SII-SWORD/CoKE huggingface dataset:
Conserved hypothetical protein CHP03034 (CHP03034)
Type: Family

Members of this protein family have been found in several species of gammaproteobacteria, including Yersinia pestis and Yersinia pseudotuberculosis, Xylella fastidiosa, and Escherichia coli (strain UTI89 / UPEC). As many as five members can be found in a single genome; their function is unknown. Recently, it was proposed that members of this family along with members of [

] should be recognised as a putative toxin-antitoxin pair in which [

] is a homologue of Colicin M and [

] acts as its cognate immunity protein .
Kynurenine formamidase, bacteria (Kynurenine_formamidase_bac)
Type: Family

One of several pathways of tryptophan degradation is as follows:

Tryptophan 2,3-dioxygenase (

) uses 02 to convert Trp to L-formylkynurenine.

Kynurenine formamidase (

) hydrolyses the product to L-kynurenine and formate.

Kynureninase (

) hydrolyses L-kynurenine to anthranilate plus alanine.

Members of this entry are predicted bacterial metal-dependent hydrolases. All are supported as kynurenine formamidase (

) by an operon structure in which kynureninase and/or tryptophan 2,3-dioxygenase genes are adjacent. The members from Bacillus cereus, Pseudomonas aeruginosa and Ralstonia metallidurans (strain CH34) have been characterised. An example from Pseudomonas fluorescens is given the gene symbol qbsH instead of kynB because of its role in quinolobactin biosynthesis, which begins with tryptophan. All members of this family should be kynurenine formamidase (

).

Synonym(s): Arylformamidase, N-formylkynurenine formamidase
Tryptophan 2,3-dioxygenase, bacterial (Trp_2-3-dOase_bac)
Type: Family

Members of this family are tryptophan 2,3-dioxygenase, as confirmed by several experimental characterisations, and by conserved operon structure for many of the other members. This enzyme represents the first of a two-step degradation to L-kynurenine, and a three-step pathway (via kynurenine) to anthranilate plus alanine .
Photosystem II CP47 reaction centre protein (PSII_PsbB)
Type: Family

This entry contains the photosystem II P680 chlorophyll A apoprotein, PsbB.

Photosystem II light-harvesting proteins are the intrinsic transmembrane antenna proteins CP43 (PsbC) and CP47 (PsbB) found in the reaction centre of PSII. These polypeptides bind to chlorophyll a and beta-carotene and pass the excitation energy on to the reaction centre . This family also includes the iron-stress induced chlorophyll-binding protein CP43 (IsiA), which evolved in cyanobacteria from a PSII protein to cope with light limitations and stress conditions .
Photosystem II PsbQ, cyanobacteria (PSII_PsbQ_cyanobac)
Type: Family

This entry represents a family of CyanoQ proteins (PsbQ) from cyanobacteria. PsbQ is one of the extrinsic, lumenal subunits of photosystem II (PSII), which stabilise and protect the oxygen-evolving complex. It plays a role in the stability of the oxygen-evolving centre (OEC) on the luminal side of PSII and is required for optimal photoautotrophic growth in the absence of Ca2+ or Cl- .
Photosystem II Psb27, cyanobacteria (PSII_Psb27_cyano_bac)
Type: Family

This entry represents the cyanobacterial Psb27, a small thylakoid lumen-localized protein known to serve as an assembly factor for the biogenesis and repair of the PSII complex . It is closely related to chloroplast Psb27.
Photosystem I protein PsaC (PSI_PsaC)
Type: Family

Members of this family are PsaC, an essential component of photosystem I (PS-I) reaction centre in Cyanobacteria and chloroplasts. This small protein, about 80 amino acids in length, contains two copies of the ferredoxin-like 4Fe-4S binding site and therefore eight conserved Cys residues. This protein is also called photosystem I subunit VII.
Photosystem I reaction center subunit PsaK (PSI_PsaK)
Type: Family

Photosystem I (PSI) is an integral membrane protein complex that uses light energy to mediate electron transfer from plastocyanin to ferredoxin. It is found in the chloroplasts of plants and cyanobacteria. PSI is composed of at least 14 different subunits, two of which are small hydrophobic proteins of about 7 to 9 Kd and evolutionary related, PsaG (also known as PSI-G) and PsaK (also known as PSI-K), both integral membrane proteins. Cyanobacteria contain only PsaK . While cyanobacterial PSI have phycobilisomes to harvest light, eukaryotic PSI have a membrane-imbedded peripheral antenna .

