SII-SWORD/CoKE huggingface dataset:
V0 complex accessory subunit Ac45 (Ac45_acc_su)
Type: Family

V-ATPases (also known as V1V0-ATPase or vacuolar ATPase) are found in the eukaryotic endomembrane system, and in the plasma membrane of prokaryotes and certain specialised eukaryotic cells. V-ATPases hydrolyse ATP to drive a proton pump, and are involved in a variety of vital intra-and inter-cellular processes such as receptor mediated endocytosis, protein trafficking, active transport of metabolites, homeostasis and neurotransmitter release . V-ATPases are composed of two linked complexes: the V1 complex (subunits A-H) contains the catalytic core that hydrolyses ATP, while the V0 complex (subunits a, c, c', c'', d) forms the membrane-spanning pore. V-ATPases may have an additional role in membrane fusion through binding to t-SNARE proteins .

This entry represents the V0 complex Ac45 accessory subunit (ATP6AP1, also known as V-type proton ATPase subunit S1), an ER/Golgi membrane protein. This subunit is synthesized as an N-glycosylated 60kDa precursor that is intracellularly cleaved to a protein of about 45kDa. This subunit plays a crucial role on V0 assembly, stability and function as it connects to multiple V0 subunits and phospholipids in the c-ring . This subunit assists the V-ATPase in the acidification of neuroendocrine granules and guides the V-ATPase into specialized subcellular compartments such as neuroendocrine regulated secretory vesicles or the ruffled border of the osteoclast . In humans, mutations of ATP6AP1 cause immunodeficiency with hypogammaglobulinemia, hepatopathy and neurocognitive abnormalities .
ATPase, V0 complex, subunit e1/e2 (ATPase_V0-cplx_e1/e2_su)
Type: Family

Transmembrane ATPases are membrane-bound enzyme complexes/ion transporters that use ATP hydrolysis to drive the transport of protons across a membrane. Some transmembrane ATPases also work in reverse, harnessing the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP.

V-ATPases (also known as V1V0-ATPase or vacuolar ATPase) are found in the eukaryotic endomembrane system, and in the plasma membrane of prokaryotes and certain specialised eukaryotic cells. V-ATPases hydrolyse ATP to drive a proton pump, and are involved in a variety of vital intra-and inter-cellular processes such as receptor mediated endocytosis, protein trafficking, active transport of metabolites, homeostasis and neurotransmitter release . V-ATPases are composed of two linked complexes: the V1 complex (subunits A-H) contains the catalytic core that hydrolyses ATP, while the V0 complex (subunits a, c, c', c'', d) forms the membrane-spanning pore. V-ATPases may have an additional role in membrane fusion through binding to t-SNARE proteins .

This entry represents subunit e (or subunit M9.2) found in the V0 complex of certain V-ATPases. The V0 complex contains subunit c (proton-conducting pore), as well as accessory subunits that function in assembly, targeting or regulation of the V-ATPase complex. Subunit e is an extremely hydrophobic protein of approximately 9kDa, which may be required for assembly of vacuolar ATPases . The amino terminal domain of subunit E interacts with the H subunit and is required fo V-ATPase function . Different isoforms of this subunit exist sometimes annotated as e1 and e2 also a neuron-specific isoform, NM9.2 has been identified .
AWPM-19-like (AWPM-19)
Type: Family

Members of this family are 19kDa membrane proteins. The levels of the plant protein AWPM-19 increase dramatically when there is an increase level of abscisic acid. The increase presence of this protein leads to greater tolerance of freezing . The rice homologue, OsPM19L1, is induced by osmotic stress and may be associated with stress tolerance through ABA-dependent pathway .
Acetyl xylan esterase domain (AXE1_dom)
Type: Domain

This domain can be found in several bacterial acetyl xylan esterase proteins. Acetyl xylan esterases are enzymes that hydrolyse the ester linkages of the acetyl groups in position 2 and/or 3 of the xylose moieties of natural acetylated xylan from hardwood. These enzymes are one of the accessory enzymes which are part of the xylanolytic system, together with xylanases, beta-xylosidases, alpha-arabinofuranosidases and methylglucuronidases; these are all required for the complete hydrolysis of xylan .
Drosophila accessory gland-specific peptide 26Ab (Acp26Ab)
Type: Family

