SII-SWORD/CoKE huggingface dataset:
Stage II sporulation protein M (SpoIIM)
Type: Family

This entry represents the stage II sporulation protein M, which is encoded in a spore formation operon . SpoIIM is one of the three genes (spoIID, spoIIM and spoIIP, ), under the control of sigma E, that have been shown to be essential for the engulfment of the forespore by the mother cell. Their products are involved in degradation of the septal peptidoglycan and mutations in spoIID, spoIIM or spoIIP block sporulation at morphological stage II, prior to the stage of engulfment. These three genes are absolutely conserved (sometimes even duplicated) in all endospore formers .
Sporulation protein YunB (Sporulation_prot_YunB)
Type: Family

This entry represents the sporulation protein YunB. In Bacillus subtilis its expression is controlled by sigmaE. The gene yunB seems to code for a protein involved, at least indirectly, in the pathway leading to the activation of sigmaK. Inactivation of yunB delays sigmaK activation and results in reduced sporulation efficiency .
Stage III sporulation protein AB (Spore_III_AB)
Type: Family

This entry represents the stage III sporulation protein AB, which is encoded in a spore formation operon: spoIIIAABCDEFGH that is under sigma G regulation . A comparative genome analysis of all sequenced genomes of Firmicutes shows that the proteins are strictly conserved among the sub-set of endospore-forming species.
Sporulation protein YtxC (Spore_YtxC)
Type: Family

This uncharacterised protein is one of a number of proteins conserved in all known endospore-forming Firmicutes (low-GC Gram-positive bacteria), including Carboxydothermus hydrogenoformans, and it is not found in non-endospore forming species. It is uniformly distributed in the mother cell cytoplasm in Bacillus subtilis .
RNA polymerase sigma-E type (RNA_pol_sigma-E)
Type: Family

Members of this entry represent the endospore formation-specific sigma factor SigE, also called SpoIIGB and sigma-29. In Bacillus subtilis, sigma-29 is synthesized as a precursor (P31), specifically in the mother cell compartment, and is activated by a cleavage that removes the N-terminal 29 amino acids .

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 .
Sporulation stage IV, protein A (Spore_IV_A)
Type: Family

This entry represents the stage IV sporulation protein A (

), an ATPase that has a role at an early stage in the morphogenesis of the spore coat and is required for proper coat localisation to the forespore . A comparative genome analysis of all sequenced genomes of Firmicutes shows that the proteins are strictly conserved among the subset of endospore-forming species. This protein contains an ATPase domain at the N-terminal, a structural middle domain and a C-terminal domain that is key for targeting SpoIVA to the outer forespore membrane .
Sporulation stage II, protein R (Spore_II_R)
Type: Family

This entry is designated stage II sporulation protein R. A comparative genome analysis of all sequenced genomes of Firmicutes shows that the proteins are strictly conserved among the sub-set of endospore-forming species. SpoIIR is a signalling protein that links the activation of sigma E to the transcriptional activity of sigma F during sporulation .
Sporulation stage V, protein AC (Spore_V_AC)
Type: Family

This entry describes stage V sporulation protein AC; a paralog of stage V sporulation protein AE. Both are proteins found to be present in a species, if and only if, that species is one of the Firmicutes capable of endospore formation, as of the time of the publication of the genome of Carboxydothermus hydrogenoformans. Mutants in spoVAC have a stage V sporulation defect.
Sporulation stage V, protein AE (Spore_V_AE)
Type: Family

This entry describes stage V sporulation protein AE; a paralog of stage V sporulation protein AC. Both are proteins found to be present in a species, if and only if, that species is one of the Firmicutes capable of endospore formation, as of the time of the publication of the genome of Carboxydothermus hydrogenoformans. Mutants in spoVAE have a stage V sporulation defect.
Sporulation protein YtaF (Spore_YtaF)
Type: Family

This entry represents YtaF, which represents a protein family identified, at the time of the publication of the Carboxydothermus hydrogenoformans genome . The phylogenetic profile of the members matches the subset of the Firmicutes capable of forming endospores. These species include Bacillus anthracis, Clostridium tetani, Thermoanaerobacter tengcongensis, and Geobacillus kaustophilus.
Cytochrome o ubiquinol oxidase, subunit III (Cyt_c_ubiqinol_oxidase_su3)
Type: Family

This entry represents subunit 3 (CyoC) of the cytochrome o terminal oxidase complex, which is a component of the aerobic respiratory chain that reacts with oxygen, reducing it to water with the concomitant transport of 4 protons across the membrane. Also known as the cytochrome bo complex, cytochrome o ubiquinol oxidase contains four subunits, two haem B cofactors and a copper atom which is believed to be the oxygen active site. This complex is structurally related to the cytochrome caa3 oxidases which utilise cytochrome c as the reductant and contain haem Acofactors, as well as the intermediate form aa3 oxidases which also react directly with quinones as the reductant.
Cytochrome o ubiquinol oxidase, subunit I (Cyt_c_ubiqinol_oxidase_su1)
Type: Family