Photosystems I and II occur together in the same sets of organisms. Photosystem I uses light energy to transfer electrons from plastocyanin to ferredoxin, while photosystem II uses light energy to split water and releases molecular oxygen.

This entry represents Photosystem I reaction centre subunit PsaK from Cyanobacteria and Rhodophyta (red algae).
Photosystem I reaction center subunit psaK, plant (PSI_PsaK_pln)
Type: Family

Photosystem I (PSI) is an integral membrane protein complex that uses light energy to mediate electron transfer from plastocyanin to ferredoxin. It is found in the chloroplasts of plants and cyanobacteria. PSI is composed of at least 14 different subunits, two of which are small hydrophobic proteins of about 7 to 9 Kd and evolutionary related, PsaG (also known as PSI-G) and PsaK (also known as PSI-K), both integral membrane proteins. Cyanobacteria contain only PsaK . While cyanobacterial PSI have phycobilisomes to harvest light, eukaryotic PSI have a membrane-imbedded peripheral antenna .

This entry represents Photosystem I reaction center subunit psaK found in plants, predominantly in Streptophytes. PsaK is important for stable interaction and proper function of the antenna . The crystal structure of the plant PSI complex show this protein is closely related to the similar subunit PsaG .
Photosystem I reaction center subunit V (PSI_PsaG)
Type: Family

Photosystem I (PSI) is an integral membrane protein complex that uses light energy to mediate electron transfer from plastocyanin to ferredoxin. It is found in the chloroplasts of plants and cyanobacteria. PSI is composed of at least 14 different subunits, two of which are small hydrophobic proteins of about 7 to 9 Kd and evolutionary related, PsaG (also known as PSI-G) and PsaK (also known as PSI-K), both integral membrane proteins. Cyanobacteria contain only PsaK . While cyanobacterial PSI have phycobilisomes to harvest light, eukaryotic PSI have a membrane-imbedded peripheral antenna .

This protein family represents Photosystem I reaction center subunit V (PsaG) found in plants, predominantly in Streptophytes. In Arabidopsis thaliana, PsaG is involved in the binding dynamics of plastocyanin to PSI, in the stability of the PSI complex and in light-harvesting . The crystal structure of the plant PSI complex show this protein is closely related to the similar subunit PsaK .
Photosynthetic complex assembly protein PuhC (PuhC)
Type: Family

PuhC regularly is found encoded near PuhA, which encodes a component of the photosynthetic reaction centre, among other genes associated with photosynthesis . Members of this entry are predominantly found in alpha- and betaproteobacteria.
Photosynthetic complex assembly protein 2, putative (Photo_alph_chp2)
Type: Family

This uncharacterised protein family was identified, by the method of partial phylogenetic profiling, as having a matching phylogenetic distribution to that of the photosynthetic reaction centre of the alpha-proteobacterial type. It is nearly always encoded near other photosynthesis-related genes, including puhA.
Magnesium-chelatase 30 kDa subunit (BchO)
Type: Family

This family represents a group of proteins found in bacteria that encode anoxygenic photosynthetic systems similar to that found in Rhodobacter capsulatus (Rhodopseudomonas capsulata), including Magnesium-chelatase 30 kDa subunit (BchO). Members of this entry belong to the α/β fold family of hydrolases.

Co-occurrence with 2-vinyl bacteriochlorophyllide hydratase (

) is almost perfect, suggesting a role in the biosynthesis of a specific form of chlorophyll. It is typically encoded immediately downstream of protoporphyrin IX magnesium chelatase subunits BchI and BchD, and have been designated BchO. Surprisingly, member protein RPA1511 from Rhodopseudomonas palustris (

) was shown to be able to depolymerise polylactic acid (PLA) plastic .
Photosystem I PsaO (PSI_PsaO)
Type: Family

Members of this family are the PsaO protein of photosystem I. This protein is found in chloroplasts but not in Cyanobacteria.
Protein Thf1 (Thf1)
Type: Family

Thf1 protein (also known as Psb29) is found in Cyanobacteria and in the plastids of vascular plants. They may function in the biogenesis of Photosystem II complexes .

