SII-SWORD/CoKE huggingface dataset:
ATP synthase protein 8, fungal type (ATP_synth_su8_fun)
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.

F-ATPases (also known as ATP synthases, F1F0-ATPase, or H(+)-transporting two-sector ATPase) (

) are composed of two linked complexes: the F1 ATPase complex is the catalytic core and is composed of 5 subunits (alpha, beta, gamma, delta, epsilon), while the F0 ATPase complex is the membrane-embedded proton channel that is composed of at least 3 subunits (A-C), with additional subunits in mitochondria. Both the F1 and F0 complexes are rotary motors that are coupled back-to-back. In the F1 complex, the central gamma subunit forms the rotor inside the cylinder made of the α(3)β(3) subunits, while in the F0 complex, the ring-shaped C subunits forms the rotor. The two rotors rotate in opposite directions, but the F0 rotor is usually stronger, using the force from the proton gradient to push the F1 rotor in reverse in order to drive ATP synthesis . These ATPases can also work in reverse in bacteria, hydrolysing ATP to create a proton gradient.

In yeast, the F0 complex is composed of at least nine polypeptides which are nucleus-encoded: b, OSCP, d, e, f, g, h, i/j and k, together with three subunits, 6, 8 and 9, which are mitochondrion-encoded. The bovine enzyme also includes subunit F6 for which no homologue has been found in yeast .

This entry represents subunit 8 found in the F0 complex of mitochondrial F-ATPases from fungi. This subunit appears to be an integral component of the stator stalk in yeast mitochondrial F-ATPases . The stator stalk is anchored in the membrane, and acts to prevent futile rotation of the ATPase subunits relative to the rotor during coupled ATP synthesis/hydrolysis. This subunit differs in sequence between fungi, Metazoa (

) and plants (

).
Chloride channel CLIC-like (Chloride_chnl_CLIC-like)
Type: Family

This entry consists of several Chloride channel CLIC-like proteins, which function as a chloride channel when incorporated in the planar lipid bilayer .
EB-1 binding (EB1-bd)
Type: Domain

This region at the C terminus of the APC proteins binds the microtubule-associating protein EB-1 . At the C terminus of the alignment is also a PDZ-binding domain. A short motif in the middle of the region appears to be found in the APC2 proteins (e.g.

).
Competence pheromone ComX, Bacillus-type (Competence_ComX_Bacillus)
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 .

Natural genetic competence in Bacillus subtilis is controlled by quorum-sensing (QS). The ComP- ComA two-component system detects the signalling molecule ComX, and this signal is transduced by a conserved phosphotransfer mechanism. ComX is synthesised as an inactive precursor and is then cleaved and modified by ComQ before export to the extracellular environment .
Adenomatous polyposis coli protein basic domain (APC_basic_dom)
Type: Domain

This region of the APC family of proteins is known as the basic domain. It contains a high proportion of positively charged amino acids and interacts with microtubules .
Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf146 (AcMNPV_Orf146)
Type: Family

This entry is represented by Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf146; it is a family of uncharacterised viral proteins.
Chordopoxvirus A13L (Chordopox_A13L)
Type: Family

The major components of the vaccinia virus membrane consists of the A17L, A14L, A13L, L1L, D8R, and H3L proteins. This entry represents the A13L protein, also known as Virion membrane protein OPG139, which is 70 amino acids long and has an N-terminal hydrophobic region that is implicated in cotranslational insertion of the protein into the membranes of the ER. It is dispensable for the early biogenesis of the virion membrane but is essential for virion maturation .
Herpesvirus US2/US3 (Herpes_US2/US3)
Type: Family

Unique short glycoprotein 2 (US2) and US3 are Herpesviral proteins that interfere with the expression of major histocompatibility complex (MHC) class I molecules on the surface of infected cells. US2 is an endoplasmic reticulum resident transmembrane protein that binds to newly synthesized MHC class I heavy chains in the endoplasmic reticulum, redirecting them to the cytosol for proteasome-dependent destruction, thereby preventing their expression at the cell surface . US3 is similarly an endoplasmic reticulum resident transmembrane glycoprotein that binds MHC class I molecules and prevents their departure. The endoplasmic reticulum retention signal of the US3 protein is contained in the luminal domain of the protein .
Chordopoxvirus A33R (Chordopox_A33R)
Type: Family

