SII-SWORD/CoKE huggingface dataset:
Ethanolamine utilization, putative (Eut_put)
Type: Family

Proteins in this entry are encoded in operons for the polyhedral organelle-based degradation of ethanolamine. This family is not found in proteobacterial species, which otherwise have the same suite of genes in the eut operon. Proteobacteria have two genes that are not found in other species which encode proteins which may complement this family's function -a phosphotransacetylase (

), and EutJ (

) which is of unknown function.
Flagellin/pilin, N-terminal site, archaea (Flagellin/pilin_N_arc)
Type: Conserved_site

This entry describes a hydrophobic N-terminal conserved site of archaeal flagellins and pilins . This site is directly analogous to the bacterial N-terminal methylation site

, which has a cleavage motif resembling G^FxxxE followed by a strongly hydrophobic sequence. The bacterial domain is a recognition site for cleavage and methylation, found in pilus components, competence proteins and type II secretion proteins. This archaeal domain may play a similar role.
ATPase, type IV, pilus assembly, PilB (ATPase_typ4_pilus-assembl_PilB)
Type: Family

This model describes a protein involved in type IV pilus biogenesis designated PilB in Pseudomonas aeruginosa but PilF in Neisseria gonorrhoeae; the more common usage, reflected here, is PilB. This protein is an ATPase involved in protein export for pilin assembly, and is closely related to GspE (

) of type II secretion systems (also referred to as the main terminal branch of the general secretion pathway). Note that type IV pilus systems are often divided into type IV-A and IV-B, with the latter group including bundle-forming pilus, mannose-sensitive haemagglutinin, etc. Members of this family are found in type IV-A systems.
O-phosphoseryl-tRNA:Cys-tRNA synthase, archaea (Sep_Cys-tRNA_synth_arc)
Type: Family

Aminoacylation of tRNA(Cys) with Cys, and cysteine biosynthesis in the process, happens in Methanocaldococcus jannaschii and several other archaea by misacylation of tRNA(Cys) with O-phosphoserine (Sep), followed by modification of the phosphoserine to cysteine. In some species, direct tRNA-cys aminoacylation also occurs but this pathway is required for Cys biosynthesis. Members of this protein family catalyze the second step in this two step pathway, using pyridoxal phosphate and a sulphur donor to synthesize Cys from Sep while attached to the tRNA .
Glutathione peroxidase Gpx7, putative (Glut_perox_Gpx7)
Type: Family

This model represents one of several families of known and probable glutathione peroxidases. It is restricted to animals and designated GPX7.
Peptidoglycan hydrolase FlgJ (FlgJ)
Type: Family

FlgJ is a flagellum-specific muramidase which hydrolyses the peptidoglycan layer to assemble the rod structure in the periplasmic space . The N-terminal region of this protein acts directly in flagellar rod assembly, while the C-terminal region is a flagellum-specific muramidase (peptidoglycan hydrolase) required for formation of the outer membrane L ring .
Internalin B-like, B-repeat (InlB-like_B-rpt)
Type: Repeat

This entry represents the B-repeat described in internalins of Listeria species . These are 70-residue repeats, found in one copy in internalin B, three in internalin A and two in internalin H . The B-repeat plays an important role in protein-protein interactions, as it probably binds a host cell receptor and thereby it may enhance signaling downstream of the host cell receptor tyrosine kinase Met. This entry also include 78-residue repeats which occur from 2 to 15 times in some proteins of Tannerella forsythensis ATCC 43037. In Fibrobacter succinogenes, these repeats are found between one and four copies, while a single copy is found in Geobacter sulfurreducens, and a few other bacteria.
Type 3 secretion system ATPase SctN (ATPase_T3SS_SctN)
Type: Family

Proteins in this entry are found in a variety of bacteria, and are ATPases that occurs as a cytoplasmic component of the type III secretion system (T3SS) found in many pathogenic bacteria. This entry includes SctN (also known as YscN) from Yersinia enterocolitica, which is a component of the Yop (Yersinia outer protein) secretion machinery that acts as a molecular motor to provide the energy that is required for the export of proteins . It may be required for type III secretion apparatus formation, proper protein secretion, host cell invasion and virulence . This protein is required for the stabilization of the major sorting platform component (or C-ring component) .
CRISPR-associated protein Cse1 (CRISPR-assoc_prot_Cse1)
Type: Family

This entry represents the Cse1 family of Cas proteins, which includes CT1972 from Chlorobium tepidum . These proteins are found in the CRISPR/Cas subtype Escherichia coli regions of many bacteria (most of which are mesophiles), and not in Archaea. This is also known as CasA, or Cse1 Type I-E .

