SII-SWORD/CoKE huggingface dataset:
Sporulation protein YhbH (Spore_YhbH)
Type: Family

Proteins in this entry, typified by YhbH from Bacillus subtilis, are found in the genomes of nearly every endospore-forming bacterium, and in no other genomes. The gene in B. subtilis was shown to be a member of the sigma-E regulon, with mutation leading to a sporulation defect .
Sporulation protein YpjB (Spore_YpjB)
Type: Family

Proteins in thie entry, typified by YpjB, are restricted to a subset of the endospore-forming bacteria which includes Bacillus species, but not species. In Bacillus subtilis, ypjB was found to be part of the sigma-E regulon . Sigma-E is a sporulation sigma factor that regulates expression in the mother cell compartment. Null mutants of ypjB show a sporulation defect, but this gene is not, however, a part of the endospore formation minimal gene set.
Sporulation stage V, protein K (Spore_V_K)
Type: Family

Proteins in this entry include the stage V sporulation protein K (SpoVK), a close homologue of the Rubisco expression protein CbbX (

), and are members of an ATPase family associated with various cellular activities. These proteins are strictly limited to bacterial endospore-forming species, but are not found universally among members of this group; they are missing from the Clostridium species.
Quinol oxidase subunit I (QoxB)
Type: Family

This entry represents subunit I of the aa3-type quinone oxidase, one of several terminal oxidases found in bacteria . This complex couples the oxidation of reduced quinones to the reduction of molecular oxygen to water, and the pumping of protons to form a proton gradient utilised for ATP production. aa3-type oxidases contain two haem A cofactors as well as copper atoms at the active site.
N-acetylmuramoyl-L-alanine amidase CwlD (Spore_CwlD)
Type: Family

This entry represents the germination-specific N-acetylmuramoyl-L-alanine amidase CwlD. CwlD from Bacillus subtilis is required, along with the putative deactylase PdaA, to make muramic delta-lactam, a novel peptidoglycan constituent found only in bacterial endospores. CwlD mutants show a germination defect.
Peptidoglycan-N-acetylmuramic acid deacetylase PdaA (Spore_PdaA)
Type: Family

Muramic delta-lactam is an unusual constituent of peptidoglycan, found only in bacterial spores, in the peptidoglycan wall or spore cortex. This entry represents a subset of the larger polysaccharide deacetylase family that is specifically involved in delta-lactam biosynthesis. PdaA from Bacillus subtilis acts immediately after CwlD, an N-acetylmuramoyl-L-alanine amidase and performs a de-N-acetylation . PdaA may also perform the subsequent transpeptidation that leads to lactam ring formation, as heterologous expression in Escherichia coli of CwlD and PdaA together is sufficient for delta-lactam production .
RNA polymerase sigma-F type (RNA_pol_sigma-F)
Type: Family

The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes.

With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors .

The plastids of higher plants originating from an ancestral cyanobacterial endosymbiont also contain sigma factors that are encoded by a small family of nuclear genes. All plastid sigma factors belong to the superfamily of sigmaA/sigma70 and have sequences homologous to the conserved regions 1.2, 2, 3, and 4 of bacterial sigma factors .

Members of this entry represent RNA polymerase sigma factor F. Within the Firmicutes, Sigma-F is specifically, and universally, a component of the endospore formation program, and is expressed in the forespore to turn on the expression of dozens of genes. It is closely related to sigma-G, which is also expressed in the forespore.
Anti-sigma F factor antagonist (Anti-sigma_F_ant)
Type: Family

This represents the anti-sigma F factor antagonist, also known as stage II sporulation protein AA. This protein is universally conserved in the endospore-forming bacteria, all of which belong to the Firmcutes.
Sporulation protein YlmC/YmxH (Spore_YlmC/YmxH)
Type: Family

Proteins in this entry belong to the broader family of PRC-barrel domain proteins, but are found only in endospore-forming bacteria within the Firmicutes (low-GC, Gram-positive bacteria). Most species encode two of these proteins, though their function is unknown. In Bacillus subtilis, which encodes YlmC and YmxH, YmxH is strongly induced by the mother cell-specific sigma-E factor .
Sporulation protein YpeB, PepSY1 and PepSY2 domains (YpeB_PepSY1-2)
Type: Domain

Proteins in this entry include the sporulation protein YpeB from Bacillus subtilis. YpeB and the spore-cortex-lytic enzyme SleB are required for normal germination . These proteins are restricted to endospore-forming species in the Firmicutes lineage of bacteria, and have been found in all such species to date except Clostridium perfringens. This protein is essential in stabilising SleB enzyme in Bacillus spores and may regulate its activity during spore germination . It consists of three tandemly repeated PepSY domains at the C-terminal, being the first two (PepSY1 and PepSY2) represented in this entry and the last one in