This family consists of several Chordopoxvirus A33R proteins. A33R, also known as Protein OPG161, plays a role in promoting Ab-resistant cell-to-cell spread of virus and interacts with A36R to incorporate the protein into the outer membrane of intracellular enveloped virions (IEV) and, subsequently, the production of actin tails .
Bacillus PapR (Bacillus_PapR)
Type: Family

This family consists of the Bacillus species-specific PapR protein. The papR gene belongs to the PlcR regulon and is located 70 bp downstream from plcR. It encodes a 48-amino-acid peptide. Disruption of the papR gene abolishes expression of the PlcR regulon, resulting in a large decrease in haemolysis and virulence in insect larvae. A processed form of PapR activates the PlcR regulon by allowing PlcR to bind to its DNA target. This activating mechanism is strain specific .
Adenomatous polyposis coli protein, 15 residue repeat (APC_15aa_rpt)
Type: Repeat

The 15 aa repeat is found in the APC protein family. It is involved in binding beta-catenin along with the

repeats. Many human cancer mutations map to the region around these motifs, and may be involved in disrupting their binding of beta-catenin.
Toxin HigB-like (HigB-like)
Type: Family

This entry consists of putative toxins, including probable endoribonuclease HigB1 . HigB1 is a toxic component of an atypical, type II toxin-antitoxin chaperone (TAC) module. Upon expression in M.smegmatis it inhibits colony formation and cell growth .
Protein of unknown function DUF896 (DUF896)
Type: Family

In Bacillus subtilis, one small SOS response operon under the control of LexA, the yneA operon, is comprised of three genes: yneA, yneB, and ynzC . This family consists of several short, hypothetical bacterial proteins of unknown function. These proteins are mainly found in Gram-positive Firmicutes. Structures show that the N terminus is composed of two α-helices forming a helix-loop-helix motif. The structure of ynzC from B. subtilis forms a trimeric complex . Structural modelling suggests this domain may bind nucleic acids . This family is also known as UPF0291.
Mediator complex, subunit Med7 (Mediatior_Med7)
Type: Family

The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins.

The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11.

This family consists of several eukaryotic proteins, which are homologues of the yeast MED7 protein. Activation of gene transcription in metazoans is a multistep process that is triggered by factors that recognise transcriptional enhancer sites in DNA. These factors work with co-activators such as MED7 to direct transcriptional initiation by the RNA polymerase II apparatus .
Herpesvirus UL22A (Cytomegalo_UL22A)
Type: Family

This family consists of several Cytomegalovirus UL20A proteins. UL20A is thought to be a glycoprotein .
Ethanolamine ammonia-lyase small subunit (EutC)
Type: Family

This family consists of several bacterial ethanolamine ammonia-lyase small subunit (EutC) sequences. Ethanolamine ammonia-lyase is a bacterial enzyme that catalyses the adenosylcobalamin-dependent conversion of certain vicinal amino alcohols to oxo compounds and ammonia .
Chordopoxvirus A35R (Chordopox_A35R)
Type: Family

This family consists of several Chordopoxvirus sequences homologous to the Vaccinia virus A35R protein, also known as Protein OPG163, which affects the expression of MHC class II molecules on the surface of host antigen presenting cells (APCs) .
SbmA/BacA-like (SbmA_BacA)
Type: Family

The Rhizobium meliloti (Sinorhizobium meliloti) bacA gene encodes a function that is essential for bacterial differentiation into bacteroids within plant cells in the symbiosis between R. meliloti and alfalfa. An Escherichia coli homologue of BacA, SbmA, is implicated in the uptake of microcins and bleomycin. This family is likely to be a subfamily of the ABC transporter family.
Ferredoxin-dependent bilin reductase (Ferredoxin-dep_bilin_Rdtase)
Type: Family

This family consists of several different but closely related proteins which include phycocyanobilin:ferredoxin oxidoreductase