This entry represents subunit 1 (CyoB) of the cytochrome o terminal oxidase complex, which is a component of the aerobic respiratory chain that reacts with oxygen, reducing it to water with the concomitant transport of 4 protons across the membrane. Also known as the cytochrome bo complex, cytochrome o ubiquinol oxidase contains four subunits, two haem B cofactors and a copper atom which is believed to be the oxygen active site. This complex is structurally related to the cytochrome caa3 oxidases which utilise cytochrome c as the reductant and contain haem A cofactors, as well as the intermediate form aa3 oxidases which also react directly with quinones as the reductant.
Sporulation stage III, transcriptional regulator SpoIIID (Spore_III_D)
Type: Family

Members of this entry represent the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if, and only if, the species is capable of endospore formation. In Bacillus subtilis SpoIIID is a DNA binding protein that is involved in gene repression as well as activation .
RNA polymerase sigma-K type (RNA_pol_sigma-K)
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 .

The sporulation-specific transcription factor sigma-K (also called sigma-27) is expressed in the mother cell compartment of endospore-forming bacteria such as Bacillus subtilis. Like its close homologue sigma-E (sigma-29, see

), also specific to the mother cell compartment, it must be activated by a proteolytic cleavage.

Note: that in B. subtilis (and apparently also in Clostridium tetani), but not in other endospore forming species such as Bacillus anthracis, the sigK gene is generated by a non-germline (mother cell only) chromosomal rearrangement that recombines coding regions for the N-terminal and C-terminal regions of sigma-K .
Cytochrome o ubiquinol oxidase subunit IV (Cyt_o_ubiqinol_oxidase_su4)
Type: Family

This entry represents subunit 4 (CyoD) of cytochrome o terminal oxidase complex, which is a component of the aerobic respiratory chain that reacts with oxygen, reducing it to water with the concomitant transport of 4 protons across the membrane. Also known as the cytochrome bo complex, cytochrome o ubiquinol oxidase contains four subunits, two haem B cofactors and a copper atom which is believed to be the oxygen active site. This complex is structurally related to the cytochrome caa3 oxidases which utilise cytochrome c as the reductant and contain haem A cofactors, as well as the intermediate form aa3 oxidases which also react directly with quinones as the reductant.
Stage III sporulation protein AD (Spore_III_AD)
Type: Family

Members of this entry represent the uncharacterised protein SpoIIIAD, part of the spoIIIA operon that acts at sporulation stage III as part of a cascade of events leading to endospore formation. The operon is regulated by sigmaG . Note that the start sites of members of this family as annotated tend to be variable; quite a few members have apparent homologous protein-coding regions continuing upstream of the first available start codon.
RNA polymerase sigma-G type (RNA_pol_sigma-G)
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 comprise the Firmicutes lineage endospore formation-specific sigma factor SigG. It is also designated stage III sporulation protein G (SpoIIIG). Members of this entry are closely related to sigma-F (SpoIIAC), another sporulation sigma factor.
Sporulation stage V, protein T (SpoVT)
Type: Family

Members of this protein family are stage V sporulation protein T (SpoVT), a protein of the sporulation/germination program in Bacillus subtilis and related species. The amino-terminal 50 amino acids are nearly perfectly conserved across all endospore-forming bacteria. SpoVT is a DNA-binding transcriptional regulator related to AbrB .
Dipicolinic acid synthetase, subunit B (Dipicolinic_acid_synth_B)
Type: Family

Members of this entry represent the B subunit of dipicolinic acid synthetase, an enzyme that synthesizes a small molecule that appears to confer heat stability to bacterial endospores such as those of Bacillus subtilis. The A and B subunits are together in what was originally designated the spoVF locus for stage V of endospore formation.
Dipicolinic acid synthetase subunit A (Dipicolinic_acid_synth_A)
Type: Family

This predicted Rossman fold-containing protein is the A subunit of dipicolinic acid synthetase as found in most, though not all, endospore-forming low-GC Gram-positive bacteria; it is absent in Clostridium. The B subunit is represented by

. This protein is also known as SpoVFA.
ABC transporter, CydDC cysteine exporter (CydDC-E) family, permease/ATP-binding protein CydD (ABC_transptr_CydD)
Type: Family

The gene pair cydCD encodes an ABC-family transporter in which each gene contains an N-terminal membrane-spanning domain and a C-terminal ATP-binding domain . In Escherichia coli these genes were discovered as mutants which caused the terminal haem-copper oxidase complex cytochrome bd to fail to assemble. Recent work has shown that the transporter is involved in the export of redox-active thiol compounds such as cysteine and glutathione . The linkage to assembly of the cytochrome bd complex is further supported by the conserved operon structure found outside the gammaproteobacteria (cydABCD) containing both the transporter and oxidase genes components.
Sporulation stage III, protein AA (Spore_III_AA)
Type: Family

Proteins in this entry include the stage III sporulation protein AA that is encoded by one of several genes in the spoIIIA locus. This protein is only found in species that are capable of endospore formation.
RNA polymerase sigma-H type (RNA_pol_sigma-H)
Type: Family

Members of this entry represent the RNA polymerase sigma-H factor required for sporulation in endospore-forming bacteria. These proteins are also called Sigma-30 and SigH. Related sequences exist in Listeria, but as Listeria does not form spores the role of these related sigma factors in that genus is in doubt.