.
Regulatory protein, YteA family (YteA)
Type: Family

This entry contains predicted regulatory proteins that are found in nearly every species of the endospore-forming bacteria within the Firmicutes (low-GC Gram-positive bacteria), with the exception of Clostridium perfringens. Some (but not all) of these proteins contain an unusual DksA/TraR C4-type zinc finger, where only one of the four key Cys residues is conserved. All members of this protein family share an additional C-terminal domain.
Cytochrome c oxidase, subunit I bacterial type (Cyt_c_oxidase_su1_bac)
Type: Family

This entry represents the bacterial-type cytochrome c oxidase subunit I (CtaD, CoxA, CaaA). Cytochrome c oxidase is the component of the respiratory chain that catalyses the reduction of oxygen to water. Subunits I, II and III form the functional core of the enzyme complex. Subunit I is the catalytic subunit of the enzyme. Electrons originating in cytochrome c are transferred via the copper A centre of subunit II and haem A of subunit I to the bimetallic centre formed by haem A3 and copper B. This cytochrome c oxidase shows proton pump activity across the membrane in addition to the electron transfer activity. In the bacilli an apparent split (paralogism) has created a sister clade (

) encoding subunits (QoxA) of the aa3-type quinone oxidase complex which reacts directly with quinones, bypassing the interaction with soluble cytochrome c.
Prespore-specific transcriptional regulator RsfA-like (RsfA-like)
Type: Family

This entry represents a set of transcription factors found in some endospore-forming bacteria within the Firmicutes (low-GC Gram-positive bacteria), including Prespore-specific transcriptional regulator RsfA and Sporulation-specific transcriptional regulator GerR from Bacillus subtilis. In some species these proteins are encoded multiple times. The expression of RsfA, previously known as YwfN, is controlled by sigma factor F, and it seems to improve the efficiency of sporulation by fine-tuning the expression of genes in the sigma F regulon, particularly the timing of their expression . It also negatively regulates spoIIR and its own synthesis. GerR, its paralog, previously known as YlbO, controls genes of both sigma-E and sigma-K regulons, acting alone on some genes and in conjunction with SpoIIID or GerE on others and regulates, directly or indirectly, the expression of genes encoding coat proteins . A highly variable linker region separates two very strongly conserved sequence regions within the protein.
RNA polymerase sigma-I type (RNA_pol_sigma-I)
Type: Family

The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes.

With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors .

The plastids of higher plants originating from an ancestral cyanobacterial endosymbiont also contain sigma factors that are encoded by a small family of nuclear genes. All plastid sigma factors belong to the superfamily of sigmaA/sigma70 and have sequences homologous to the conserved regions 1.2, 2, 3, and 4 of bacterial sigma factors .

This entry represents the transcription factor Sigma-I. This protein is found in endospore-forming species in the Firmicutes lineage of bacteria, such as Bacillus subtilis, but is not universally present among such species. Sigma-I was shown to be induced by heat shock in B. subtilis and is suggested by its phylogenetic profile to be connected to the program of sporulation .
Sporulation stage III, protein AF (Spore_III_AF)
Type: Family

This family represents the stage III sporulation protein AF (SpoIIIAF) of the bacterial endospore formation program, which exists in some but not all members of the Firmicutes (formerly called low-GC Gram-positives). These proteins have the typical RBM fold conserved in T3SS/flagellar systems [1]. The RBM fold of SpoIIIAF contains two unique features, extended N-terminal helix, associated with multimerization and an insertion at a loop region that can adopt two distinct conformations .
Quinol oxidase subunit III (QoxC)
Type: Family

This entry encodes subunit III of the aa3-type quinone oxidase (QoxC), a multi-chain transmembrane protein located in the cell membrane and one of several aerobic bacterial terminal oxidases . This complex couples oxidation of reduced quinones to the reduction of molecular oxygen to water, and the pumping of protons to form the proton gradient utilised for ATP production. aa3-type oxidases contain two haem A cofactors as well as copper atoms at the active site.

Quinone oxidases feature four subunits in contrast to the 13 subunit bovine cytochrome c oxidase (CcO). Subunits I, II and III of ubiquinol oxidase are homologous to the corresponding subunits in bovine CcO . Although not required for catalytic activity, subunit III appears to be involved in assembly of the multimer complex .
Sporulation lipoprotein YhcN/YlaJ (Spore_lipoprot_YhcN/YlaJ)
Type: Family

This entry contains YhcN and YlaJ, which are predicted lipoproteins that have been detected as spore proteins but not vegetative proteins in Bacillus subtilis . YlaJ and YhcN contribute to the efficiency of spore germination in Bacillus subtilis . Both appear to be expressed under control of the RNA polymerase sigma-G factor. The YlaJ-like members of this family have a low-complexity, strongly acidic, 40-residue C-terminal domain.
Spore coat assembly protein SafA (Spore_coat_assembly_SafA)
Type: Domain