This family consists of accessory gland-specific 26Ab peptides or male accessory gland secretory protein 355B from different Drosophila species. Drosophila males, like males of most other insects, transfer a group of specific proteins (Acp26Ab and Acp26Aa in Drosophila) to the females during mating. These proteins are produced primarily in the accessory gland and are likely to influence the female's reproduction .
Adenovirus late L2 mu core (Adenovirus_late_L2_mu_core)
Type: Family

The late transcription region 2 (L2) of Adenovirus type 2 has an ORF of 80 residues positioned between nucleotides 17,676 and 17,915. It encodes an 11K polypeptide, which has the initiating methionine residue removed, leaving a 79-residue product. The L2 region that encoded 11K polypeptide is arginine rich (21%) and has a predicted molecular weight of 8,715. It was cleaved by the viral endoprotease to give two products which co-migrated on sodium dodecyl sulphate-polyacrylamide gels as virion polypeptide X .

The role of the L2 precursor, by virtue of its two domains, might be to condense the viral prochromatin for encapsidation. Subsequent cleavage within the particle after residue 31 releases the cross-link and prepares the viral chromatin for a relaxed conformation, which is required during infection and uncoating. Cleavage seems to be necessary for infectivity.

This family consists of several adenovirus late L2 mu core protein or protein X sequences .
Enterobacteria AfaD invasin (AfaD)
Type: Family

This family consists of several AfaD and related proteins from Escherichia coli and Salmonella bacteria. The afa gene clusters encode an afimbrial adhesive sheath produced by E. coli. The adhesive sheath is composed of two proteins, AfaD and AfaE, which are independently exposed at the bacterial cell surface. AfaE is required for bacterial adhesion to HeLa cells and AfaD for the uptake of adherent bacteria into these cells .
Agenet-like domain (Agenet-like_dom)
Type: Domain

Fragile X messenger ribonucleoprotein 1 (FMR1/FMRP), and its autosomal paralogues, RNA-binding proteins FXR1/2 (Fragile X-related protein 1/2), comprise a family of RNA-binding proteins that are involved the regulation of alternative mRNA splicing, mRNA stability, mRNA dendritic transport and postsynaptic local protein synthesis of a subset of mRNAs, playing a crucial role in neuronal development and synaptic plasticity . These proteins are highly similar to one another and also retain highly conserved domain architecture. The three ribonucleoprotein K homology (KH) domains and the cluster of arginine and glycine residues that constitute the RGG box, comprise a large region that is important for RNA binding and polyribosome association . In addition, two Agenet-like domains exist in tandem within the N-terminal regions of FMRP family proteins. The Agenet-like domain belongs to the "Royal" domain superfamily which contains also the Tudor, chromo, MBT, PWWP and plant Agenet domains. Biochemical analysis of the tandem Agenet-like domains reveals their ability to preferentially recognise trimethylated peptides in a sequence-specific manner .

The Tudor/Agenet-like domain folds into a bent four-stranded antiparallel β-sheet with a fifth strand closing the cavity of the sheet, similar to a thumb across a semiclosed hand . This domain is also found plant proteins, such as AGDP1 from Arabidopsis, which is required for transcriptional silencing, non-CG DNA methylation and H3K9 dimethylation (H3K9me2) at some loci . It preferentially occupies long transposons and specifically recognizes the histone H3 'Lys-9' methylation (H3K9me) marks, with a stronger affinity for dimethylated H3K9 (H3K9me2) . Plant DUF724 domain-containing proteins are also members of this entry, and they may be involved in the polar growth of plant cells via transportation of RNAs .
Alginate lyase domain (Alginate_lyase_dom)
Type: Domain

Alginate is a family of 1-4-linked copolymers of beta-D-mannuronic acid (M) and alpha-L-guluronic acid (G). It is produced by brown algae and by some bacteria belonging to the genera Azotobacter and Pseudomonas. Alginate lyases catalyse the depolymerisation of alginates by beta -elimination, generating a molecule containing 4-deoxy-L-erythro-hex-4-enepyranosyluronate at the nonreducing end . Two subfamilies of alginate lyase exist: the poly(beta-D-mannuronate) lyase,

, and the poly(alpha-L-guluronate) lyase,

.

This entry represents a domain found in the poly(beta-D-mannuronate) lyase subfamily of alginate lyase.
Allexivirus 40kDa (Allexi_40kDa)
Type: Family

This family of sequences contains the 40kDa polypeptides from garlic viruses (Allexiviruses), which do not resemble any other plant virus gene products reported so far .

