METHYLTRANSFERASE HI0333 (EC 2.1.1.-)</td><td></td></tr></tbody><thead><tr><th colspan="3">BIO12.07 Translation factors</th><th colspan="2">23 genes</th></tr></thead><tbody><tr><td>YDGI_BACSU</td><td>30%</td><td>183</td><td>PUTATIVE NAD(P)H NITROREDUCTASE (EC 1.-.-.-)</td><td></td></tr></tbody></table>
<table><caption>Table 3.</caption><thead><tr><th>Gene</th><th>Accession</th><th>Gene ID</th><th>Description</th></tr></thead><tbody><tr><td>RP3_SYNY3</td><td>47%</td><td>349</td><td>PEPTIDE CHAIN RELEASE FACTOR 3 (RF-3)</td></tr><tr><td>RF2 Helpy</td><td>25%</td><td>451</td><td>PEPTIDE CHAIN RELEASE FACTOR 2 (RF-2)</td></tr><tr><td>IF2EntFC</td><td>36%</td><td>543</td><td>TRANSLATION INITIATION FACTOR IF-2</td></tr><tr><td>RP1_BACSU</td><td>54%</td><td>584</td><td>PEPTIDE CHAIN RELEASE FACTOR 1 (RF-1)</td></tr><tr><td>PLAV_DESV</td><td>38%</td><td>595</td><td>PLAVODOXIN</td></tr><tr><td>EPP_BACSU</td><td>48%</td><td>689</td><td>ELONGATION FACTOR P (EF-P)</td></tr><tr><td>IF2EntFC</td><td>69%</td><td>775</td><td>TRANSLATION INITIATION FACTOR IF-2</td></tr><tr><td>RBFA_BACSU</td><td>37%</td><td>777</td><td>RIBOSOME-BINDING FACTOR A (P15B PROTEIN)</td></tr><tr><td>RF2_BACSU</td><td>53%</td><td>996</td><td>PEPTIDE CHAIN RELEASE FACTOR 2 (RF-2)</td></tr><tr><td>YDGT_BACSU</td><td>49%</td><td>1500</td><td>PUTATIVE NAD(P)H NITROREDUCTASE (EC 1.1.1.1-1)</td></tr><tr><td>MVIM_ECOLI</td><td>34%</td><td>1872</td><td>VIRULENCE FACTOR MVIM HOMOLOG</td></tr><tr><td>IF3_BACSU</td><td>61%</td><td>1892</td><td>TRANSLATION INITIATION FACTOR IF-3</td></tr><tr><td>EFTU_STROR</td><td>80%</td><td>1909</td><td>ELONGATION FACTOR TU (EF-TU)</td></tr><tr><td>RRF_HAEIN</td><td>43%</td><td>2066</td><td>RIBOSOME RECYCLING FACTOR (RIBOSOME RELEASING FACTOR)</td></tr><tr><td>YTHK_ECOLI</td><td>55%</td><td>2073</td><td>65.4 KD GTP-BINDING PROTEIN IN GLNA-RBN INTERGENIC REGION</td></tr><tr><td>IF1_LACLA</td><td>100%</td><td>2134</td><td>TRANSLATION INITIATION FACTOR IF-1</td></tr><tr><td>FMNB_DESVM</td><td>39%</td><td>2161</td><td>FMN-BINDING PROTEIN</td></tr><tr><td>EFTS Helpy</td><td>43%</td><td>2206</td><td>ELONGATION FACTOR TS (EF-TS)</td></tr><tr><td>EFTS_STRPN</td><td>71%</td><td>2207</td><td>ELONGATION FACTOR TS (EF-TS)</td></tr><tr><td>EFTS_BACSU</td><td>77%</td><td>2207</td><td>ELONGATION FACTOR TS (EF-TS)</td></tr><tr><td>EFC_BACSU</td><td>72%</td><td>2333</td><td>ELONGATION FACTOR G (EF-G)</td></tr><tr><td>EFG_THETA</td><td>55%</td><td>2333</td><td>ELONGATION FACTOR G (EF-G)</td></tr><tr><td colspan="4">BIO13. TRANSPORT AND BINDING PROTEINS 185 genes</td></tr><tr><td colspan="4">BIO13.01 General 35 genes</td></tr><tr><td>LCNC_LACLA</td><td>94%</td><td>84</td><td>LACTOCOCCIN A TRANSPORT ATP-BINDING PROTEIN LCNC</td></tr><tr><td>RFBB_MYXXA</td><td>40%</td><td>202</td><td>O-ANTIGEN EXPORT SYSTEM ATP-BINDING PROTEIN RFBB</td></tr><tr><td>CHVA_AGRTU</td><td>35%</td><td>260</td><td>BETA-(1-->2)GLUCAN EXPORT ATP-BINDING PROTEIN CHVA</td></tr><tr><td>P69_MYCHR</td><td>26%</td><td>296</td><td>TRANSPORT SYSTEM PERMEASE PROTEIN P69</td></tr><tr><td>ABC_ECOLI</td><td>42%</td><td>319</td><td>ATP-BINDING PROTEIN ABC</td></tr><tr><td>LCN3_LACLA</td><td>34%</td><td>517</td><td>LACTICIN 481/LACTOCOCCIN TRANSPORT ATP-BINDING PROTEIN LCNDR3</td></tr><tr><td>UUP1_HAEIN</td><td>29%</td><td>560</td><td>ABC TRANSPORTER ATP-BINDING PROTEIN UUP-1</td></tr><tr><td>LMRA_STRNL</td><td>34%</td><td>597</td><td>LINCOMYCIN RESISTANCE PROTEIN</td></tr><tr><td>KUP_ECOLI</td><td>36%</td><td>608</td><td>KUP SYSTEM POTASSIUM UPTAKE PROTEIN</td></tr><tr><td>KUP_ECOLI</td><td>29%</td><td>610</td><td>KUP SYSTEM POTASSIUM UPTAKE PROTEIN</td></tr><tr><td>CYDC_BACSU</td><td>48%</td><td>709</td><td>TRANSPORT ATP-BINDING PROTEIN CYDC</td></tr><tr><td>CYDD_BACSU</td><td>45%</td><td>711</td><td>TRANSPORT ATP-BINDING PROTEIN CYDD</td></tr><tr><td>NRDH_LACLC</td><td>99%</td><td>1003</td><td>GLUTAREDOXIN-LIKE PROTEIN NRDH</td></tr><tr><td>PERM_HAEIN</td><td>26%</td><td>1196</td><td>PUTATIVE PERMEASE PERM HOMOLOG</td></tr><tr><td>ATMB_SALTY</td><td>51%</td><td>1284</td><td>MG(2+) TRANSPORT ATPASE, P-TYPE 2 (EC 3.6.1.