SII-SWORD/CoKE huggingface dataset:
Equine arteritis virus peptidase S32 (EAV_peptidase_S32)
Type: Family

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) .

This group of serine peptidases belong to MEROPS peptidase family S32 (clan PA(S)). The type example is equine arteritis virus serine endopeptidase (equine arteritis virus), which is involved in processing of nidovirus polyproteins .
Peptidase S37, tripeptidyl aminopeptidase (Peptidase_S37)
Type: Family

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) .

These group of serine peptidases belong to MEROPS peptidase family S37 (clan SC). The members of this group of secreted peptidases are restricted to bacteria. In Streptomyces lividans the peptidase removes tripeptides from the N terminus of extracellular proteins (tripeptidyl aminopeptidase,Tap) .
Peptidase S55, SpoIVB (Peptidase_S55)
Type: Domain

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) .

This group of serine peptidases belong to the MEROPS peptidase family S55 (SpoIVB peptidase family, clan PA(S)).

The protein SpoIVB plays a key role in signalling in the final sigma-K checkpoint of Bacillus subtilis .
Peptidase U57, YabG (Peptidase_U57)
Type: Family

The peptidases families associated with clan U-have an unknown catalytic mechanism as the protein fold of the active site domain and the active site residues have not been reported.

This is a group of peptidases belong to MEROPS peptidase family U57 (clan U-). The type example is the YabG protein of Bacillus subtilis. This is a protease involved in the synthesis and maturation of the spore coat proteins SpoIVA and YrbA of B. subtilis .
Bacteriophage T4, Frd3 (Phage_T4_Frd3)
Type: Family

This is a group of proteins of unknown function from bacteriophage T4 and related phages.
Replication gene A protein-like (Replication_gene_A-like)
Type: Domain

Replication gene A proteins (also known as GpA) are found in bacteriophages and in bacteria as part of a suspected prophage. These proteins function as endonucleases during DNA replication .

This entry represents a domain found at the centre of these sequences, which may be a DNA-binding domain.
Bacteriophage SPP1, head-tail adaptor (Phage_SPP1_head-tail_adaptor)
Type: Family

This entry describes the head-tail adaptor protein of bacteriophage SPP1
and related proteins in other bacteriophage and prophage regions of bacterial genomes. Homologues are also found in Gene Transfer Agents (GTA) , including ORFg7 (RCAP_rcc01689) of the GTA of Rhodobacter capsulatus (Rhodopseudomonas capsulata) . This entry also includes gp7.

In bacteriophage SPP1, the gp16 protein functions as a stopper, locking the viral DNA into the capsid. When the tail attachment binds to the entry receptor, gp16 opens by a diaphragm-like motion, allowing the genome to exit the capsid through the tail tube to the host cell. During virion assembly, gp16 functions as a docking platform to which the preassembled tail binds .

The gp7 protein functions as a stopper within the head-tail connector, locking the viral DNA inside the capsid . Upon attachment of the tail to the host cell entry receptor, gp7 appears to open via a diaphragm-like motion, allowing the genome to exit the capsid through the tail tube and enter the host cell. During viral assembly, gp7 also acts as a docking platform for the preassembled tail, which is tapered by the head-tail joining protein gp17.

The SPP1 head-to-tail connector is composed of cyclical dodecamers of the portal protein gp6 and of the 2 head completion proteins gp15 and gp16 .
Capsid assembly scaffolding protein-like (Gp9-like)
Type: Family

This family includes the capsid assembly protein Gp9 (scaffolding protein) of bacteriophage T7, similar viral proteins and prophages from Proteobacteria. Gp9 facilitates assembly by binding to Gp10 hexamers but not the pentamers and locking them into a morphogenically correct conformation .
Poly granule associated (PhaF_PhaI)
Type: Family

Polyhydroxyalkanoates (PHAs) are storage polyesters synthesised by various bacteria as intracellular carbon and energy reserve material. PHAs are accumulated as water-insoluble inclusions within the cells. This family consists of the phasins PhaF and PhaI which act as a transcriptional regulator of PHA biosynthesis genes. PhaF has been proposed to repress expression of the phaC1 gene and the phaIF operon.
DNA terminal protein Gp3 (DNA_terminal_Gp3)
Type: Family

The DNA terminal protein Gp3, found in a number of Bacillus phages, is linked to the 5' ends of both strands of the genome through a phosphodiester bond between the β-hydroxyl group of a serine residue and the 5'-phosphate of the terminal deoxyadenylate. This protein is essential for DNA replication and is involved in the priming of DNA elongation .
Phi-29-like late genes activator (Phi-29_GP4)
Type: Family