This entry represents a subset of the LysM domain of about 40 residues long which is found in a variety of enzymes involved in bacterial cell wall degradation , and which may have a general peptidoglycan binding function. Proteins containing this domain include SafA of Bacillus subtilis, which is a protein found at the interface of the spore cortex and spore coat, and which is dependent on SpoVID for its localization. This domain is generally found towards the N terminus of these proteins. The C-terminal region of these proteins are more variable and may contain blocks of 12-residue and 13-residue repeats, or an SCP-like domain (

).
Sporulation stage V protein B (Spore_V_B)
Type: Family

This entry represents SpoVB, which is the stage V sporulation protein B of the bacterial endospore formation program in Bacillus subtilis and various other Firmcutes . It is nearly universal among endospore-formers. Paralogs with high sequence similarity to SpoVB exist, such as YkvU from B. subtilis and a number Clostridium proteins, but they are excluded from this entry.
Quinol oxidase subunit IV (QoxD)
Type: Family

This entry represents subunit IV of the aa3-type quinone oxidase (QoxD), one of several bacterial terminal oxidases . This complex couples oxidation of reduced quinones to the reduction of molecular oxygen to water, and the pumping of protons to form a proton gradient utilised for ATP production. aa3-type oxidases contain two haem A cofactors as well as copper atoms in the active site.
Sporulation protease LonB (Spore_LonB)
Type: Family

This entry represents LonB, a paralog of the ATP-dependent protease La (LonA,

). LonB proteins are unassigned peptidases belonging to the MEROPS peptidase family S16 (lon protease family, clan SJ) and are found strictly, and almost universally, in endospore-forming bacteria. This protease was shown, in Bacillus subtilis, to be expressed specifically in the forespore during sporulation, under control of sigmaF . The lonB gene, despite being located immediately upstream of lonA, was shown to be monocistronic. LonB appears to be involved in the post-translation control of sigmaH, but lonB mutation did not produce an obvious sporulation defect under the conditions tested . Note that additional paralogs of LonA and LonB occur in the Clostridium lineage and these are excluded from this entry.
Sporulation protease LonC (Spore_LonC)
Type: Family

Members of this protein family resemble the widely distributed ATP-dependent protease La, also called Lon and LonA. They resemble even more closely LonB, which is a LonA paralog found in genomes of species capable of endospore formation (such as Bacillus subtilis, Clostridium tetani, and select other members of the Firmicutes) and expressed specifically in the forespore compartment. Members of this family are restricted to a subset of spore-forming species, and are very likely to participate in the program of endospore formation. We propose the designation LonC.
Spore coat protein YsxE (Spore_coat_YsxE)
Type: Family

Members of this entry, which includes the Bacillus subtilis protein YsxE, are found only in the family Bacillaceae, part of the the endospore-forming group within the Firmicutes. As a rule, the ysxE gene is found immediately downstream of spoVID, a gene necessary for spore coat assembly. The protein has been shown to be part of the spore coat and is a homologue of CotS (

).
Spore coat putative kinase YutH (Spore_coat_YutH)
Type: Family

This entry, represented by the Bacillus subtilis protein YutH, is found only in the family Bacillaceae, part of the endospore-forming group within the Firmicutes. YutH has been shown to be involved in spore coat assmebly . Proteins in this entry are homologous to CotS (

).
Spore coat protein CotS (Spore_coat_CotS)
Type: Family

Members of this entry include the spore coat proteins CotS and YtaA from Bacillus subtilis and, from other endospore-forming bacteria, homologues that are more closely related to these two than to the spore coat proteins YutH (

) and YsxE (

). The CotS family is more broadly distributed than YutH or YsxE, but still is not universal among spore-formers.
Sporulation stage VI, protein D (Spore_VI_D)
Type: Family

This entry represents SpoVID, the stage VI sporulation protein D, which is restricted to endospore-forming bacteria, all of which are found among the Firmicutes. It is widely distributed but not quite universal in this group. Between well-conserved N-terminal and C-terminal domains is a poorly conserved, low-complexity region of variable length, rich in glutamic acid. SpoVID is involved in spore coat assembly in the mother cell compartment late in the process of sporulation.
Cytochrome c oxidase, subunit IV bacillaceae (Cyt_c_oxidase_su4_bacillaceae)
Type: Family

This entry represents a small clade of cytochrome oxidase subunit IV sequences found in the Bacillaceae.
CAP domain, YkwD-like (CAP_domain_YkwD-like)
Type: Domain