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 .
SpoIVB peptidase (SpoIVB)
Type: Family

SpoIVB, the stage IV sporulation protein B of endospore-forming bacteria such as Bacillus subtilis, is a serine proteinase expressed in the spore (rather than mother cell) compartment, that participates in a proteolytic activation cascade for Sigma-K. It appears to be universal among endospore-forming bacteria and occurs nowhere else. The members of this entry belong to MEROPS peptidase family S55 (SpoIVB peptidase, clan PA).

Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes . They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Many families of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence . Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases .

Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base . The geometric orientations of the catalytic residues are similar between families, despite different protein folds . The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) .
Small acid-soluble spore protein, SspJ (SASP_SspJ)
Type: Family

This entry represents a group of small acid-soluble proteins (SASP) from Bacillus species, which are present in spores but not in growing cells. The sspJ gene is transcribed in the forespore compartment by RNA polymerase with the forespore-specific sigmaG. Loss of SspJ causes a slight decrease in the rate of spore outgrowth in an otherwise wild-type background .
Stage II sporulation protein E (SpoII_E)
Type: Family

This entry contains the stage II sporulation protein E (SpoIIE,

), which is a multiple membrane spanning protein with two separable functions. It plays a role in the switch to polar cell division during sporulation and it has phosphatase activity, located in the C-terminal region, which is required to activate sigma-F by dephosphorylating the phosphoprotein SpoIIAA-P . All members of this entry are found in endospore-forming Gram-positive bacteria. A homologous protein, not a member of this entry, is found in the Cyanobacterium-like (and presumably non-spore-forming) photosynthesizer Heliobacillus mobilis.
Cytochrome c oxidase, subunit II (Cyt_c_oxidase_su2)
Type: Domain

This entry contains subunit II (CoxB) of cytochrome c oxidase. Cytochrome c oxidase is the terminal electron acceptor of mitochondria (and one of several possible acceptors in prokaryotes) in the electron transport chain of aerobic respiration. The enzyme couples the oxidation of reduced cytochrome c to the reduction of molecular oxygen to water. This process results in the pumping of four protons across the membrane that are used in the proton gradient powered synthesis of ATP. The oxidase contains two haem A cofactors and three copper atoms as well as other bound ions .
Spore cortex-lytic enzyme SleB (Spore_cortex_SleB)
Type: Family

The entry represents the spore cortex-lytic enzyme SleB from Bacillus subtilis and other Gram-positive, endospore-forming bacterial species. SleB is stored in an inactive form in the spore and activated during germination.
Sporulation stage II, protein D firmicutes (Spore_II_D_firmicutes)
Type: Family

This entry contains the stage II sporulation protein D (SpoIID), which is a protein involved in the endospore formation program. SpoIID is one of the three genes (spoIID, spoIIM and spoIIP, ), under the control of sigma E, that have been shown to be essential for the engulfment of the forespore by the mother cell. Their products are involved in degradation of the septal peptidoglycan - mutations in spoIID, spoIIM or spoIIP block sporulation at morphological stage II, prior to the engulfment stage. These three genes are absolutely conserved (sometimes even duplicated) in all endospore formers .
Sporulation integral membrane protein YlbJ (Spore_IM_YlbJ)
Type: Family

Members of this entry include YlbJ, from Bacillus subtilis. They are found exclusively in the Firmicutes (low-GC Gram-positive bacteria) and are known from studies in B. subtilis to be part of the sigma-E regulon . Mutation leads to a sporulation defect, confirming that members of this entry are involved in sporulation. The protein appears to be universal among endospore-forming bacteria, and in Symbiobacterium thermophilum IAM 14863, there are two ORFs encoding YlbJ that are distant from each other.
Putative transport protein YtvI-like (YtvI-like)
Type: Family

This family includes transport proteins such as sodium-lithium/proton antiporter from Halobacillus and sporulation protein YtvI from Bacillus subtilis, a putative permease . YtvI has extensive hydrophobic regions and is likely to be an integral membrane protein.
Sporulation protein, polysaccharide deacetylase, YlxY (Spore_polysacc_deacetyl_YlxY)
Type: Family

Members of this entry include YlxY, and are related to

, which represents a subset of the polysaccharide deacetylase family found in a species if, and only if, the species forms endospores e.g. Bacillus subtilis or Clostridium tetani. Proteins in this entry are likewise restricted to spore-formers, but are not universally found among endospore-forming species.
Sporulation protein YtfJ (Spore_YtfJ)
Type: Family

Proteins in this entry, exemplified by YtfJ of Bacillus subtilis, are encoded by bacterial genomes if, and only if, the species are capable of endospore formation. YtfJ was confirmed in spores of B. subtilis; it appears to be expressed in the forespore under control of SigF .