This family consists of phi-29-like late genes activator (or early protein GP4). This protein is thought to be a positive regulator of late transcription and may function as a sigma-like component of the host RNA polymerase .
Bacterial phosphonate metabolism, PhnH (Phosphonate_metab_PhnH)
Type: Family

PhnH is an essential component of the C-P lyase core complex formed through the interaction with other Phn proteins (G, I and J). This core complex is involved in the C-P lyase pathway that converts phosphonate into 5-phosphoribosyl-alpha-1-diphosphate (PRPP) and is activated upon phosphate starvation in many bacterial species including Escherichia coli. In E. coli, the 14-cistron phn operon is required for phosphonate uptake and utilisation and encodes an ATP-binding cassette transporter (PhnC, PhnD, and PhnE), a regulatory protein (PhnF) and components required for enzymatic conversion of phosphonate into PRPP (PhnGHIJKLMNOP) .
Phosphonate metabolism protein PhnI (PhnI)
Type: Family

This family consists of several proteobacterial phosphonate metabolism protein (PhnI) sequences. Bacteria that use phosphonates as a phosphorus source must be able to break the stable carbon-phosphorus bond. In Escherichia coli phosphonates are broken down by a C-P lyase that has a broad substrate specificity. The genes for phosphonate uptake and degradation in E. coli are organised in an operon of 14 genes, named phnC to phnP. Three gene products (PhnC, PhnD and PhnE) comprise a binding protein-dependent phosphonate transporter, which also transports phosphate, phosphite, and certain phosphate esters such as phosphoserine; two gene products (PhnF and PhnO) may have a role in gene regulation; and nine gene products (PhnG, PhnH, PhnI, PhnJ, PhnK, PhnL, PhnM, PhnN, and PhnP) probably comprise a membrane-associated C-P lyase enzyme complex .
Phytanoyl-CoA dioxygenase-like (Phytyl_CoA_dOase-like)
Type: Family

This family includes several eukaryotic phytanoyl-CoA dioxygenase (PhyH) proteins as well as several bacterial deoxygenases. PhyH is a peroxisomal enzyme catalysing the first step of phytanic acid alpha-oxidation. PhyH deficiency causes Refsum's disease (RD), which is an inherited neurological syndrome biochemically characterised by the accumulation of phytanic acid in plasma and tissues .

The bacterial deoxygenase 2-aminoethylphosphonate dioxygenase (PhnY) hydroxylates 2-aminoethylphosphonic acid to form (2-amino-1-hydroxyethyl)phosphonic acid, which is then oxidatively converted to inorganic phosphate and glycine by 2-amino-1-hydroxyethylphosphonate dioxygenase (PhnZ) .

Ectoine dioxygenase from Streptomyces coelicolor (EctD) is involved in the biosynthesis of 5-hydroxyectoine, called compatible solute, which helps organisms to survive extreme osmotic stress by acting as a highly soluble organic osmolyte .
Phytoreovirus Pns9Pns10 (Phyto_Pns9_10)
Type: Family

This family consists of the Phytoreovirus nonstructural proteins Pns9 and Pns10. The function of this family is unknown.
Phytoreovirus Pns1011 (Phytoreo_Pns)
Type: Family

This family consists of Phytoreovirus nonstructural proteins Pns10 and Pns11. Genome segment S11 of Rice gall dwarf virus (RGDV), a Phytoreovirus, encodes a putative protein of 40kDa that exhibits approximately 37% homology at the amino acid level to the nonstructural proteins Pns10 of rice dwarf and wound tumour viruses, which are other members of this genus .
Pirin, C-terminal domain (Pirin_C_dom)
Type: Domain

Eukaryotic pirins are highly conserved nuclear proteins that may function as transcriptional regulators with a role in apoptosis . Prokaryotic homologues have also been identified. Both bacterial and human pirins have been shown to possess quercetinase activity , although this is not universally true for all family members - YhaK (

), for example, displays no such enzymatic activity .

Pirin is composed of two structurally similar domains arranged face to face. Although the two domains are similar, the C-terminal domain of pirin differs from the N-terminal domain as it does not contain a metal binding site and its sequence does not contain the conserved metal-coordinating residues .

Pirin is considered a member of the cupin superfamily on the basis of primary sequence and structural similarity. The presence of a metal binding site in the N-terminal β-barrel of pirin, may be significant in its interaction with Bcl-3 and nuclear factor I (NFI) and role in regulating NF-kappaB transcription factor activity .