Rod-shaped flexuous viruses have been isolated from garlic plants, Allium sativum. Infection by this virus creates typical mosaic symptoms. The core-like sequence of a zinc finger protein preceded by a cluster of basic amino acid residues shows similarities to the corresponding 12K proteins of the potexviruses and carlaviruses . Viral epidemics by allexiviruses are also known to be caused by aphids and eriophyid mites (Aceria tulipae) carrying Potyviruses, Carlaviruses, and Allexiviruses .
Anthrax toxin receptor, C-terminal (Anthrax_toxin_rcpt_C)
Type: Domain

Anthrax is an acute disease in humans and animals, which is caused by the bacterium Bacillus anthracis. While the disease can be lethal, there are effective vaccines against anthrax, and some forms of the disease respond well to antibiotic treatment.

The anthrax toxin consists of the proteins protective antigen (PA), lethal factor (LF) and oedema factor (EF). The first step of toxin entry into host cells is the recognition by PA of a receptor on the surface of the target cell. The subsequent cleavage of receptor-bound PA enables EF and LF to bind and form a heptameric PA63 pre-pore, which triggers endocytosis. PA has been shown to bind to two cellular receptors, termed anthrax toxin receptor 1 (ANTXR1/TEM8) and 2 (ANTXR2). Both bind to PA with high affinity and are capable of mediating toxicity , and both are type 1 membrane proteins that include an approximately 200-aa extracellular von Willebrand factor A (VWA) domain with a metal ion-dependent adhesion site (MIDAS) motif .

This region is found in the putatively cytoplasmic C terminus of the anthrax receptor.
Anthrax toxin receptor, extracellular domain (Anthrax_toxin_rcpt_extracel)
Type: Domain

Anthrax is an acute disease in humans and animals, which is caused by the bacterium Bacillus anthracis. While the disease can be lethal, there are effective vaccines against anthrax, and some forms of the disease respond well to antibiotic treatment.

The anthrax toxin consists of the proteins protective antigen (PA), lethal factor (LF) and oedema factor (EF). The first step of toxin entry into host cells is the recognition by PA of a receptor on the surface of the target cell. The subsequent cleavage of receptor-bound PA enables EF and LF to bind and form a heptameric PA63 pre-pore, which triggers endocytosis. PA has been shown to bind to two cellular receptors, termed anthrax toxin receptor 1 (ANTXR1/TEM8) and 2 (ANTXR2). Both bind to PA with high affinity and are capable of mediating toxicity , and both are type 1 membrane proteins that include an approximately 200-aa extracellular von Willebrand factor A (VWA) domain with a metal ion-dependent adhesion site (MIDAS) motif .

This region is found in the putatively extracellular N-terminal half of the anthrax receptor. It is probably part of the Ig superfamily and most closely related to

.
Apc13 (Apc13)
Type: Family

The anaphase-promoting complex (APC) is a conserved multi-subunit ubiquitin ligase required for the degradation of key cell cycle regulators. Members of this family are components of the anaphase-promoting complex homologous to Apc13 .
Anaphase-promoting complex subunit 15/mnd2 (APC_su15/mnd2)
Type: Family

This entry includes budding yeast Mnd2 and its homologue, anaphase-promoting complex subunit 15 (Apc15), from fission yeasts . They are part of the anaphase promoting complex/cyclosome (APC/C) .

The anaphase-promoting complex (APC) or cyclosome is a multi-subunit E3 protein ubiquitin ligase that regulates important events in mitosis, such as the initiation of anaphase and exit from telophase. The APC, in conjunction with other enzymes, assembles multi-ubiquitin chains on a variety of regulatory proteins, thereby targeting them for proteolysis by the 26S proteasome .
Apolipoprotein CIII (Apo-CIII)
Type: Family

Apolipoprotein C-III is a 79-residue glycoprotein synthesised in the intestine and liver as part of the very low density lipoprotein (VLDL) and the high density lipoprotein (HDL) particles. Owing to its positive correlation with plasma triglyceride (Tg) levels, Apo-CIII is suggested to play a role in Tg metabolism and is therefore of interest regarding atherosclerosis. However, unlike other apolipoproteins such as Apo-AI, Apo E or CII for which many naturally occurring mutations are known, the structure-function relationships of apo C-III remains a subject of debate. One possibility is that apo C-III inhibits lipoprotein lipase (LPL) activity, as shown by
in vitro
experiments. Another suggestion, is that elevated levels of Apo-CIII displace other apolipoproteins at the lipoprotein surface, modifying their clearance from plasma .
Apovitellenin I (Apo-VLDL-II)
Type: Family