In Synechocystis it was isolated and partially sequenced from purified photosystem II (PS II). Deletion of psb29 in Synechocystis 6803 results in slower growth rates under high light intensities, increased light sensitivity, and lower PSII efficiency, without affecting the PSII core electron transfer activities .
Phage infection protein, YhgE, N-terminal (Phage_infect_YhgE_N)
Type: Domain

This entry represents the N-terminal domain of a family of multiple membrane-spanning proteins from Gram-positive bacteria. One member was shown to be a host protein essential for phage infection, so many members of this family are called "phage infection protein". A separate entry,

, represents the conserved C-terminal domain. The domains are separated by regions highly variable in both length and sequence, often containing extended heptad repeats as described in

.
Phage infection protein, YhgE, C-terminal (Phage_infect_YhgE_C)
Type: Domain

This entry contains proteins that have the C-terminal domain of a family of multiple membrane-spanning proteins of Gram-positive bacteria. One member was shown to be a host protein essential for phage infection, so many members of this family are called "phage infection protein". A separate model,

, represents the conserved N-terminal domain. The domains are separated by regions highly variable in both length and sequence, often containing extended heptad repeats as described in

.
Sortase B cell surface sorting signal (Sortase_SrtB_target)
Type: Domain

Two different classes of sorting signal, both analogous to the sortase A signal LPXTG, can be recognised by the sortase, SrtB. These are given as NXZTN and NPKXZ. Proteins sorted by this class of sortase are less common than the sortase A and LPXTG system. This entry describes a number of cell surface proteins regions from Gram-positive bacteria, having a C-terminal region that appears to be sortase B (SrtB) sorting signals.
Sortase B signal domain, QVPTGV class (Sortase_SrtB_sig_QVPTGV)
Type: Domain

This entry represents an unusual sorting signal, recognised by a member of the sortase SrtB family rather than by the housekeeping sortase, SrtA.
Conserved hypothetical protein CHP03067, planctomycetes (CHP03067_Planctomycetes)
Type: Domain

This domain occurs in several species, mostly from the Planctomycetes division of the bacteria. It has expanded into a paralogous family of at least twenty-five members in Gemmata obscuriglobus UQM 2246. This family appears related to

, which has also expanded into a large paralogous family in G. obscuriglobus.
Sortase B signal domain, NPQTN class (Sortase_SrtB_sig_NPQTN)
Type: Domain

This entry represents one of the rare sortase signals, recognised by sortase B (SrtB) rather than by the housekeeping-type SrtA class sortase. This sequence, beginning NPQTN, shows little similarity to several other SrtB substrates.
Photosystem II S4 (PSII_S4)
Type: Family

Members of this protein family are about 265 residues long and each contains an S4 RNA-binding domain of about 48 residues. The member from the Cyanobacterium, Synechocystis sp. (strain PCC 6803), was detected as a novel polypeptide in a highly purified preparation of active photosystem II . The phylogenetic distribution, including Cyanobacteria and Arabidopsis, supports a role in photosystem II, although the high bit score cut-off for this model excludes similar sequences in non-photosynthetic organisms such as Carboxydothermus hydrogenoformans, a Gram-positive bacterium.
Transcription regulator, HipB-like (Tscrpt_reg_HipB-like)
Type: Family

Members of this family belong to a clade of helix-turn-helix DNA-binding proteins. Members are similar in sequence to the HipB protein of Escherichia coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.
HipA, N-terminal subdomain 1 (HipA_N1)
Type: Domain

HipA is a bacterial serine/threonine protein kinase involved in multidrug tolerance. In HipA, a P loop motif forms a central strand that disrupts the N-terminal β-sheet region, leading to the creation of two N-subdomains . This entry represents subdomain 1, and hits the N-terminal region of HipA and its homologues.
Peptide chain release factor homolog (PrfH)
Type: Family

Members of this protein family are bacterial proteins homologous to peptide chain release factors 1 (RF-1, product of the prfA gene), and 2 (RF-2, product of the prfB gene). This class I release factor is always found as the downstream gene of a two-gene operon. PrfH acts on 70S ribosomes with specific damage to their decoding centre. The PrfH-RtcB2 pair restores growth in the presence of ribotoxins that specifically create this damage .
RNA-splicing ligase RtcB2 (RtcB2)
Type: Family

This family includes RNA-splicing ligase RtcB2 from Escherichia coli and similar sequences mainly found in bacteria. RtcB2 is a GTP-dependent RNA ligase involved in rRNA repair that does not repair damaged tRNA. In vivo the PrfH(

)-RtcB2 pair restores growth in the presence of ribotoxins that specifically create this damage .
PQQ-dependent membrane bound dehydrogenase (PQQ_mDH)
Type: Family

This bacterial subfamily of enzymes belongs to the dehydrogenase family with pyrroloquinoline quinone (PQQ) as cofactor, and is the only subfamily that is bound to the membrane. It includes glucose dehydrogenase, which converts D-glucose to D-glucono-1,5-lactone in a reaction that is coupled with the respiratory chain in the periplasmic oxidation of sugars and alcohols in Gram-negative bacteria . It also includes glycerol dehydrogenase SldA .
PQQ-dependent dehydrogenase, methanol/ethanol family (PQQ_MeOH/EtOH_DH)
Type: Family