(PcyA), 15,16-dihydrobiliverdin:ferredoxin oxidoreductase

(PebA) and phycoerythrobilin:ferredoxin oxidoreductase

(PebB). Phytobilins are linear tetrapyrrole precursors of the light-harvesting prosthetic groups of the phytochrome photoreceptors of plants and the phycobiliprotein photosynthetic antennae of cyanobacteria, red algae, and cryptomonads. It is known that that phytobilins are synthesised from haem via the intermediacy of biliverdin IX alpha (BV), which is reduced subsequently by ferredoxin-dependent bilin reductases with different double-bond specificities .
Alpha-2,3-sialyltransferase (A-2_3-sialyltransferase)
Type: Family

This entry represents several alpha-2,3-sialyltransferase (

) proteins, most of which are found in the food-borne pathogen Campylobacter jejuni. Sialyltransferases transfer a sialic acid moiety from cytidine-5'-monophospho-N-acetyl-neuraminic acid (CMP-NeuAc) to terminal positions of various key glycoconjugates, which play critical roles in cell recognition and adherence . The structure of Cst-II alpha-2,3-sialyltransferase from C. jejuni consists of a 3-layer α/β/α topology. Cst-II catalytic mechanism involves an essential histidine (general base) and two tyrosine residues (coordination of the phosphate leaving group) to carry out substrate binding and glycosyl transfer.
Cell division protein ZapB (Cell_div_ZapB)
Type: Family

Cell division protein ZapB is a non-essential, abundant cell division factor that is required for proper Z-ring formation. It is recruited early to the divisome by direct interaction with FtsZ, stimulating Z-ring assembly and thereby promoting cell division earlier in the cell cycle. Its recruitment to the Z-ring requires functional FtsA or ZipA .
Protein of unknown function DUF905 (DUF905)
Type: Family

This family consists of several short hypothetical proteobacterial proteins of unknown function.
Laminin alpha, domain I (Laminin_aI)
Type: Domain

Laminins are glycoproteins that are major constituents of the basement membrane of cells. Laminins are trimeric molecules; laminin-1 is an alpha1 beta1 gamma1 trimer. It has been suggested that the domains I and II from laminin A, B1 and B2 may come together to form a triple helical coiled-coil structure . Binding to cells via a high affinity receptor, laminin is thought to mediate the attachment, migration and organisation of cells into tissues during embryonic development by interacting with other extracellular matrix components.
YqgQ-like (YqgQ-like)
Type: Family

This family consists of short proteins predominantly found in Firmicutes, including Uncharacterized protein YqgQ from Bacillus subtilis. YqgQ folds into a three-helical bundle, with the helix order being left-handed and with the third helix flanked by a loop. Based on sequence and structural homology, this protein is thought to be involved in single-stranded nucleic acid binding .
Chordopoxvirus A30L (Chordopox_A30L)
Type: Family

This family consists of several short Chordopoxvirus proteins which are homologous to the A30L protein of Vaccinia virus, also known as Protein OPG157. The vaccinia virus A30L protein is required for the association of electron-dense, granular, proteinaceous material with the concave surfaces of crescent membranes, an early step in viral morphogenesis. A30L is known to interact with the G7L protein and it has been shown that the stability of each is dependent on its association with the other .
Bacteriophage T4, Gp30.8 (Phage_T4_Gp30.8)
Type: Family

This entry is represented by Bacteriophage T4, Gp30.8; it is a family of uncharacterised viral proteins.
Drosophila roughex (Roughex)
Type: Family

This family consists of several roughex (RUX) proteins specific to Drosophila species. Roughex can influence the intracellular distribution of cyclin A and is therefore defined as a distinct and specialised cell cycle inhibitor for cyclin A-dependent kinase activity . Rux is though to regulate the metaphase to anaphase transition during development .
CRISPR-associated exonuclease Csa1 (CRISPR-ass_Csa1)
Type: Family

CRISPR (clustered regularly interspaced short palindromic repeats) elements and cas (CRISPR-associated) genes are widespread in Bacteria and Archaea. The CRISPR/Cas system operates as a defense mechanism against mobile genetic elements (i.e., viruses or plasmids). Csa1 is part of the archaeal subtype I-A system. Cas1 has not yet been enzymatically characterised .
Autographa californica nuclear polyhedrosis virus (AcMNPV), Protein AC78 (AcMNPV_AC78)
Type: Family