This family consists of several avian apovitellenin I sequences. As part of the avian reproductive effort, large quantities of triglyceride-rich very-low-density lipoprotein (VLDL) particles are transported by receptor-mediated endocytosis into the female germ cells. Although the oocytes are surrounded by a layer of granulosa cells harbouring high levels of active lipoprotein lipase, non-lipolysed VLDL is transported into the yolk. This is because VLDL particles from laying chickens (Gallus gallus) are protected from lipolysis by apolipoprotein (apo)-VLDL-II, a potent dimeric lipoprotein lipase inhibitor . Apo-VLDL-II is produced in the liver and secreted into the blood stream when induced by estrogen production in female birds.
Apolipoprotein L (ApoL)
Type: Family

Apo L belongs to the high density lipoprotein family that plays a central role in cholesterol transport. The cholesterol content of membranes is important in cellular processes such as modulating gene transcription and signal transduction both in the adult brain and during neurodevelopment. There are six apo L genes located in close proximity to each other on chromosome 22q12 in humans. 22q12 is a confirmed high-susceptibility locus for schizophrenia and close to the region associated with velocardiofacial syndrome that includes symptoms of schizophrenia .
The various functions of apoL are still not entirely clear. Apolipoprotein L-I has been identified as a trypanolytic agent and displays similar phylogenetic distribution to the programmed cell death protein Bcl-2 and BH-3 domain-containing proteins, suggesting a possible role in apoptosis .
Dormancy/auxin associated protein (DRM/ARP)
Type: Family

This family contains several plant dormancy-associated and auxin-repressed proteins . The expression of the DRM/ARP family members may be regulated by stress and environmental factors .
Branched-chain amino acid transport, AzlD (Brnchd-chn_aa_trnsp_AzlD)
Type: Family

This family consists of a number of bacterial and archaeal branched-chain amino acid transport proteins. AzlD, a member of this group, is encoded by a gene part of the of the azl operon which is involved in branched-chain amino acid transport . AzlCD is a bipartite histidine exporter consisting of AzlC and AzlD subunits . Overexpression of this gene results in resistance to a leucine analog, 4-azaleucine.
Brain acid soluble protein 1 (BASP1)
Type: Family

This family consists of several brain acid soluble protein 1 (BASP1) or neuronal axonal membrane protein NAP-22. The BASP1 is a neuron enriched Ca
2+
-dependent calmodulin-binding protein of unknown function .
Pre-mRNA-splicing factor SPF27 (SPF27)
Type: Family

Proteins in this family are involved in mRNA splicing . This family includes pre-mRNA-splicing factor SPF27, SNT309 and Cwf7. In humans, SPF27 is a component of the PRP19-CDC5L complex that forms an integral part of the spliceosome and is required for activating pre-mRNA splicing. It may have a scaffolding role in the spliceosome assembly as it contacts all other components of the core complex .
Cellulose synthase operon C, C-terminal (BCSC_C)
Type: Domain

This entry contains the C-terminal regions of several bacterial cellulose synthase operon C (BCSC) proteins. BCSC is involved in cellulose synthesis although the exact function of this protein is unknown .
Integrin-binding sialoprotein (IBSP)
Type: Family

This entry represents human Integrin-binding sialoprotein, also known as Bone sialoprotein 2, and similar proteins mainly found in animals.

The major non-collagenous matrix proteins (chondroitin-sulphate glycoproteins decorin and biglycan, sialoproteins osteopontin and bone sialoprotein, osteocalcin and osteonectin) have important roles in formation and organisation of the collagen matrix and nucleation and growth of hydroxyapatite crystals.