The CRISPR-Cas system is a prokaryotic defence mechanism against foreign genetic elements. The key elements of this defence system are the Cas proteins and the CRISPR RNA.
CRISPR-associated protein Cse2 (CRISPR-assoc_prot_Cse2)
Type: Family

This entry represents the Cse2 family of Cas proteins, which includes CT1973 from Chlorobium tepidum. These proteins are found in the CRISPR/Cas subtype Ecoli regions of many bacteria (most of which are mesophiles), and not in Archaea . This is also known as CasB or Cse2 Type I-E .

The CRISPR-Cas system is a prokaryotic defence mechanism against foreign genetic elements. The key elements of this defence system are the Cas proteins and the CRISPR RNA.
CRISPR-associated protein DxTHG, conserved site (CRISPR-assoc_prot_DxTHG_CS)
Type: Conserved_site

The CRISPR-Cas system is a prokaryotic defence mechanism against foreign genetic elements. The key elements of this defence system are the Cas proteins and the CRISPR RNA.

This entry represents a conserved site found in two otherwise substantially different families of Cas proteins . This site includes the motif [VIL]-D-x-[ST]-H-[GS].
Flagellar hook-associated protein 3 (Flagell_FlgL)
Type: Family

FlgL (or hook-associated protein 3, HAP3) proteins are flagellar hook-associated proteins encoded in bacterial flagellar operons . An N-terminal region of about 150 residues and a C-terminal region of about 85 residues are conserved in this family, though members show considerable length heterogeneity between these two well-conserved terminal regions -proteins in this family range from 287 to more than 500 residues in length.
Type III secretion system apparatus protein YscQ/HrcQ/SpaO (T3SS_SpaO/YscQ/SpaO)
Type: Family

Proteins in this entry are encoded within type III secretion operons and are involved in many different functions. For example, YscQ in Yersinia is essential for YOPs secretion , while SpaO in Shigella is involved in the surface presentation of antigens apparatus found on the virulence plasmid , and HrcQ is involved in the Harpin secretory system in organisms like Pseudomonas syringae .
Type III secretion system, PrgH/EprH (T3SS_PrgH/EprH)
Type: Family

In Salmonella, the gene encoding this protein is part of a four-gene operon PrgHIJK, while in other organisms it is found in type III secretion operons. PrgH has been shown to be required for type III secretion and is a structural component of the needle complex, which is the core component of type III secretion systems .
Type III secretion apparatus protein OrgA/MxiK (T3SS_OrgA/MxiK)
Type: Family

This protein is encoded by genes which are found in type III secretion operons, and has been shown to be essential for the invasion phenotype in Salmonella and a component of the secretion apparatus . The protein is known as OrgA in Salmonella due to its oxygen-dependent expression pattern in which low-oxygen levels up-regulate the gene . In Shigella it is called MxiK and has been shown to be essential for the proper assembly of the needle complex, which is the core component of type III secretion systems . The putative uncharacterised protein YgeO from E. coli is also included in this entry. YgeO' is reported in ecogene as being homologous to OrgA and MxiK.
CRISPR-associated protein Cas8b (CRISPR-assoc_prot_Cas8b)
Type: Family

The CRISPR-Cas system is a prokaryotic defence mechanism against foreign genetic elements. The key elements of this defence system are the Cas proteins and the CRISPR RNA.

This entry represents a minor class of Cas proteins, known as Cas8b , found in at least five prokaryotic genomes: Methanosarcina mazei, Sulfurihydrogenibium azorense, Thermotoga maritima, Carboxydothermus hydrogenoformans, and Dictyoglomus thermophilum, the first of which is archaeal while the rest are bacterial . Cas8b is a large subunit of the Type-I-B Cascade complex found in Clostridium thermocellum and Methanococcus maripaludis .
Type III secretion protein HpaP (T3SS_HpaP)
Type: Family

This entry represents proteins encoded by genes which are always found in type III secretion operons , which are described as SctP (Secretion and Cellular Translocation P) proteins in many pathogenic bacteria. Lineage-specific names for SctP include HpaP in Ralstonia solanacearum, YscP in Yersinia, HrpP in Pseudomonas syringae, EscP in enteropathogenic Escherichia coli, etc. SctP is homologous to flagellar hook-length control protein FliK, and member protein YscP has been described as a molecular ruler, but it appears to have other functions as well .
Type III secretion protein HrpB2 (T3SS_HrpB2)
Type: Family