-)</td></tr><tr><td>MGLA_HAEIN</td><td>23%</td><td>1352</td><td>GALACTOSIDE TRANSPORT ATP-BINDING PROTEIN MGLA</td></tr><tr><td>MGLA_MYCGE</td><td>32%</td><td>1364</td><td>GALACTOSIDE TRANSPORT ATP-BINDING PROTEIN MGLA HOMOLOG</td></tr><tr><td>AC22_STRCO</td><td>26%</td><td>1383</td><td>PROBABLE ACTINORHODIN TRANSPORTER</td></tr><tr><td>LPLC_BACSU</td><td>42%</td><td>1527</td><td>LPLC PROTEIN</td></tr><tr><td>LPLB_BACSU</td><td>27%</td><td>1528</td><td>LPLB PROTEIN</td></tr><tr><td>LCN3_LACLA</td><td>41%</td><td>1559</td><td>LACTICIN 481/LACTOCOCCIN TRANSPORT ATP-BINDING PROTEIN LCNDR3</td></tr><tr><td>COMA_STRPN</td><td>24%</td><td>1560</td><td>TRANSPORT ATP-BINDING PROTEIN COMA</td></tr><tr><td>AC22_STRCO</td><td>28%</td><td>1584</td><td>PROBABLE ACTINORHODIN TRANSPORTER</td></tr><tr><td>UUP_ECOLI</td><td>31%</td><td>1592</td><td>ABC TRANSPORTER ATP-BINDING PROTEIN UUP</td></tr><tr><td>YJJK_HAEIN</td><td>38%</td><td>1593</td><td>ABC TRANSPORTER ATP-BINDING PROTEIN HI1252</td></tr><tr><td>MVAA_PSEMV</td><td>42%</td><td>1607</td><td>3-HYDROXY-3-METHYLGLUTARYL-COENZYME A REDUCTASE (EC 1.1.1.88)</td></tr><tr><td>YQGI_BACSU</td><td>54%</td><td>1753</td><td>PROBABLE ABC TRANSPORTER PERMEASE PROTEIN IN SODA-COMGA</td></tr><tr><td colspan="4">INTERGENIC REGION (ORF73)</td></tr><tr><td>YQGH_BACSU</td><td>32%</td><td>1754</td><td>PROBABLE ABC TRANSPORTER PERMEASE PROTEIN IN SODA-COMGA</td></tr><tr><td colspan="4">INTERGENIC REGION (ORF72)</td></tr><tr><td>YQGG_BACSU</td><td>47%</td><td>1755</td><td>PROBABLE ABC TRANSPORTER BINDING PROTEIN IN SODA-COMGA</td></tr><tr><td colspan="4">INTERGENIC REGION PRECURSOR (ORF108)</td></tr><tr><td>NOCQ_AGR5</td><td>32%</td><td>1835</td><td>NOPALINE TRANSPORT SYSTEM PERMEASE PROTEIN NOCQ</td></tr><tr><td>PERM_ECOLI</td><td>27%</td><td>1863</td><td>PUTATIVE PERMEASE PERM</td></tr><tr><td>UVRA_NEIGO</td><td>59%</td><td>1866</td><td>EXCINUCLEASE ABC SUBUNIT A</td></tr><tr><td>ECSB_BACSU</td><td>28%</td><td>2054</td><td>PROTEIN ECSB</td></tr><tr><td>ECSA_BACSU</td><td>60%</td><td>2055</td><td>ABC-TYPE TRANSPORTER ATP-BINDING PROTEIN ECSA</td></tr><tr><td>FLIP_BORBU</td><td>27%</td><td>2113</td><td>FLAGELLAR BIOSYNTHETIC PROTEIN FLIP</td></tr><tr><td colspan="4">BIO13.02 Amino acids, peptides and amines 52 genes</td></tr><tr><td>YW40_MYCTU</td><td>25%</td><td>70</td><td>HYPOTHETICAL TRANSPORT PROTEIN CY39.40 (FRAGMENT)</td></tr><tr><td>GABP_ECOLI</td><td>23%</td><td>70</td><td>GABA PERMEASE (4-AMINO BUTYRATE TRANSPORT CARRIER)</td></tr><tr><td>LYSP_ECOLI</td><td>27%</td><td>111</td><td>LYSINE-SPECIFIC PERMEASE</td></tr><tr><td>PTHP_STRSL</td><td>81%</td><td>113</td><td>PHOSPHOCARRIER PROTEIN HPR (HISTIDINE-CONTAINING PROTEIN)</td></tr><tr><td>PT1_STRSL</td><td>82%</td><td>119</td><td>PHOSPHOENOLPYRUVATE-PROTEIN PHOSPHOTRANSFERASE (EC 2.7.3.9)</td></tr><tr><td>ALYS_ENTFA</td><td>49%</td><td>267</td><td>AUTOLYSIN (EC 3.5.1.28)</td></tr><tr><td>YQIZ_BACSU</td><td>34%</td><td>322</td><td>PROBABLE AMINO-ACID ABC TRANSPORTER ATP-BINDING PROTEIN IN</td></tr><tr><td colspan="4">BMRU-ANSR INTERGENIC REGION</td></tr><tr><td>AMIA_STRPN</td><td>31%</td><td>341</td><td>OLIGOPEPTIDE-BINDING PROTEIN AMIA PRECURSOR</td></tr><tr><td>OPPA_ECOLI</td><td>28%</td><td>343</td><td>PERIPLASMIC OLIGOPEPTIDE-BINDING PROTEIN PRECURSOR</td></tr><tr><td>OPPB_BACSU</td><td>46%</td><td>345</td><td>OLIGOPEPTIDE TRANSPORT SYSTEM PERMEASE PROTEIN OPPB</td></tr></tbody></table>