This entry represents the Pirin C-terminal domain.
Plasmodium histidine-rich (Plasmodium_HRP)
Type: Family

This family consists of several histidine-rich protein II and III sequence from Plasmodium falciparum .
Plasmodium vivax Vir (Plasmodium_Vir)
Type: Family

This family consists of several Vir proteins specific to the genus Plasmodium and Plasmodium vivax in particular. The vir genes are present at about 600-1,000 copies per haploid genome and encode proteins that are immunovariant in natural infections, indicating that they may have a functional role in establishing chronic infection through antigenic variation .
Pneumovirinae attachment membrane glycoprotein G (Pneumo_att_G)
Type: Family

This family of proteins contain the major surface glycoprotein of turkey rhinotracheitis virus (TRTV), avian pneumovirus (APV), the aetiological agent of turkey rhinotracheitis (TRT), and other Metapneumoviruses. The major surface glycoprotein is the attachment (G) protein, which, by analogy with other respiratory syncytial viruses (RSV), has been proposed to be responsible for virus binding to its cell receptor. The APV G gene and its predicted protein have several features in common with their RSV counterparts. Both G proteins are type II glycoproteins and both the RSV G and APV G proteins are heavily O-glycosylated. In both RSV and APV, the G protein is the most variable protein and is a major target for neutralizing antibodies .
Podovirus DNA packaging protein (Podovirus_Gp16)
Type: Family

This family includes several DNA encapsidation protein sequences from the phi-29-like viruses (gene product 16, Gp16). Gp16 is the primary ATPase of the motor assembly of phi-29; it binds to the prohead RNA to form a pentameric ring to complete the assembly of the DNA packaging motor . The characteristics of the protein distribution suggest prophage matches.
Poxvirus A14, virion envelope (Poxvirus_A14)
Type: Family

This entry represents Protein A14 from Vaccinia virus, also known as Virion membrane protein OPG140, and similar sequences from poxvirus. A14 is a component of the virion membrane and has been found to be an H1 phosphatase substrate
in vivo
and
in vitro
. A14 is hyperphosphorylated on serine residues in the absence of H1 expression .
Poxvirus A31 (Poxvirus_A31)
Type: Family

This family contains the vaccinia virus A31R protein, also known as Protein OPG159, the function of which is not known.
Poxvirus G7-like (Poxvirus_G7)
Type: Family

This family of proteins which include vaccinia virus G7L and fowlpox virus FPV120 are associated with the intracellualar mature virus particle. The function of this family of proteins is not known.
Poxvirus intermediate transcription factor (Poxvirus_intermed-TF)
Type: Family

This family consists of several highly related Poxvirus sequences which are thought to be intermediate transcription factors .
Poxvirus serine/threonine kinase (Poxvirus_ser/thr_kinase)
Type: Family

This family of proteins contain poxvirus serine/threonine protein kinases, which are essential for phosphorylation of virion proteins during virion assembly .
Orthopoxvirus interleukin 18 binding (Orthopox_IL18-bd)
Type: Family

Interleukin-18 (IL-18) is a proinflammatory cytokine that plays a key role in the activation of natural killer and T helper 1 cell responses principally by inducing interferon-gamma (IFN-gamma). Several poxvirus genes encode proteins with sequence similarity to IL-18BPs. It has been shown that vaccinia, ectromelia and cowpox viruses secrete from infected cells a soluble IL-18BP (vIL-18BP) that may modulate the host antiviral response. The expression of vIL-18BPs by distinct poxvirus genera that cause local or general viral dissemination, or persistent or acute infections in the host, emphasises the importance of IL-18 in response to viral infections .
Coenzyme PQQ synthesis protein D (PQQD)
Type: Family

This family contains several bacterial coenzyme PQQ synthesis protein D (PqqD) sequences. This protein is required for coenzyme pyrrolo-quinoline-quinone (PQQ) biosynthesis . PqqD functions as a PqqA binding protein that would serve as a chaperone to deliver PqqA to PqqE .
Proline racemase family (Pro_racemase_fam)
Type: Family

This family consists of proline racemase (

), 4-hydroxyproline epimerase (

), and trans-L-3-hydroxyproline dehydratase (

).