This entry represents proteins encoded by genes which are found in type III secretion operons in a narrow group of species including Xanthomonas, Burkholderia and Ralstonia.
Type III secretion protein HrpB7 (T3SS_HrpB7)
Type: Family

This entry represents proteins encoded by genes which are found in type III secretion operons in a narrow range of species including Xanthomonas, Burkholderia and Ralstonia.
Type III secretion protein HrpB4 (T3SS_HrpB4)
Type: Family

This entry represents proteins encoded by genes which are found in type III secretion operons in a narrow range of species including Xanthomonas, Burkholderia and Ralstonia.
Type III secretion system, HrpB1/HrpK (T3SS_HrpB1/HrpK)
Type: Family

This family of proteins is encoded by genes found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia.
CRISPR-associated Cas3, Yersinia-type (CRISPR-assoc_Cas3_yers)
Type: Family

This entry represents the Yersinia-type Cas3 family of helicases. The Yersinia-type Cas3 helicases differ from the more common Cas3 proteins by being considerably larger, though they still share a number of motifs, and replace Cas3 in some CRISPR/cas loci in a number of Proteobacteria, including Yersinia pestis, Chromobacterium violaceum, Erwinia carotovora subsp. atroseptica SCRI1043, Photorhabdus luminescens subsp. laumondii TTO1, Legionella pneumophila, etc.

The CRISPR-Cas system is a prokaryotic defence mechanism against foreign genetic elements. The key elements of this defence system are the Cas proteins and the CRISPR RNA.
CRISPR-associated endoribonuclease Cas6/Csy4, subtype I-F/YPEST (CRISPR-assoc_prot_Csy4)
Type: Family

This protein family, typified by YPO2462 of Yersinia pestis, is a CRISPR-associated (Cas) family strictly associated with the Ypest subtype of CRISPR/Cas locus. It is designated Csy4, for CRISPR/Cas Subtype Ypest protein 4. In Pseudomonas aeruginosa, crRNA biogenesis requires the endoribonuclease Csy4, which binds and cleaves the repetitive sequence of the CRISPR transcript .

The CRISPR-Cas system is a prokaryotic defence mechanism against foreign genetic elements. The key elements of this defence system are the Cas proteins and the CRISPR RNA.
Type I-F CRISPR-associated protein Csy1 (CRISPR-assoc_prot_Csy1)
Type: Family

This entry represents type I-F CRISPR-associated protein Csy1 (CRISPR/Cas Subtype Ypest protein 1, also known as Cas8f), typified by YPO2465 of Yersinia pestis, is a CRISPR-associated (Cas) entry strictly associated with the Ypest subtype of CRISPR/Cas locus. Csy1 is part of the type I-F CRISPR system yersinia (Csy) surveillance complex in which the binding of target dsDNA leads to large quaternary and tertiary structural changes in the complex that are likely necessary in the pathway leading to target dsDNA degradation by a trans-acting helicase-nuclease . The Csy complex folds into an asymmetric spiral; in the tail region, one Csy1/Cas8f and one Csy2/Cas5f form a stable heterodimer in which the 5' handle of the crRNA is anchored .

The CRISPR-Cas system is a prokaryotic defence mechanism against foreign genetic elements. The key elements of this defence system are the Cas proteins and the CRISPR RNA.
Type I-F CRISPR-associated protein Csy2 (CRISPR-assoc_prot_Csy2)
Type: Family

This entry represents ty I-F CRISPR-associated protein Csy2 (also known as Cas5f), typified by YPO2464 of Yersinia pestis, which is part of the type I-F CRISPR system yersinia (Csy) surveillance complex in which the binding of target dsDNA leads to large quaternary and tertiary structural changes in the complex that are likely necessary in the pathway leading to target dsDNA degradation by a trans-acting helicase-nuclease . The Csy complex folds into an asymmetric spiral; in the tail region, one Csy1/Cas8f and one Csy2/Cas5f form a stable heterodimer in which the 5' handle of the crRNA is anchored .

The CRISPR-Cas system is a prokaryotic defence mechanism against foreign genetic elements. The key elements of this defence system are the Cas proteins and the CRISPR RNA.
Type I-F CRISPR-associated protein Csy3 (CRISPR-assoc_prot_Csy3)
Type: Family

This entry represents type I-F CRISPR-associated protein Csy3 (also known as Cas7f) , typified by YPO2463 of Yersinia pestis. Csy3 is part of the type I-F CRISPR system yersinia (Csy) surveillance complex in which the binding of target dsDNA leads to large quaternary and tertiary structural changes in the complex that are likely necessary in the pathway leading to target dsDNA degradation by a trans-acting helicase-nuclease . The Csy complex folds into an asymmetric spiral in which six Cys3/Cas7f subunits form the spiral backbone with extensive interactions with the crRNA .