<table><caption>Table 3.</caption><thead><tr><th>DB</th><th>NAME</th><th>PROTEIN</th><th>FUNCTION</th></tr></thead><tbody><tr><td>DFPC_BACSU</td><td>43%</td><td>346</td><td>DIGESTIVE TRANSPORT SYSTEM PERMEASE PROTEIN DPPC</td></tr><tr><td>OPPF_BACSU</td><td>61%</td><td>348</td><td>OLIGOPEPTIDE TRANSPORT ATP-BINDING PROTEIN OPPF</td></tr><tr><td>CYCA_ECOLI</td><td>28%</td><td>358</td><td>D-SERINE/D-ALANINE/GLYCINE TRANSPORTER</td></tr><tr><td>APA_BACSU</td><td>47%</td><td>360</td><td>AMINO ACID PERMEASE APA</td></tr><tr><td>LYSP_ECOLI</td><td>48%</td><td>368</td><td>LYSINE-SPECIFIC PERMEASE</td></tr><tr><td>OPPA_BACSU</td><td>30%</td><td>523</td><td>OLIGOPEPTIDE-BINDING PROTEIN OPPA PRECURSOR</td></tr><tr><td>ALYS_ENTFA</td><td>35%</td><td>525</td><td>AUTOLYSIN (EC 3.5.1.28)</td></tr><tr><td>DEF_HELPY</td><td>39%</td><td>553</td><td>POLYPEPTIDE DEFORMYLASE (EC 3.5.1.31)</td></tr><tr><td>YQIX_BACSU</td><td>36%</td><td>556</td><td>PROBABLE AMINO-ACID ABC TRANSPORTER BINDING PROTEIN IN BMRU-ANSR INTERGENIC REGION PRECURSOR</td></tr><tr><td>BRNQ_LACDL</td><td>47%</td><td>683</td><td>BRANCHED-CHAIN AMINO ACID TRANSPORT SYSTEM CARRIER PROTEIN (BRANCHED-CHAIN AMINO ACID UPTAKE CARRIER)</td></tr><tr><td>DTPT_LACLA</td><td>97%</td><td>703</td><td>DI-/TRIPEPTIDE TRANSPORTER</td></tr><tr><td>YDGF_BACSU</td><td>33%</td><td>817</td><td>HYPOTHETICAL TRANSPORT PROTEIN IN EXPZ-DINB INTERGENIC REGION</td></tr><tr><td>OPUA_BACSU</td><td>34%</td><td>863</td><td>GLYCINE BETAINE TRANSPORT ATP-BINDING PROTEIN OPUAA</td></tr><tr><td>PROW_BACSU</td><td>42%</td><td>863</td><td>GLYCINE BETAINE/L-PROLINE TRANSPORT SYSTEM PERMEASE PROTEIN PROW</td></tr><tr><td>YCKK_BACSU</td><td>28%</td><td>960</td><td>PROBABLE AMINO-ACID ABC TRANSPORTER BINDING PROTEIN PRECURSOR</td></tr><tr><td>Y4TG_RHISN</td><td>32%</td><td>961</td><td>PROBABLE AMINO-ACID ABC TRANSPORTER PERMEASE PROTEIN Y4TG</td></tr><tr><td>GLTL_HAEIN</td><td>59%</td><td>962</td><td>GLUTAMATE/ASPARTATE TRANSPORT ATP-BINDING PROTEIN GLTL</td></tr><tr><td>POTA_HAEIN</td><td>45%</td><td>1173</td><td>SPERMIDINE/PUTRESCINE TRANSPORT ATP-BINDING PROTEIN POTA</td></tr><tr><td>POTC_HAEIN</td><td>35%</td><td>1175</td><td>SPERMIDINE/PUTRESCINE TRANSPORT SYSTEM PERMEASE PROTEIN POTC</td></tr><tr><td>POTD_ECOLI</td><td>43%</td><td>1176</td><td>SPERMIDINE/PUTRESCINE-BINDING PERIPLASMIC PROTEIN PRECURSOR (SPBP)</td></tr><tr><td>GRSB_BACSR</td><td>30%</td><td>1290</td><td>GRAMICIDIN S SYNTHETASE II (GRAMICIDIN S BIOSYNTHESIS GRSB PROTEIN) (EC 6.---.-)</td></tr><tr><td>XASA_ECOLI</td><td>50%</td><td>1323</td><td>AMINO ACID ANTIPORTER (EXTREME ACID SENSITIVITY PROTEIN)</td></tr><tr><td>OPUC_BACSU</td><td>47%</td><td>1471</td><td>GLYCINE BETAINE-BINDING PROTEIN PRECURSOR</td></tr><tr><td>OPUB_BACSU</td><td>51%</td><td>1471</td><td>GLYCINE BETAINE TRANSPORT SYSTEM PERMEASE PROTEIN OPUAB</td></tr><tr><td>OPUA_BACSU</td><td>58%</td><td>1473</td><td>GLYCINE BETAINE TRANSPORT ATP-BINDING PROTEIN OPUAA</td></tr><tr><td>PMGR_BACSU</td><td>54%</td><td>1590</td><td>PUTATIVE PEPTIDE METHIONINE SULFOSIDE REDUCTASE (PEPTIDE MET GLN3_ECOLI)</td></tr><tr><td>GLNH_ECOLI</td><td>36%</td><td>1797</td><td>GLUTAMINE-BINDING PERIPLASMIC PROTEIN PRECURSOR (GLNBP)</td></tr><tr><td>YA79_HAEIN</td><td>38%</td><td>1798</td><td>HYPOTHETICAL AMINO-ACID ABC TRANSPORTER PERMEASE PROTEIN HI0179</td></tr><tr><td>YQIZ_BACSU</td><td>64%</td><td>1799</td><td>PROBABLE AMINO-ACID ABC TRANSPORTER ATP-BINDING PROTEIN IN BMRU-ANSR INTERGENIC REGION</td></tr><tr><td>GLNQ_ECOLI</td><td>56%</td><td>1833</td><td>GLUTAMINE TRANSPORT ATP-BINDING PROTEIN GLNQ</td></tr><tr><td>HISP_ECOLI</td><td>51%</td><td>1835</td><td>HISTIDINE TRANSPORT ATP-BINDING PROTEIN HISP</td></tr><tr><td>PEPT_LACLC</td><td>95%</td><td>1857</td><td>PEPTIDASE T (EC 3.4.11.