Bone sialoprotein (BSP) is a major structural protein of the bone matrix that is specifically expressed by fully differentiated osteoblasts and is highly specific for mineralising tissues. The expression of bone sialoprotein (BSP) is normally restricted to mineralised connective tissues of bones and teeth; it is thought to be responsible for nucleation of hydroxyapatite crystals. BSP also displays a high affinity for calcium ions. The mature protein has a molecular weight of around 33kDa and consists predominantly of Glu and Gly residues. It is subject to extensive post-translational modification, and is predominantly phosphorylated at Ser residues. Post-translational modifications can also cause BSP to act as an inhibitor of hydroxyapatite crystal formation. Ectopic expression of BSP occurs in various lesions, including oral and extraoral carcinomas, in which it has been associated both with the formation of microcrystalline deposits and with the metastasis of cancer cells to bone. The expression of this protein may be altered with the cancer secretome . It has also been related to osteoarthritis .
Hemolysin BL-binding component (HBL)
Type: Family

This entry consists of the hemolysin BL-binding component. Hemolysin BL is an enterotoxin and is composed of a binding component, B, and two lytic components, L1 and L2. Hemolysin BL is responsible for binding to erythrocytes and is thought to be the cause of the diarrheal form of gastroenteritis caused by food-borne strains of B. cereus .
Nucleopolyhedrovirus late expression factor 3 (Baculo_LEF-3)
Type: Family

This family consists of LEF-3 Orgyia pseudotsugata multicapsid polyhedrosis virus (OpMNPV) late expression factor 3 (LEF-3) sequences which are known to be ssDNA-binding proteins . Alkaline nuclease (AN) and LEF-3 may participate in homologous recombination of the baculovirus genome in a manner similar to that of exonuclease (Redalpha) and DNA-binding protein (Redbeta) of the Red-mediated homologous recombination system of bacteriophage lambda .
Baculovirus VP1054 (Baculo_VP1054)
Type: Family

This family consists of several VP1054 proteins from the Baculoviruses. VP1054 (also known as AC54) is a virus structural protein required for nucleocapsid assembly . It is necessary for localization of the major capsid protein VP39 at the site of nucleocapsid assembly .
B-cell receptor-associated protein 29/31 (BAP29/BAP31)
Type: Family

The mammalian B-cell receptor-associated proteins of 29 and 31kDa (BAP29 and BAP31) are integral membrane proteins with a role in endoplasmic reticulum (ER) quality control and sorting . BAP31 is also involved in apoptosis . Saccharomyces cerevisiae possesses three homologues of BAP31 known as Yet1, Yet2, and Yet3 .
Benyvirus p25/p26 (BNYVV_p25/p26)
Type: Family

This entry consists of p25 and p26 proteins from the Beet necrotic yellow vein virus (BNYVV), which is a plant pathogenic virus . It is characterised by a positive-stranded single stranded RNA genome that is rod-shaped and non-enveloped in nature. The virus is transmitted by Polymyxa betae, a fungus from the order Plasmodiophorales.

p25 is an RNA-3-encoded protein that is responsible for the production of rhizomania symptoms of sugar beet roots . An estimate of the ratio between synonymous and non-synonymous substitution rates (omega) with maximum-likelihood models showed that the p25 sequences presented the highest (of three benyvirus proteins) mean omega values with strong positive selection acting on 14 amino acids, and particularly on amino acid 68, where the omega value was the highest so far encountered in plant viruses .
Borrelia membrane P13 (Borrelia_P13)
Type: Family

Lyme borreliosis (or Lyme's disease) is one of the most common tick-borne diseases. It is caused by bacteria from the genus Borrelia.

This family consists of P13 proteins from Borrelia species. P13 is a 13kDa integral membrane protein which is post-translationally processed at both ends and modified by an unknown mechanism .
Borrelia lipoprotein paralogus family 54/60 (Borrelia_lipoprotein_PFam54/60)
Type: Family

This family contains lipoproteins from the Lyme disease spirochete Borrelia burgdorferi and related bacteria, including proteins from Paralogous family 54 (PFam54) and 60 (PFam60). The first crystal structure of B. burgdorferi PFam54 member BBA68 revealed a previously unseen novel fold, which, according to the CATH protein domain classification, was named the Bbcrasp-1 fold because of the common name used for the protein BBA68 .
KN homeodomain (KN_HD)
Type: Domain

This entry represents a homeodomain (HD) present in transcription factors conserved from fungi to human and plants . Genes encoding these proteins were first identified as TALE homeobox proteins in eukaryotes, (including KNOX and MEIS genes) . They have been classified .
P21 molecular chaperone, Bacillus thuringiensis (P21_molc_chaperone_B_thur)
Type: Family

This family contains several Bacillus thuringiensis P21 proteins. These proteins are thought to be molecular chaperones and have mosquitocidal properties .