The CRISPR-Cas system is a prokaryotic defence mechanism against foreign genetic elements. The key elements of this defence system are the Cas proteins and the CRISPR RNA.
Type III secretion regulator, YopN/LcrE/InvE/MxiC (T3SS_LcrE)
Type: Domain

This protein is found in type III secretion operons and, in Yersinia, is localized to the cell surface and is involved in the Low-Calcium Response (LCR), possibly by sensing the calcium concentration . In Salmonella, the gene is known as InvE and is believed to perform an essential role in the secretion process and interacts with the proteins SipBCD and SicA . Negative regulation of type III secretion in Yersinia pestis is mediated in part by a multiprotein complex that has been proposed to act as a physical impediment to type III secretion by blocking the entrance to the secretion apparatus prior to contact with mammalian cells. This complex is composed of YopN, its heterodimeric secretion chaperone SycN-YscB, and TyeA .
Conserved hypothetical protein CHP02569 (CHP02569)
Type: Family

This entry has so far only been found in Actinobacteria, including at least five species of Mycobacterium, three of Corynebacterium, and Nocardia farcinica -always in a single copy per genome. The function is unknown.
Type I-U CRISPR-associated RAMP protein Csb1/Cas7u (CRISPR-assoc_prot_Csb1/Cas7u)
Type: Family

Members of this family, previously called Csx4 and now called Csb1 or Cas7u, are found in association with CRISPR repeats and other CRISPR-associated (cas) genes. Its CRISPR/Cas type, now called type I-U, originally was designated Dpsych. It was first seen in the genomes of Geobacter sulfurreducens PCA and Desulfotalea psychrophila LSv54 (both Desulfobacterales from the Deltaproteobacteria), Gemmata obscuriglobus (a Planctomycete), and Actinomyces naeslundii MG1 (Actinobacteria).

The CRISPR-Cas system is a prokaryotic defence mechanism against foreign genetic elements. The key elements of this defence system are the Cas proteins and the CRISPR RNA.
Competence operon E, ComEB (Competence_ComEB)
Type: Family

Competence is the ability of a cell to take up exogenous DNA from its environment, resulting in transformation. It is widespread among bacteria and is probably an important mechanism for the horizontal transfer of genes. DNA usually becomes available by the death and lysis of other cells. Competent bacteria use components of extracellular filaments called type 4 pili to create pores in their membranes and pull DNA through the pores into the cytoplasm. This process, including the development of competence and the expression of the uptake machinery, is regulated in response to cell-cell signalling and/or nutritional conditions .

The development of genetic competence in Bacillus subtilis is a highly regulated adaptive response to stationary-phase stress. For competence to develop, the transcriptional regulator, ComK, must be activated. ComK is required for the expression of genes encoding proteins that function in DNA uptake. In log-phase cultures, ComK is inactive in a complex with MecA and ClpC. The comS gene is induced in response to high culture cell density and nutritional stress and its product functions to release active ComK from the complex. ComK then stimulates the transcription initiation of its own gene as well as that of the late competence operons .

This entry represents proteins encoded in the comE operon for "late competence" as characterised in B. subtilis . It is under competence control and is required for both DNA binding to the competent cell surface, and for uptake. The presence of a cytidine/deoxycytidine deaminase domain in these proteins suggests that they may perform this activity. comE contains three open reading frames (ORF1-3) read in the forward direction, preceded by a long untranslated leader sequence and an E sigma A promoter. The comE transcript is present at a very low level during growth and at an elevated level in stationary-phase cells. Conversely, the reverse transcript is present during exponential growth and disappears during the stationary phase. ORF1 and ORF3 are predicted to be integral membrane proteins. The latter is specifically required for DNA uptake but not for binding .
Type III secretion system regulator, LcrR (T3SS_LcrR)
Type: Family

This family of proteins are encoded within type III secretion operons and have been characterised in Yersinia as a regulator of the Low-Calcium Response (LCR) .
Conserved hypothetical protein CHP02574, addiction module (CHP02574_addiction_mod)
Type: Family

This entry defines several short bacterial proteins, typically about 75 amino acids long, which are always found as part of a pair (at least) of small genes. The other protein in the pair always belongs to a family of plasmid stabilisation proteins (

). It is likely that this protein and its partner comprise some form of addiction module -a pair of genes consisting of a stable toxin and an unstable antitoxin which mediate programmed cell death -although these gene pairs are usually found on the bacterial main chromosome.
CRISPR-associated protein Cmr2 (CRISPR-assoc_prot_Cmr2)
Type: Family