-)</td></tr><tr><td>YDGF_BACSU</td><td>35%</td><td>1870</td><td>HYPOTHETICAL TRANSPORT PROTEIN IN EXPZ-DINB INTERGENIC REGION</td></tr><tr><td>OPPA_LACLA</td><td>90%</td><td>1885</td><td>OLIGOPEPTIDE-BINDING PROTEIN OPPA PRECURSOR</td></tr><tr><td>OPPC_LACLA</td><td>100%</td><td>1887</td><td>OLIGOPEPTIDE TRANSPORT SYSTEM PERMEASE PROTEIN OPPC</td></tr><tr><td>OPPB_LACLC</td><td>100%</td><td>1888</td><td>OLIGOPEPTIDE TRANSPORT SYSTEM PERMEASE PROTEIN OPPB</td></tr><tr><td>OPPF_LACLA</td><td>100%</td><td>1889</td><td>OLIGOPEPTIDE TRANSPORT ATP-BINDING PROTEIN OPPF</td></tr><tr><td>OPPD_LACLC</td><td>100%</td><td>1890</td><td>OLIGOPEPTIDE TRANSPORT ATP-BINDING PROTEIN OPPD</td></tr><tr><td>PMSR_BACSU</td><td>53%</td><td>2064</td><td>PUTATIVE PEPTIDE METHIONINE SULFOSIDE REDUCTASE (PEPTIDE MET ARGD_PSEAE)</td></tr><tr><td>ARCD_PSEAE</td><td>35%</td><td>2092</td><td>ARGININE/ORNITHINE ANTIPORTER</td></tr><tr><td>YXEM_BACSU</td><td>33%</td><td>2118</td><td>PROBABLE AMINO-ACID ABC TRANSPORTER BINDING PROTEIN IN IDH-DEOR INTERGENIC REGION PRECURSOR</td></tr><tr><td>LYSP_ECOLI</td><td>37%</td><td>2257</td><td>LYSINE-SPECIFIC PERMEASE</td></tr><tr><td colspan="4"><strong>BIO13.03 Anions</strong></td></tr><tr><td>MEGL_PSEPU</td><td>38%</td><td>77</td><td>METHIONINE GAMMA-LYASE (EC 4.4.1.11)</td></tr><tr><td>ATZN_ECOLI</td><td>28%</td><td>95</td><td>ZINC-TRANSPORTING ATPASE (EC 3.6.1.-)</td></tr><tr><td>5NTD_HAEIN</td><td>25%</td><td>180</td><td>PROBABLE 5'-NUCLEOTIDASE PRECURSOR (EC 3.1.3.5)</td></tr><tr><td>DHAK_CITFR</td><td>35%</td><td>243</td><td>DIHYDROXYACETONE KINASE (EC 2.7.1.29)</td></tr><tr><td>CN16_VEREN</td><td>31%</td><td>298</td><td>2',3'-CYCLIC-NUCLEOTIDE 2'-PHOSPHODIESTERASE PRECURSOR (EC 3.1.4.16)</td></tr><tr><td>GLPT_BACSU</td><td>34%</td><td>546</td><td>GLYCEROL-3-PHOSPHATE TRANSPORTER (G-3-P TRANSPORTER)</td></tr><tr><td>MANA_STRMU</td><td>65%</td><td>777</td><td>MANNOSE-6-PHOSPHATE ISOMERASE (EC 5.3.1.8)</td></tr><tr><td>ATKA_ENTFA</td><td>41%</td><td>845</td><td>POTASSIUM/COPPER-TRANSPORTING ATPASE A (EC 3.6.1.36)</td></tr><tr><td>CADA_BACFI</td><td>28%</td><td>869</td><td>PROBABLE CADMIUM-TRANSPORTING ATPASE (EC 3.6.1.-)</td></tr><tr><td>5NTD_HAEIN</td><td>33%</td><td>1098</td><td>PROBABLE 5'-NUCLEOTIDASE PRECURSOR (EC 3.1.3.5)</td></tr><tr><td>SCRK_STRMU</td><td>62%</td><td>1516</td><td>FRUCTOKINASE (EC 2.7.1.4)</td></tr><tr><td>PTA_BACSU</td><td>61%</td><td>1704</td><td>PROBABLE PHOSPHATE ACETYLTRANSFERASE (EC 2.3.1.8)</td></tr><tr><td>SPHX SYNPT</td><td>28%</td><td>1756</td><td>SPHX PROTEIN PRECURSOR</td></tr><tr><td colspan="4"><strong>BIO13.04 Carbohydrates, organic alcohols and acids</strong></td></tr><tr><td>GLPF_ECOLI</td><td>35%</td><td>245</td><td>GLYCEROL UPTAKE FACILITATOR PROTEIN</td></tr><tr><td>FECE_ECOLI</td><td>42%</td><td>324</td><td>IRON(III) DICITRATE TRANSPORT ATP-BINDING PROTEIN FECE</td></tr><tr><td>FECD_ECOLI</td><td>35%</td><td>326</td><td>IRON(III) DICITRATE TRANSPORT SYSTEM PERMEASE PROTEIN FECD</td></tr><tr><td>CITN_LACLA</td><td>48%</td><td>921</td><td>CITRATE-SODIUM SYMPOR (CITRATE