This entry represents Protein AC78 from Autographa californica nuclear polyhedrosis virus (AcMNPV) and similar proteins from Baculovirus. AC78 is a late gene in the viral life cycle and encodes an envelope structural protein that plays an essential role in embedding the occlusion-derived virus (ODV) in the occlusion body . Although AC78 is not essential for budding virus formation or nucleocapsid assembly and ODV formation, number are significantly reduced if the gene is knocked-out .
Solute carrier family 35 member SLC35F1/F2/F6 (SLC35_F1/F2/F6)
Type: Family

This entry contains some of the solute carrier family 35 members, including SLC35F1, SLC35F2 and SLC35F6. In humans, SLC35F6 is involved in the maintenance of mitochondrial membrane potential in pancreatic ductal adenocarcinoma (PDAC) cells. It promotes pancreatic ductal adenocarcinoma (PDAC) cell growth and may play a role as a nucleotide-sugar transporter .
SERTA domain (SERTA_dom)
Type: Domain

The SERTA (for SEI-1, RBT-1, and TARA) domain is a motif of ~47 residues corresponding to the largest conserved region among TRIP-Br (transcriptional regulator interacting with the PHD-bromodomain) proteins, an evolutionarily conserved family restricted to higher eukaryotes. In proteins of the TRIP-Br family, the SERTA domain is found in association with a cyclin A-binding domain and a PHD-bromo binding domain. The SERTA domain is also found in some other proteins with no conservation with TRIP-Br proteins outside of the SERTA motif. The cyclin-dependent kinase CDK4-interacting segment of TRIP-Br1 includes most of the SERTA domain .
Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf57 (AcMNPV_Orf57)
Type: Family

This entry is represented by Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf57; it is a family of uncharacterised viral proteins.
Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf29 (AcMNPV_Orf29)
Type: Family

This entry is represented by Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf29. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

This family consists of several short baculovirus proteins of unknown function.
Adenovirus E3 (Adeno_E3)
Type: Family

This family consists of several Adenovirus E3 proteins. The E3 protein does not seem to be essential for virus replication in cultured cells suggesting that the protein may function in virus-host interactions .
Putative nucleotidyltransferase (NTP_transf_6)
Type: Family

This family consists of several hypothetical bacterial proteins of unknown function. This family was recently identified as belonging to the nucleotidyltransferase superfamily .
Reovirus P9-like (Reo_P9)
Type: Family

These proteins of unknown function are found in Rice black streaked dwarf virus (RBSDV) and other viruses.
NF-kappa-B-activating protein, C-terminal (NKAP_C)
Type: Domain

This is the C-terminal domain found in NF-kappa-B-activating protein (Nkap) and a hypothetical open reading frame on chromosome 6, c6orf194. It is the HDAC3 binding domain required for transcriptional repression . Nkap functions as a transcriptional repressor on Notch target genes, and is required for T cell development and acquisition of functional competency .
Domain of unknown function DUF927 (DUF927)
Type: Domain

This entry represents a domain found in bacterial proteins of unknown function. The crystal stucture has been solved for a protein containing this domain

.
Coagulation factor V, LSPD (Coagulation_factor_V_LSPD)
Type: Repeat

The name LSPD derives from the conserved residues in the middle of the repeat. These repeats are found in coagulation factor V and occur in the B domain, which is cleaved prior to activation of the protein. It has been suggested that domain B bring domains A and C together for activation .