This entry represents PQQ-dependent dehydrogenases from the methanol/ethanol family, which has a phylogenetic distribution very similar to that coenzyme PQQ biosynthesis enzymes, as shown by partial phylogenetic profiling. Genes in this family often are found adjacent to the PQQ biosynthesis genes themselves. An unusual, strained disulphide bond between adjacent Cys residues contributes to PQQ-binding, as does a Trp residue that is part of a PQQ enzyme repeat (see

). Characterised members include the dehydrogenase subunit of a membrane-anchored, three subunit alcohol (ethanol) dehydrogenase of Gluconobacter oxydans (Gluconobacter suboxydans), a homodimeric ethanol dehydrogenase in Pseudomonas aeruginosa, and the large subunit of an α2/β2 heterotetrameric methanol dehydrogenase in Methylobacterium extorquens.
Conserved hypothetical protein CHP03076, glycine cleavage (CHP03076_Gly-cleavage)
Type: Family

The H protein (GcvH) of the glycine cleavage system shuttles the methylamine group of glycine from the P protein to the T protein. Most Chlamydia lack the P and T proteins, and have a single homologue of GcvH that appears deeply split from canonical GcvH in molecular phylogenetic trees. The proteins in this entry are only found in the Chlamydiae, and always are part of a two-gene operon, upstream of the homologue of GcvH. Its function is unknown.
Glycine cleavage system protein H-related, Chlamydia (GcvH_Chlamydia)
Type: Family

The H protein (GcvH) of the glycine cleavage system shuttles the methylamine group of glycine from the P protein to the T protein. Most Chlamydia lack the P and T proteins, and have a single homologue of GcvH that appears deeply split from canonical GcvH in molecular phylogenetic trees. This protein family represents the Chlamydial GcvH homologue, which is always seen as part of a two-gene operon, downstream of a member of the uncharacterised protein family

. The function of the proteins in this entry are unknown.
Methylmalonyl-CoA epimerase (MeMalonyl-CoA_epimerase)
Type: Family

Members of this protein family are the enzyme methylmalonyl-CoA epimerase (

), also called methylmalonyl-CoA racemase. This enzyme converts (2R)-methylmalonyl-CoA to (2S)-methylmalonyl-CoA, which is then a substrate for methylmalonyl-CoA mutase (

). It is known in bacteria, archaea, and as a mitochondrial protein in animals. It is closely related to lactoylglutathione lyase (

), which is also called glyoxylase I, and is also a homodimer.
AbrB duplication (AbrB_dup)
Type: Domain

The entry describes a hydrophobic sequence region that is duplicated to form the AbrB protein of Escherichia coli (not to be confused with a Bacillus subtilis protein with the same gene symbol). In some species, notably the Cyanobacteria and Thermus thermophilus, proteins consist of a single copy rather than two copies. The member from Pseudomonas putida, PP_1415 (

), was suggested to be an ammonia monooxygenase characteristic of heterotrophic nitrifiers, based on an experimental indication of such activity in the organism and a glimmer of local sequence similarity between parts of the P. putida protein and an instance of the AmoA protein (

) from Nitrosomonas europaea ; we do not believe the sequence similarity to be meaningful. The member from E. coli (b0715, ybgN) appears to be the largely uncharacterised AbrB (aidB regulator) protein of E. coli , although we did not manage to trace the origin of association of the article to the sequence.
Maleylpyruvate isomerase, mycothiol-dependent enzyme (Maleyloyr_isom)
Type: Family

This protein family pulls together several groups of proteins, each very different from the others. They share in common three conserved regions. The first is a region of about 38 amino acids, nearly always at the N terminus of a protein. This region has a bulky hydrophobic residue, usually Trp, at position 29, and a His residue at position 37 that is invariant, so far, in over 150 instances. The second conserved region has a motif [DE]xxxHxxD. The third conserved region contains a hydrophobic patch and a well-conserved Arg residue. Most examples are found in the Actinobacteria, including the genera Mycobacterium, Corynebacterium, Streptomyces, Nocardia, Frankia, etc. The pattern of near-invariant residues against a backdrop of extreme sequence divergence suggests enzymatic activity and conservation of active site residues, and therefore, members of this entry have been described as maleylpyruvate isomerase, mycothiol-dependent enzymes .
Conserved hypothetical protein CHP03084 (CHP03084)
Type: Family

This family belongs to the larger set of enzymes modeled by

. Members are found primarily in the Actinobacteria (Mycobacterium, Streptomyces, etc.). The family of metal-binding proteins is uncharacterised.
Conserved hypothetical protein CHP03085 (CHP03085)
Type: Family

This family belongs to the larger set of probable enzymes defined by

. Members are found primarily in the Actinobacteria (Mycobacterium, Streptomyces, etc.). The family of metal-binding proteins is uncharacterised.
Conserved hypothetical protein CHP03086 (CHP03086)
Type: Family

This family belongs to the larger set of probable enzymes defined by

. Members are found primarily in the Actinobacteria (Mycobacterium, Streptomyces, etc.). The family of metal-binding proteins is uncharacterised.
Sugar transferase, PEP-CTERM, Stp1 (Sugar_tfrase_PEP-CTERM_Stp1)
Type: Family

Members of this family contain a glycosyl transferase group 1 domain. Nearly all are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria. In particular, these transferases are found proximal to a particular variant of exosortase, EpsH1, which appears to travel with a conserved group of genes summarized by

. The nature of the sugar transferase reaction catalysed by members of this clade is unknown and may conceivably be variable with respect to substrate by species, but we hypothesize a conserved substrate.
Sugar transferase, PEP-CTERM, Stp2 (Sugar_tfrase_PEP-CTERM_Stp2)
Type: Family

Members of this family contain a glycosyl transferase group 1 domain. Nearly all are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria. In particular, these transferases are found proximal to a particular variant of exosortase, EpsH1, which appears to travel with a conserved group of genes summarized by

. The nature of the sugar transferase reaction catalysed by members of this clade is unknown and may conceivably be variable with respect to substrate by species, but we hypothesize a conserved substrate.
Rv3268-like (Rv3268)
Type: Family

This protein family is found, so far, only in the Actinobacteria (Streptomyces, Mycobacterium, Corynebacterium, Nocardia, Propionibacterium, etc.) and never more than one to a genome. Members show twilight-level sequence similarity to family of AMP-binding enzymes described by

.
Small acid-soluble spore protein, thioredoxin-like (SASP_thioredoxin-like)
Type: Family

This protein family is restricted to a subset of endospore-forming bacteria such as Bacillus subtilis, all of which are in the Firmicutes (low-GC Gram-positive) lineage. Although previously designated tlp (thioredoxin-like protein), the B. subtilis protein was shown to be a minor small acid-soluble spore protein SASP, unique to spores. The motif E[VIL]XDE near the C terminus probably represents at a germination protease cleavage site.
Small, acid-soluble spore protein I (SspI)
Type: Family

This protein family is restricted to a subset of endospore-forming bacteria, such as Bacillus subtilis, all of which are in the Firmicutes (low-GC Gram-positive) lineage. It is a minor SASP (small, acid-soluble spore protein) designated SspI. The gene in B. subtilis was previously designated ysfA.
Small acid-soluble spore protein, SspL (SASP_SspL)
Type: Family

This protein family is restricted to a subset of endospore-forming bacteria such as Bacillus subtilis, all of which are in the Firmicutes (low-GC Gram-positive) lineage. It is a minor SASP (small, acid-soluble spore protein) designated SspL .
Nitrosocyanin (Nitrosocyanin)
Type: Family

Nitrosocyanin, as described from the obligate chemolithoautotroph Nitrosomonas europaea, is a red copper protein of unknown function with sequence similarity to a number of blue copper redox proteins .

The structure of nitrosocyanin is a trimer of single domain cupredoxins . Nitroscocyanin may mediate electron transfer. It could have a novel role as a nitric oxide dehydrogenase or a nitric oxide reductase in the oxidation of ammonia .
Conserved hypothetical protein CHP03097, O-antigen ligase-related (CHP03097O-antigen_lig-rel)
Type: Family

These proteins in this entry all have multiple transmembrane domains and are related to or are members of the O-antigen ligase family. This group is associated with genomes and usually genomic contexts containing elements of the exosortase/PEP-CTERM protein export system , specifically the type 1 variety of this system described by

.
Acyl-CoA ligase (AMP-forming), exosortase system type 1 associated (AcylCoA_ligase_PEP_1)
Type: Family

This group of proteins contains an AMP-binding domain associated with acyl CoA-ligases. These proteins are generally found in genomes containing the exosortase/PEP-CTERM protein export system , specifically the type 1 variant of this system described by

. When found in this context they are invariably present next to a decarboxylase enzyme. A number of sequences from Burkholderia species are also present in this entry, but the genomic context is obviously different. The hypothesis of a constant substrate for this family is only strong where the exosortase context is present.