Proline racemase catalyses the interconversion of L- and D-proline in bacteria . Although the mechanisms of aminoacid racemisation and epimerisation are conserved between proline racemase and hydroxyproline epimerase, substrate specificity partly rely on constraints imposed by certain residues distinctively belonging to the catalytic pocket . A human proline racemase-like gene, lacking a specific cysteine residue critical for racemase activity, has been identified as a trans-3-hydroxy-L-proline dehydratase . This family also contains several proteins that remain uncharacterised.
Prominin (Prominin)
Type: Family

The prominins are an emerging family of proteins that, among the multispan membrane proteins, display a novel topology. Mouse and Homo sapiens prominin and (Mus musculus) prominin-like 1 (PROML1) are predicted to contain five membrane spanning domains, with an N-terminal domain exposed to the extracellular space followed by four, alternating small cytoplasmic and large extracellular, loops and a cytoplasmic C-terminal domain . The exact function of prominin is unknown although in humans defects in PROM1, the gene coding for prominin, cause retinal degeneration .
Photosystem I reaction centre subunit N, chloroplastic (PSAN)
Type: Family

Photosystem I reaction centre subunit N (PSAN, also known as PSI-N) may function in mediating the binding of the antenna complexes to the PSI reaction centre and core antenna . PSI-N subunit does not bind pigments .
Oxygen-evolving enhancer protein 3 (PSII_PsbQ)
Type: Family

In PSII, the oxygen-evolving complex (OEC) is responsible for catalysing the splitting of water to O(2) and 4H+. The OEC is composed of a cluster of manganese, calcium and chloride ions bound to extrinsic proteins. In cyanobacteria there are five extrinsic proteins in OEC (PsbO, PsbP-like, PsbQ-like, PsbU and PsbV), while in plants there are only three (PsbO, PsbP and PsbQ), PsbU and PsbV having been lost during the evolution of green plants .

This family represents the PSII OEC protein PsbQ from cyanobacteria and plants. Both PsbQ and PsbP (

) are regulators that are necessary for the biogenesis of optically active PSII. The crystal structure of PsbQ from spinach revealed a 4-helical bundle polypeptide. The distribution of positive and negative charges on the protein surface might explain the ability of PsbQ to increase the binding of chloride and calcium ions and make them available to PSII .

Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product .

PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane . Within the core of the complex, the chlorophyll and β-carotene pigments are mainly bound to the antenna proteins CP43 (PsbC) and CP47 (PsbB), which pass the excitation energy on to the reaction centre proteins D1 (Qb, PsbA) and D2 (Qa, PsbD) that bind all the redox-active cofactors involved in the energy conversion process. The PSII oxygen-evolving complex (OEC) oxidises water to provide protons for use by PSI, and consists of OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ). The remaining subunits in PSII are of low molecular weight (less than 10kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection .
Avirulence B/C (Avirulence_B/C)
Type: Family

This entry represents the avirulence B and C proteins from Pseudomonas syringae and related proteins from Xanthomonas campestris . avrB and avrC encode these proteins, which are 36 and 39 kilodaltons in size respectively . Pathogenic bacterial effectors suppress pathogen-associated molecular pattern (PAMP)-triggered host immunity, thereby promoting parasitism. AvrB suppresses PAMP-triggered immunity (PTI) through RAR1, which is for effector-triggered immunity (ETI) .
Pseudomonas avirulence D (Pseudomon_AvrD)
Type: Family

This family consists of several avirulence D (AvrD) proteins primarily found in Pseudomonas syringae .
PufQ cytochrome subunit (PufQ_cyt-su)
Type: Family

This family consists of bacterial PufQ proteins. PufQ is required for bacteriochlorophyll biosynthesis serving a regulatory function in the formation of photosynthetic complexes .
Rapid ALkalinization Factor (RALF)
Type: Family

The plant RAPID ALKALINIZATION FACTOR (RALF) family consists of extracellular peptides that serve as extracellular signals. RALF1, a 5kDa ubiquitous polypeptide in plants, arrests root growth and development . RALF4/19 peptides interact with LRX proteins to control pollen tube growth .
Rubber elongation factor (REF)
Type: Family

This family consists of the highly related rubber elongation factor (REF), small rubber particle protein (SRPP) and stress-related protein (SRP) sequences. REF and SRPP are released from the rubber particle membrane into the cytosol during osmotic lysis of the sedimentable organelles (lutoids). The exact function of this family is unknown .
RHD3/Sey1 (RHD3/Sey1)
Type: Family

This family consists of plant root hair defective 3 (RHD3) protein and its homologues from other eukaryotes. RHD3 is a conserved protein with GTP-binding motifs that is implicated in the control of vesicle trafficking between the endoplasmic reticulum and the Golgi compartments and is also involved in homotypic ER membrane fusion, being classified as a dynamin-like GTPase together with its homologues Sey1 and atlastin . It is required for appropriate root and root hair cells enlargement . It may play a role in cell wall biosynthesis and actin organisation . Its homologue from Saccharomyces cerevisiae, Sey1, mediates homotypic ER fusion .