SII-SWORD/CoKE huggingface dataset:
Major structural subunit of bundle-forming pilus (Bundlin)
Type: Family

This family consists of Major structural subunit of bundle-forming pilus (Bundlin) from Escherichia coli and similar proteins from Proteobacteria. Bundlin is a type IV pilin protein that is the only known structural component of enteropathogenic E. coli bundle-forming pili (BFP). BFP play a role in virulence, antigenicity, autoaggregation, and localised adherence to epithelial cells .
Mitochondrial fission regulator 1 (Mtfr1)
Type: Family

Mitochondrial fission regulator 1 has been described in mammals, where it induces mitochondrial fission .
Pilus assembly TraE (Pilus_assembly_TraE)
Type: Family

This family consists of several bacterial sex pilus assembly and synthesis proteins (TraE). Conjugal transfer of plasmids from donor to recipient cells is a complex process in which a cell-to-cell contact plays a key role. Many genes encoded by self-transmissible plasmids are required for various processes of conjugation, including pilus formation, stabilisation of mating pairs, conjugative DNA metabolism, surface exclusion and regulation of transfer gene expression . The exact function of the TraE protein is unknown.
Tenuivirus movement protein (Tenui_movmnt_prot)
Type: Family

This family of ssRNA negative-strand crop plant tenuivirus proteins appears to combine PV2 , NS2 , NS3, and PV3 proteins.

Plant viruses encode specific proteins known as movement proteins (MPs) to control their spread through plasmodesmata (PD) in walls between cells as well as from leaf to leaf via vascular-dependent transport. During this movement process, the virally encoded MPs interact with viral genomes for transport from the viral replication sites to the PDs in the walls of infected cells along the cytoskeleton and/or endoplasmic reticulum (ER) network. The virus is then thought to move through the PDs in the form of MP-associated ribonucleoprotein complexes or as virions . The NS3 protein appears to function as an RNA silencing suppressor .
Baculovirus pp39 (Baculo_pp39)
Type: Family

Autographa californica nuclear polyhedrosis virus (AcMNPV) pp31 is a nuclear phosphoprotein that accumulates in the virogenic stroma, which is the viral replication centre in the infected-cell nucleus. Deletion of the pp31 gene does not seem to affect viral DNA replication, but results in a modest down-regulation of both early and late genes .
Poxvirus Virion membrane protein OPG144 precursor (Poxvirus_OPG144)
Type: Family

This entry represents the Virion membrane protein OPG144 precursor from poxvirus, encoded by the A17L (or A18L) gene is cleaved into the Mature 21 kDa protein OPG144, which has been
reported to localise on the inner of the two membranes of the intracellular mature virus (IMV). It has
also been shown that it acts as a membrane anchor for the externally located fusion protein P14
(A27L gene) . This envelope protein participates in virus morphogenesis. Its interaction with OPG125 scaffold protein leads to the formation of rigid, crescent-shaped membranes that assemble around the cytoplasmic virus factory .
Baculovirus occlusion-derived virus envelope EC27 (Baculo_ODV-E27)
Type: Family

This family consists of several baculovirus occlusion-derived virus envelope proteins (EC27 or E27) which appear to act as a multifuntional cyclins during the host cell cycle. The ODV-E27 protein has distinct functional characteristics compared to cellular and viral cyclins. When associated with cdc2, it exhibits cyclin B-like activity; when associated with cdk6, the complex possesses cyclin D-like activity and binds PCNA (proliferating cell nuclear antigen) .
Type II restriction enzyme NlaIII/ICEA1 (NlaIII/ICEA1)
Type: Family

Endonuclease NlaIII recognises the double-stranded sequence CATG and cleaves after G-4 . This family also includes ICEA1, a CATG-recognising restriction endonuclease from Helicobacter pylori . ICEA1 is speculated to be associated with peptic ulcer disease .
Small ribosomal subunit protein uS3m, fungi (Ribosomal_uS3m_fun)
Type: Family

This entry represents the fungal small ribosomal subunit protein uS3m, previously known as VAR1.