TRANSPORTER)</td></tr><tr><td>GLPF STRPN</td><td>58%</td><td>1267</td><td>GLYCEROL UPTAKE FACILITATOR PROTEIN</td></tr><tr><td>RBSB_HAEIN</td><td>45%</td><td>1679</td><td>D-RIBOSE-BINDING PERIPLASMIC PROTEIN PRECURSOR</td></tr><tr><td>RBSC_BACSU</td><td>60%</td><td>1680</td><td>RIBOSE TRANSPORT SYSTEM PERMEASE PROTEIN RBSC</td></tr><tr><td>RBSA_BACSU</td><td>42%</td><td>1681</td><td>RIBOSE TRANSPORT ATP-BINDING PROTEIN RBSA</td></tr><tr><td>RBSD_BACSU</td><td>56%</td><td>1682</td><td>HIGH AFFINITY RIBOSE TRANSPORT PROTEIN RBSD</td></tr><tr><td>LACY STRTR</td><td>43%</td><td>2043</td><td>LACTOSE PERMEASE (LACTOSE-PROTON SYMPOR)</td></tr></tbody></table>
<table><caption>Table 3.</caption><thead><tr><th></th><th></th><th></th><th></th></tr></thead><tbody><tr><td>RBSA_HAEIN</td><td>24%</td><td>2163</td><td>RIBOSE TRANSPORT ATP-BINDING PROTEIN RBSA</td></tr><tr><td>EBA2 Flame</td><td>27%</td><td>2238</td><td>ENDO-BETA-N-ACETYLGLUCOSAMINIDASE F2 PRECURSOR (EC 3.2.1.96)</td></tr><tr><td>GNTP_BACLI</td><td>59%</td><td>2246</td><td>GLUCONATE PERMEASE</td></tr><tr><td colspan="4"><strong>BIO13.05 Cations</strong></td></tr><tr><td>PEOB_ECOLI</td><td>39%</td><td>188</td><td>PERROUS IRON TRANSPORT PROTEIN B</td></tr><tr><td>PEOA_ECOLI</td><td>38%</td><td>190</td><td>PERROUS IRON TRANSPORT PROTEIN A</td></tr><tr><td>TCRI_ECOLI</td><td>41%</td><td>303</td><td>TETRACYCLINE RESISTANCE PROTEIN, CLASS A (TRANSPOSON TN1721)</td></tr><tr><td>FHUB_BACSU</td><td>37%</td><td>325</td><td>FERRICHROME TRANSPORT PERMEASE PROTEIN FHUB</td></tr><tr><td>YIB2_MYCTU</td><td>36%</td><td>567</td><td>PUTATIVE CATION-TRANSPORTING ATPASE CY21C12.02 (EC 3.6.1.-)</td></tr><tr><td>ATA1_SYNY3</td><td>40%</td><td>675</td><td>CATION-TRANSPORTING ATPASE PMA1 (EC 3.6.1.-)</td></tr><tr><td>NHAA_ECOLI</td><td>42%</td><td>1148</td><td>NA(+)/H</td></tr><tr><td>PBUX_BACSU</td><td>48%</td><td>1158</td><td>XANTHINE PERMEASE</td></tr><tr><td>YIB2_MYCTU</td><td>35%</td><td>1188</td><td>PUTATIVE CATION-TRANSPORTING ATPASE CY21C12.02 (EC 3.6.1.-)</td></tr><tr><td>ATCLSYNPT</td><td>37%</td><td>1402</td><td>CATION-TRANSPORTING ATPASE PAC1 (EC 3.6.1.-)</td></tr><tr><td>FUR_CAMJE</td><td>30%</td><td>1503</td><td>FERRIC UPTAKE REGULATION PROTEIN</td></tr><tr><td>UIDB_ECOLI</td><td>33%</td><td>1541</td><td>GLUCURONIDE CARRIER PROTEIN (GLUCURONIDE PERMEASE)</td></tr><tr><td>Y058_METJA</td><td>31%</td><td>1632</td><td>PUTATIVE AMMONIUM TRANSPORTER MJ0058</td></tr><tr><td>URAA_HAEIN</td><td>36%</td><td>1643</td><td>PROBABLE URACIL PERMEASE (URACIL TRANSPORTER)</td></tr><tr><td>FER_CLOTH</td><td>38%</td><td>1741</td><td>FERREDOXIN</td></tr><tr><td>NAPA_ENTHR</td><td>48%</td><td>1973</td><td>NA(+)/H</td></tr><tr><td>ATCS_SYNY3</td><td>36%</td><td>2061</td><td>CATION-TRANSPORTING ATPASE PACS (EC 3.6.1.-)</td></tr><tr><td>ATA1_SYNY3</td><td>36%</td><td>2315</td><td>CATION-TRANSPORTING ATPASE PMA1 (EC 3.6.1.-)</td></tr><tr><td colspan="4"><strong>BIO13.06 Nucleosides, purines and pyrimidines</strong></td></tr><tr><td>PDP_BACST</td><td>56%</td><td>1463</td><td>PYRIMIDINE-NUCLEOSIDE PHOSPHORYLASE (EC 2.4.2.2)</td></tr><tr><td colspan="4"><strong>BIO13.07 PTS system</strong></td></tr><tr><td>PTMA_ECOLI</td><td>46%</td><td>31</td><td>PTS SYSTEM, MANNITOL-SPECIFIC IIABC COMPONENT (EIIABC-MTL)</td></tr><tr><td>PTCC_BACSU</td><td>34%</td><td>175</td><td>PTS SYSTEM, CELLOBIOSE-SPECIFIC IIC COMPONENT (EIIIC-CEL)</td></tr><tr><td>PTCB_BACSU</td><td>52%</td><td>416</td><td>PTS SYSTEM, CELLOBIOSE-SPECIFIC IIB COMPONENT (EIIIB-CEL)</td></tr><tr><td>PTCA_BACSU</td><td>48%</td><td>417</td><td>PTS SYSTEM, CELLOBIOSE-SPECIFIC IIA COMPONENT (EIIA-CEL)</td></tr><tr><td>PTSA STRMU</td><td>48%</td><td>435</td><td>PTS SYSTEM, SUCROSE-SPECIFIC IIABC COMPONENT (EIIABC-SCR)</td></tr><tr><td>PTSA STRMU</td><td>31%</td><td>436</td><td>PTS SYSTEM, SUCROSE-SPECIFIC IIABC COMPONENT (EIIABC-SCR)</td></tr><tr><td>PTCC_BACSU</td><td>31%</td><td>830</td><td>PTS SYSTEM, CELLOBIOSE-SPECIFIC IIC COMPONENT (EIIIC-CEL)</td></tr><tr><td>PTPB_RHOCA</td><td>52%</td><td>984</td><td>PTS SYSTEM, FRUCTOSE-SPECIFIC IIBC COMPONENT (EIIIB-FRU)</td></tr><tr><td>PTBA_BACSU</td><td>37%</td><td>1144</td><td>PTS SYSTEM, BETA-GLUCOSIDES-SPECIFIC IIABC COMPONENT (EIIABC-BGL)</td></tr><tr><td>PTBA ERWCH</td><td>41%</td><td>1489</td><td>PTS SYSTEM, BETA-GLUCOSIDES-SPECIFIC IIABC COMPONENT (EIIABC-BGL)</td></tr><tr><td>PTNA_ECOLI</td><td>41%</td><td>1742</td><td>PTS SYSTEM, MANNOSE-SPECIFIC IIAB COMPONENT (EIIAB-MAN)</td></tr><tr><td>PTNC_ECOLI</td><td>46%</td><td>1743</td><td>PTS SYSTEM, MANNOSE-SPECIFIC IIC COMPONENT (EIIIC-MAN)</td></tr><tr><td>PTND_ECOLI</td><td>57%</td><td>1744</td><td>PTS SYSTEM, MANNOSE-SPECIFIC IID COMPONENT (EIIID-MAN)</td></tr><tr><td colspan="4"><strong>BIO13.08 Multidrug resistance</strong></td></tr><tr><td>HMR2_BACSU</td><td>46%</td><td>123</td><td>MULTIDRUG RESISTANCE PROTEIN 2 (MULTIDRUG-EFFLUX TRANSPORTER 2)</td></tr><tr><td>EMRB_ECOLI</td><td>26%</td><td>930</td><td>MULTIDRUG RESISTANCE PROTEIN B</td></tr><tr><td>MDL_ECOLI</td><td>36%</td><td>1302</td><td>MULTIDRUG RESISTANCE-LIKE ATP-BINDING PROTEIN MDL</td></tr><tr><td colspan="4"><strong>BIO13.09 Other</strong></td></tr><tr><td>YBJZ_ECOLI</td><td>34%</td><td>15</td><td>HYPOTHETICAL ABC TRANSPORTER ATP-BINDING PROTEIN YBJZ</td></tr><tr><td>YCHM_ECOLI</td><td>37%</td><td>53</td><td>HYPOTHETICAL 58.4 KD PROTEIN IN PTH-PRSA INTERGENIC REGION</td></tr><tr><td>YBIT_ECOLI</td><td>32%</td><td>74</td><td>HYPOTHETICAL ABC TRANSPORTER ATP-BINDING PROTEIN YBIT</td></tr><tr><td>YHES_ECOLI</td><td>35%</td><td>100</td><td>HYPOTHETICAL ABC TRANSPORTER ATP-BINDING PROTEIN YHES</td></tr><tr><td>YHIH_ECOLI</td><td>50%</td><td>248</td><td>HYPOTHETICAL ABC TRANSPORTER ATP-BINDING PROTEIN YHIH</td></tr><tr><td>YFIB_BACSU</td><td>39%</td><td>257</td><td>HYPOTHETICAL ABC TRANSPORTER ATP-BINDING PROTEIN 1 IN GLVBC</td></tr><tr><td colspan="4"><strong>3' REGION</strong></td></tr><tr><td>Y179_MYCGE</td><td>44%</td><td>273</td><td>HYPOTHETICAL ABC TRANSPORTER ATP-BINDING PROTEIN MG179</td></tr><tr><td>Y180_MYCGE</td><td>47%</td><td>274</td><td>HYPOTHETICAL ABC TRANSPORTER ATP-BINDING PROTEIN MG180</td></tr><tr><td>Y412_METJA</td><td>37%</td><td>295</td><td>HYPOTHETICAL ABC TRANSPORTER ATP-BINDING PROTEIN MJ0412</td></tr><tr><td>YFIB_BACSU</td><td>33%</td><td>307</td><td>HYPOTHETICAL ABC TRANSPORTER ATP-BINDING PROTEIN 1 IN GLVBC</td></tr><tr><td colspan="4"><strong>3' REGION</strong></td></tr><tr><td>YFIC_BACSU</td><td>41%</td><td>309</td><td>HYPOTHETICAL ABC TRANSPORTER ATP-BINDING PROTEIN 2 IN GLVBC</td></tr><tr><td colspan="4"><strong>3' REGION</strong></td></tr><tr><td>YARE_ECOLI</td><td>44%</td><td>320</td><td>HYPOTHETICAL ABC TRANSPORTER PERMEASE PROTEIN YAE</td></tr><tr><td>YHIH_ECOLI</td><td>27%</td><td>321</td><td>HYPOTHETICAL ABC TRANSPORTER ATP-BINDING PROTEIN YHIH</td></tr><tr><td>Y081_MYCTU</td><td>44%</td><td>347</td><td>HYPOTHETICAL ABC TRANSPORTER ATP-BINDING PROTEIN CY50.01</td></tr><tr><td>YCVJ_ECOLI</td><td>60%</td><td>426</td><td>HYPOTHETICAL ABC TRANSPORTER ATP-BINDING PROTEIN YCVJ</td></tr><tr><td>YCFV_ECOLI</td><td>41%</td><td>650</td><td>HYPOTHETICAL ABC TRANSPORTER ATP-BINDING PROTEIN YCFV</td></tr><tr><td>YWJA_BACSU</td><td>35%</td><td>715</td><td>HYPOTHETICAL