Coagulation factor V is a central regulator of hemostasis and serves as a critical cofactor for the prothrombinase activity of factor Xa that results in the activation of prothrombin to thrombin.
Protein of unknown function DUF929 (DUF929)
Type: Family

This is a family of proteins from the archaeon Sulfolobus, with undetermined function.
Protein of unknown function DUF930 (DUF930)
Type: Family

This is a family of proteins with undetermined function from bacteria, mainly from the Rhizobiales order.
Host-nuclease inhibitor Gam (Gam)
Type: Family

This superfamily represents the host-nuclease inhibitor protein Gam. Structurally, it consists of 4 α helices, 2 long and 2 short.
Within bacteriophage lambda protein Gam, one of the long helices (H4) acts as a dimerisation interface to form an antiparallel helix. The two short helices (H2 and H3) from each dimer form a 'cross-brace', while the other long helix (H1) protrudes out of the protein . Within bacteriophage lambda, Gam is involved in inhibiting host nucleases.
SepZ (SepZ)
Type: Family

SepZ is a component of the type III secretion system use in bacteria. SepZ is a gene within the enterocyte effacement locus. SepZ mutants exhibit reduced invasion efficiency and lack of tyrosine phosphorylation of Hp90 .
Herpesvirus US9 (Herpes_US9)
Type: Family

This family consists of several US9 and related proteins from the Alphaherpesviruses. The function of the US9 protein is unknown although in Bovine herpesvirus 5 Us9 is essential for the anterograde spread of the virus from the olfactory mucosa to the bulb . Together with the gE/gI heterodimer, US9 is involved in the sorting and transport of viral structural components toward axon tips .
Portal protein, Mu bacteriophage (Portal_Mu)
Type: Family

This entry represents phage portal proteins found in bacteriophage Mu (gp29 protein) and related proteins. This protein forms the portal vertex of the capsid. This portal plays critical roles in head assembly, genome packaging, neck/tail attachment, and genome ejection. The portal protein multimerizes as a single ring-shaped homododecamer arranged around a central channel.
Orthopoxvirus F14 (Orthopox_F14)
Type: Family

This family consists of several short Orthopoxvirus F14 proteins. F14 is also known as Protein OPG058. The function of this protein is unknown.
Transmembrane protein 176A/B (TMEM176A/TMEM176B)
Type: Family

Transmembrane (TMEM)-176A and 176B proteins are closely related to MS4A (membrane-spanning 4-domains subfamily A) proteins . Their levels are significantly elevated in certain cancers . TMEM176B (LR8, Torid, Clast1) is broadly expressed, but was up regulated in antigen presenting cells in a rat model of allograft tolerance . Their role in the immune system is unclear.
Protein of unknown function DUF937 (DUF937)
Type: Family

This entry consists of several hypothetical bacterial proteins of unknown function.
Apyrase (Apyrase)
Type: Family

This family consists of several eukaryotic apyrase (or adenosine diphosphatase) proteins (

), and related nucleoside diphosphatases (

). The salivary apyrases of blood-feeding arthropods are nucleotide hydrolysing enzymes implicated in the inhibition of host platelet aggregation through the hydrolysis of extracellular adenosine diphosphate . Soluble calcium-activated nucleotidase 1 (CANT1) is the human homologue .
Cytomegalovirus TRL10 (Cytomega_TRL10)
Type: Family

This family consists of several Cytomegalovirus TRL10 proteins. TRL10 represents a structural component of the virus particle and like the other HCMV envelope glycoproteins, is present in a disulphide-linked complex .
Poxvirus A26L (Poxvirus_A26L)
Type: Family

This family represents A26L from Vaccinia virus, also known as Envelop protein OPG153, and similar sequences from poxvirus. A26L is an envelop protein that mediates acid-dependent endocytosis into host cells . It plays an important role in endocytic entry of the virus by acting as an acid-sensitive membrane fusion suppressor . Low pH in host endosomes triggers conformational changes to allow de-repression of viral fusion complex activity and membrane fusion within vesicles .
Inositol-pentakisphosphate 2-kinase (Ins_P5_2-kin)
Type: Family

This is a family of inositol-pentakisphosphate 2-kinases (also known as inositol 1,3,4,5,6-pentakisphosphate 2-kinase, Ins(1,3,4,5,6)P5 2-kinase) and InsP5 2-kinase). This enzyme phosphorylates Ins(1,3,4,5,6)P5 to form Ins(1,2,3,4,5,6)P6 (also known as InsP6 or phytate). InsP6 is involved in many processes such as mRNA export, nonhomologous end-joining, endocytosis and ion channel regulation .