The cysteine-rich secretory proteins, antigen 5, and pathogenesis-related 1 proteins (CAP) superfamily proteins are found in a wide range of organisms, including prokaryotes and non-vertebrate eukaryotes , The nine subfamilies of the mammalian CAP superfamily include: the human glioma pathogenesis-related 1 (GLIPR1), Golgi associated pathogenesis related-1 (GAPR1) proteins, peptidase inhibitor 15 (PI15), peptidase inhibitor 16 (PI16), cysteine-rich secretory proteins (CRISPs), CRISP LCCL domain containing 1 (CRISPLD1), CRISP LCCL domain containing 2 (CRISPLD2), mannose receptor like and the R3H domain containing like proteins. Members are most often secreted and have an extracellular endocrine or paracrine function and are involved in processes including the regulation of extracellular matrix and branching morphogenesis, potentially as either proteases or protease inhibitors; in ion channel regulation in fertility; as tumour suppressor or pro-oncogenic genes in tissues including the prostate; and in cell-cell adhesion during fertilisation. The overall protein structural conservation within the CAP superfamily results in fundamentally similar functions for the CAP domain in all members, yet the diversity outside of this core region dramatically alters the target specificity and, thus, the biological consequences . The Ca2-chelating function would fit with the various signalling processes (e.g. the CRISP proteins) that members of this family are involved in, and also the sequence and structural evidence of a conserved pocket containing two histidines and a glutamate. It also may explain how

blocks the Ca2 transporting ryanodine receptors.

This entry represents a subgroup of the CAP domains found only in bacteria capable of endospore formation. Proteins containing this domain include YkwD of Bacillus subtilis. This domain is generally found at the C-terminal region of these proteins, while the N-terminal region sometimes contains a domain homologous to the spore coat assembly protein SafA (

).
Sulphite reductase, subunit A (Sulphite_reductase_A)
Type: Family

This entry represents subunit A, one of the three subunits of the anaerobic sulphite reductase of Salmonella, and close homologues from various Clostridium species, where the three-gene neighbourhood is preserved. Two such gene clusters are found in Clostridium perfringens, but it may be that these sets of genes correspond to the distinct assimilatory and dissimilatory forms seen in Clostridium pasteurianum. Note that any one of these enzymes may have secondary substrates such as NH2OH, SeO3(2-), and SO3(2-). Heterologous expression of the anaerobic sulphite reductase of Salmonella confers on Escherichia coli the ability to produce hydrogen sulphide gas from sulphite.
Sulphite reductase, subunit B (Sulphite_reductase_B)
Type: Family

This entry represents subunit B, one of the three subunits of the anaerobic sulphite reductase of Salmonella, and close homologues from various Clostridium species, where the three-gene neighbourhood is preserved. Two such gene clusters are found in Clostridium perfringens, but it may be that these sets of genes correspond to the distinct assimilatory and dissimilatory forms seen in Clostridium pasteurianum. Note that any one of these enzymes may have secondary substrates such as NH2OH, SeO3(2-), and SO3(2-). Heterologous expression of the anaerobic sulphite reductase of Salmonella confers on Escherichia coli the ability to produce hydrogen sulphide gas from sulphite.
Sulphite reductase, subunit C (Sulphite_reductase_C)
Type: Family

This entry represents subunit C, one of the three subunits of the anaerobic sulphite reductase of Salmonella, and close homologues from various Clostridium species, where the three-gene neighbourhood is preserved. Two such gene clusters are found in Clostridium perfringens, but it may be that these sets of genes correspond to the distinct assimilatory and dissimilatory forms seen in Clostridium pasteurianum. Note that any one of these enzymes may have secondary substrates such as NH2OH, SeO3(2-), and SO3(2-). Heterologous expression of the anaerobic sulphite reductase of Salmonella confers on Escherichia coli the ability to produce hydrogen sulphide gas from sulphite.
HAF repeat (HAF_rpt)
Type: Repeat

This repeat is approximately 40 amino acids in length and the spacing between repeats is usually is four residues. Proteins generally have a least two tandem copies, and can have as many as seven. This repeat is named after a conserved tripeptide motif, HAF, found in most of the proteins. Some proteins containing the repeat are found in species with no outer membrane (archaea and Gram-positive bacteria) while others have C-terminal autotransporter domains that suggest that the repeat region is transported across the outer membrane. This repeat seems likely to be associated with extracellular proteins.
Methanolan biosynthesis EpsI (Methanolan_biosynth_EpsI)
Type: Domain

This entry represents a domain that covers the whole protein sequence in EpsI from Methylobacillus sp. 12S. EpsI is encoded immediately downstream of the multiple-membrane-spanning putative transporter EpsH, and is predicted to be a periplasmic protein involved in, but not required for, expression of the exopolysaccharide methanolan. In a number of other species, protein homologues to EpsI are encoded either next to epsH or, more often, combined in a fused gene .