ABC TRANSPORTER ATP-BINDING PROTEIN IN ACDA</td></tr><tr><td colspan="4"><strong>5' REGION</strong></td></tr><tr><td>YBJZ_ECOLI</td><td>40%</td><td>718</td><td>HYPOTHETICAL ABC TRANSPORTER ATP-BINDING PROTEIN YBJZ</td></tr><tr><td>Y796_METJA</td><td>35%</td><td>892</td><td>HYPOTHETICAL ABC TRANSPORTER ATP-BINDING PROTEIN MJ0796</td></tr><tr><td>Y415_SYNY3</td><td>35%</td><td>990</td><td>HYPOTHETICAL ABC TRANSPORTER ATP-BINDING PROTEIN SLL0415</td></tr><tr><td>YRHG_BACSU</td><td>43%</td><td>993</td><td>HYPOTHETICAL 28.5 KD PROTEIN IN SIGV-GREA INTERGENIC REGION</td></tr><tr><td>YBJZ_ECOLI</td><td>25%</td><td>998</td><td>HYPOTHETICAL ABC TRANSPORTER ATP-BINDING PROTEIN YBJZ</td></tr><tr><td>YDIF_BACSU</td><td>52%</td><td>1072</td><td>HYPOTHETICAL ABC TRANSPORTER ATP-BINDING PROTEIN YDIF</td></tr></tbody></table>
<table><caption>Table 3.</caption><tbody><tr><td>Y796_METJA</td><td>48%</td><td>1108</td><td>HYPOTHETICAL ABC TRANSPORTER ATP-BINDING PROTEIN MJ0796</td></tr><tr><td>YLUD_LACLA</td><td>100%</td><td>1242</td><td>HYPOTHETICAL ABC TRANSPORTER ATP-BINDING PROTEIN IN LEUD</td></tr><tr><td colspan="4">3' REGION</td></tr><tr><td>YSC1_STRGC</td><td>62%</td><td>1349</td><td>HYPOTHETICAL ABC TRANSPORTER ATP-BINDING PROTEIN IN SCAA</td></tr><tr><td colspan="4">5' REGION (ORF1)</td></tr><tr><td>YXBC_BACSU</td><td>51%</td><td>1538</td><td>HYPOTHETICAL METABOLITE TRANSPORT PROTEIN IN HTPG-IOLR</td></tr><tr><td colspan="4">INTERGENIC REGION</td></tr><tr><td>YJEM_ECOLI</td><td>22%</td><td>1736</td><td>HYPOTHETICAL 56.3 KD PROTEIN IN GENX-PSD INTERGENIC REGION (0514)</td></tr><tr><td>YEJF_ECOLI</td><td>27%</td><td>1751</td><td>HYPOTHETICAL ABC TRANSPORTER ATP-BINDING PROTEIN YEJF</td></tr><tr><td>YQGJ_BACSU</td><td>60%</td><td>1751</td><td>HYPOTHETICAL ABC TRANSPORTER ATP-BINDING PROTEIN IN SODA-COMGA</td></tr><tr><td colspan="4">INTERGENIC REGION (ORF74)</td></tr><tr><td>YQGJ_BACSU</td><td>59%</td><td>1752</td><td>HYPOTHETICAL ABC TRANSPORTER ATP-BINDING PROTEIN IN SODA-COMGA</td></tr><tr><td colspan="4">INTERGENIC REGION (ORF74)</td></tr><tr><td>YXDL_BACSU</td><td>49%</td><td>1789</td><td>HYPOTHETICAL ABC TRANSPORTER ATP-BINDING PROTEIN IN IDH</td></tr><tr><td colspan="4">3' REGION</td></tr><tr><td>YATR_BACFI</td><td>43%</td><td>1815</td><td>HYPOTHETICAL ABC TRANSPORTER ATP-BINDING PROTEIN</td></tr><tr><td>YJEM_ECOLI</td><td>39%</td><td>1855</td><td>HYPOTHETICAL 56.3 KD PROTEIN IN GENX-PSD INTERGENIC REGION (0514)</td></tr><tr><td>YXDL_BACSU</td><td>35%</td><td>2076</td><td>HYPOTHETICAL ABC TRANSPORTER ATP-BINDING PROTEIN IN IDH</td></tr><tr><td colspan="4">3' REGION</td></tr><tr><td>YYBJ_BACSU</td><td>28%</td><td>2265</td><td>HYPOTHETICAL ABC TRANSPORTER ATP-BINDING PROTEIN IN COTF-TETB</td></tr><tr><td colspan="4">INTERGENIC REGION</td></tr><tr><td>Y796_METJA</td><td>42%</td><td>2329</td><td>HYPOTHETICAL ABC TRANSPORTER ATP-BINDING PROTEIN MJ0796</td></tr></tbody></table>

## BIO14. OTHER CATEGORIES

94 genes

### BIO14.01 Adaptations and atypical conditions

13 genes

<table><tbody><tr><td>CSP2_LACPL</td><td>82%</td><td>170</td><td>COLD SHOCK PROTEIN 2</td></tr><tr><td>TCMA_STRGA</td><td>28%</td><td>233</td><td>TETRACENOMYCIN C RESISTANCE AND EXPORT PROTEIN</td></tr><tr><td>MMR_BACSU</td><td>30%</td><td>382</td><td>METHYLENOMYCIN A RESISTANCE PROTEIN (MMR PEPTIDE)</td></tr><tr><td>CSPC_BACSU</td><td>75%</td><td>515</td><td>COLD SHOCK PROTEIN CSPC</td></tr><tr><td>TCMA_STRGA</td><td>25%</td><td>596</td><td>TETRACENOMYCIN C RESISTANCE AND EXPORT PROTEIN</td></tr><tr><td>VANZEntFC</td><td>42%</td><td>1097</td><td>VANZ PROTEIN</td></tr><tr><td>FSR_ECOLI</td><td>25%</td><td>1182</td><td>FOSMIDOMYCIN RESISTANCE PROTEIN</td></tr><tr><td>ARSC_BACSU</td><td>51%</td><td>1409</td><td>PUTATIVE ARSENATE REDUCTASE</td></tr><tr><td>TCMA_STRGA</td><td>29%</td><td>1553</td><td>TETRACENOMYCIN C RESISTANCE AND EXPORT PROTEIN</td></tr><tr><td>TCMA_STRGA</td><td>27%</td><td>1678</td><td>TETRACENOMYCIN C RESISTANCE AND EXPORT PROTEIN</td></tr><tr><td>CMCT_NOCLA</td><td>34%</td><td>1925</td><td>CEPHAMYCIN EXPORT PROTEIN CMCT</td></tr><tr><td>FRI_LISIN</td><td>44%</td><td>2082</td><td>NON-HEME IRON-CONTAINING FERRITIN</td></tr><tr><td>MSCL_ECOLI</td><td>44%</td><td>2150</td><td>LARGE CONDUCTANCE MECHANOSENSITIVE CHANNEL</td></tr></tbody></table>

### BIO14.02 Drug and analog sensitivity

1 genes

<table><tbody><tr><td>KKIH_LACLA</td><td>100%</td><td>1232</td><td>PROBABLE AMINOGLYCOSIDE 3'-PHOSPHOTRANSFERASE (EC 2.7.1.95)</td></tr></tbody></table>

### BIO14.03 Phage related functions and prophages

21 genes

<table><tbody><tr><td>TERS_BPSF6</td><td>37%</td><td>36</td><td>TERMINASE SMALL SUBUNIT (G1P)</td></tr><tr><td>Y367_METJA</td><td>26%</td><td>49</td><td>PROBABLE INTEGRASE/RECOMBINASE PROTEIN MJ0367</td></tr><tr><td>VINT_BPL54</td><td>25%</td><td>445</td><td>INTEGRASE</td></tr><tr><td>VG64_BPML5</td><td>45%</td><td>460</td><td>GENE 64 PROTEIN (GP64)</td></tr><tr><td>VP3_BPHK7</td><td>21%</td><td>464</td><td>PORTAL PROTEIN (GP3)</td></tr><tr><td>VP4_BPHK7</td><td>31%</td><td>465</td><td>PUTATIVE PROHEAD PROTEASE (GP4)</td></tr><tr><td>VINT_BPL54</td><td>31%</td><td>501</td><td>INTEGRASE</td></tr><tr><td>XERC_SALTY</td><td>32%</td><td>633</td><td>INTEGRASE/RECOMBINASE XERC</td></tr><tr><td>YHGE_BACSU</td><td>31%</td><td>902</td><td>HYPOTHETICAL 84.1 KD PROTEIN IN HEMY-GLTT INTERGENIC REGION (ORFB)</td></tr><tr><td>TNPA_STAAU</td><td>45%</td><td>1034</td><td>TRANSPOSASE A (TRANSPOSON TN554)</td></tr><tr><td>VP4_BPHK7</td><td>27%</td><td>1053</td><td>PUTATIVE PROHEAD PROTEASE (GP4)</td></tr><tr><td>VG13_BPPH2</td><td>33%</td><td>1064</td><td>MORPHOGENESIS PROTEIN 1 (LATE PROTEIN GP13)</td></tr><tr><td>VINT_BPL54</td><td>32%</td><td>1210</td><td>INTEGRASE</td></tr><tr><td>CODV_BACSU</td><td>31%</td><td>1256</td><td>PROBABLE INTEGRASE/RECOMBINASE CODV</td></tr><tr><td>XERC_HAEIN</td><td>37%</td><td>1257</td><td>INTEGRASE/RECOMBINASE XERC</td></tr><tr><td>SBCC_ECOLI</td><td>44%</td><td>1350</td><td>EXONJCLEASE SBCC</td></tr><tr><td>MCP_BPF41</td><td>48%</td><td>1358</td><td>MAJOR CAPSID PROTEIN (MCP)</td></tr><tr><td>VINT_BPSF6</td><td>26%</td><td>1454</td><td>INTEGRASE</td></tr><tr><td>PIP_LACLA</td><td>96%</td><td>1716</td><td>PHAGE INFECTION PROTEIN</td></tr><tr><td>VG37_BPML5</td><td>48%</td><td>1873</td><td>GENE 37 PROTEIN (GP37)</td></tr><tr><td>VINT_BPL54</td><td>25%</td><td>2005</td><td>INTEGRASE</td></tr></tbody></table>

### BIO14.04 Transposon related functions

59 genes

<table><tbody><tr><td>YI3A_LACJO</td><td>30%</td><td>53</td><td>INSERTION ELEMENT IS1223 HYPOTHETICAL 20.7 KD PROTEIN (ORFA)</td></tr><tr><td>T150_ECOLI</td><td>41%</td><td>53</td><td>PUTATIVE TRANSPOSASE FOR INSERTION SEQUENCE IS150</td></tr><tr><td>TRA4_LACLA</td><td>100%</td><td>54</td><td>TRANSPOSASE FOR INSERTION SEQUENCE ELEMENT IS904</td></tr><tr><td>YI91_SHIDY</td><td>25%</td><td>55</td><td>INSERTION ELEMENT IS911 HYPOTHETICAL 12.7 KD PROTEIN</td></tr><tr><td>TRA9_MYCTU (ORFB)</td><td>30%</td><td>89</td><td>PUTATIVE TRANSPOSASE FOR INSERTION SEQUENCE ELEMENT IS986</td></tr><tr><td>TRA4_LACLA</td><td>39%</td><td>91</td><td>TRANSPOSASE FOR INSERTION SEQUENCE ELEMENT IS904</td></tr></tbody></table>