This entry is encoded within the CRISPR-associated RAMP module, a set of six genes found together in prokaryotic genomes . This gene cluster is found only in species with CRISPR repeats, usually near the repeats themselves. Because most of the six genes (but not those encoding this entry) contain RAMP domains, and because its appearance in a genome appears to depend on other CRISPR-associated Cas genes, the set is designated the CRISPR RAMP module. This entry represents Cmr2, the largest and an essential subunit of a CRISPR RNA-Cas protein complex (the Cmr complex) which was originally thought to be the catalytic subunit of the effector complex, however, in vitro studies showed that Cmr2 is not required for cleavage and suggested that another component provides the catalytic function. Therefore, the essential role by Cmr2 does not require the ADP- or metal-binding or HD domains .

The CRISPR-Cas system is a prokaryotic defence mechanism against foreign genetic elements. The key elements of this defence system are the Cas proteins and the CRISPR RNA.
CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 (Cas10/Csm1)
Type: Family

The CRISPR-Cas system is a prokaryotic defence mechanism against foreign genetic elements. The key elements of this defence system are the Cas proteins and the CRISPR RNA.

This entry represents Csm1 (CRISPR/Cas Subtype Mtube Protein 1), which is a single-strand-specific deoxyribonuclease (ssDNase) which digests both linear and circular ssDNA .
CRISPR-associated protein Crn3/Csx3 (CRISPR-assoc_prot_Crn3/Csx3)
Type: Family

This entry represents the Crn3/Csx3 family of Cas proteins, which is encoded in CRISPR-associated gene cluster near CRISPR repeats in the genomes of several different thermophiles: Archaeoglobus fulgidus (archaeal), Aquifex aeolicus (Aquificae), Dictyoglomus thermophilum (Dictyoglomi), and a thermophilic Synechococcus (Cyanobacteria). These are ring nucleases that cleave and degrade cyclic tetra-adenylate (cA4), a second messenger generated by Cas10 in type III CRISPR systems

The CRISPR-Cas system is a prokaryotic defence mechanism against foreign genetic elements. The key elements of this defence system are the Cas proteins and the CRISPR RNA.
CRISPR-associated RAMP Cmr4 (CRISPR-assoc_RAMP_Cmr4)
Type: Family

This entry represents the CRISPR system Cmr endoribonuclease Cmr4 which is part of the broad RAMP superfamily collection of CRISPR-associated proteins. The Cmr complex is an RNA-guided endonuclease that cleaves foreign RNA targets as part of the CRISPR prokaryotic defense system . Cmr4 is required for target-cleavage activity, identified as the conserved endoribonuclease of the Cmr complex.

The CRISPR-Cas system is a prokaryotic defence mechanism against foreign genetic elements. The key elements of this defence system are the Cas proteins and the CRISPR RNA.
CRISPR-associated RAMP protein Csx7 (CRISPR-assoc_RAMP_Csx7)
Type: Family

This entry represents a family of Cas proteins that are found in the RAMP-2 subtype of CRISPR/cas locus which includes the representative protein SSO1426 from Saccharolobus solfataricus P2, was designated Csx7 in .

The CRISPR-Cas system is a prokaryotic defence mechanism against foreign genetic elements. The key elements of this defence system are the Cas proteins and the CRISPR RNA.
CRISPR-associated RAMP Csm3 (CRISPR-assoc_RAMP_Csm3)
Type: Family

This entry represents the Csm3 (CRISPR/cas Subtype Mtube, protein 3) family of Cas proteins encoded by genes found in the mtube subtype CRISPR/cas locus and designated. This is also known as Csm3 Type III-A . Csm3 binds unstructured RNAs in a sequence non-specific manner, which suggests that it interacts with the variable spacer sequence of the crRNA and that it functions as an endoribonuclease that acts to cleave the ssRNA target in a periodic manner .

The CRISPR-Cas system is a prokaryotic defence mechanism against foreign genetic elements. The key elements of this defence system are the Cas proteins and the CRISPR RNA.
CRISPR-associated protein, NE0113 (CRISPR-assoc_prot_NE0113)
Type: Family

This entry represents a minor family of Cas proteins that are now called Csm6 and previously called Csx6, with both CARF (CRISPR-associated Rossman Fold) and HEPN domains, is a ring nuclease for cyclic-oligoadenylates that are generated as second messengers involved in activation of CRISPR systems .

The CRISPR-Cas system is a prokaryotic defence mechanism against foreign genetic elements. The key elements of this defence system are the Cas proteins and the CRISPR RNA.