This family consists of the VAR1 mitochondrial ribosomal proteins found in yeast and related proteins which are essential for mitochondrial protein synthesis and required for the maturation of small ribosomal subunits . Mitochondria possess their own ribosomes responsible for the synthesis of a small number of proteins encoded by the mitochondrial genome. VAR1 is the only protein in the yeast mitochondrial ribosome to be encoded in the mitochondria - the remaining approximately 80 ribosomal proteins are encoded in the nucleus . VAR1 along with 15S rRNA are necessary for the formation of mature 37S subunits .

Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.

Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome .
Tombusvirus movement (Tombusvirus_movement)
Type: Family

This family consists of several Tombusvirus movement proteins. These proteins allow the virus to move from cell-to-cell and allow host-specific systemic spread .
DNA-directed RNA polymerase, 19kDa subunit, poxviral (DNA-dir_RNA_Pol_19kDa_poxvir)
Type: Family

DNA-directed RNA polymerases

(also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length . The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel.

RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3' direction, is known as the primary transcript.

Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise:

RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs.

RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors.

RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs.

Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700kDa, contain two non-identical large (>100kDa) subunits and an array of up to 12 different small (less than 50kDa) subunits.

The poxvirus DNA-directed RNA polymerase (

) catalyses the transcription of DNA into RNA. It consists of at least eight subunits, this is the 19kDa subunit.
Haemolysin expression modulating, HHA (Hemolysn_expr_modulating_HHA)
Type: Family

This family consists of haemolysin expression modulating protein (Hha) from Escherichia coli and its enterobacterial homologues, such as YmoA from Yersinia enterocolitica, and RmoA encoded on the R100 plasmid. These proteins act as modulators of bacterial gene expression. Members of the Hha/YmoA/RmoA family act in conjunction with members of the H-NS family, participating in the thermoregulation of different virulence factors and in plasmid transfer . Hha, along with the chromatin-associated protein H-NS, is involved in the regulation of expression of the toxin alpha-haemolysin in response to osmolarity and temperature . YmoA modulates the expression of various virulence factors, such as Yop proteins and YadA adhesin, in response to temperature. RmoA is a plasmid R100 modulator involved in plasmid transfer . The HHA family of proteins display striking similarity to the oligomerization domain of the H-NS proteins.
NINE (NINE)
Type: Family

This family consists of NINE proteins from several bacteriophage and from Escherichia coli.
Poxvirus A21 (Poxvirus_A21)
Type: Family

This entry represents A21 from Vaccinia virus, also known as Virion membrane protein OPG147, and similar proteins from poxvirus. A21 is an envelope protein part of the entry-fusion complex responsible for the virus membrane fusion with host cell membrane during virus entry. It also plays a role in cell-cell fusion (syncytium formation) .
Sperm-associated antigen 11 A/B (Sperm_Ag_11A_B)
Type: Family

This family consists of several variants of the human and chimpanzee (Pan troglodytes) sperm antigen proteins (HE2 and EP2 respectively). The EP2 gene codes for a family of androgen-dependent, epididymis-specific secretory proteins, known as sperm-associated antigen 11. The EP2 gene uses alternative promoters and differential splicing to produce a family of variant messages. The translated putative protein variants differ significantly from each other. Some of these putative proteins have similarity to beta-defensins, a family of antimicrobial peptides .
Protein of unknown function DUF730 (DUF730)
Type: Family

This family consists of several uncharacterised proteins of unknown function, from Arabidopsis and Brassica genera.
Prolactin-inducible protein (PIP)
Type: Family

Prolactin-inducible (PIP) is a 17kDa glycoprotein that binds to many proteins including fibrinogen, actin, keratin, myosin, immunoglobulin G, CD4, and human zinc-alpha-2 glycoprotein . It forms a complex with human serum albumin (HSA) in seminal plasma and may affect male fertility/infertility . It also acts as a factor capable of suppressing T-cell apoptosis through its interaction with CD4 .
RNA polymerase I specific transcription initiation factor RRN3 (RNA_pol_I_trans_ini_fac_RRN3)
Type: Family

This family consists of several eukaryotic proteins which are homologous to the Saccharomyces cerevisiae RRN3 protein. RRN3 is one of the RRN genes specifically required for the transcription of rDNA by RNA polymerase I (Pol I) in the S. cerevisiae RNA polymerase I complex within the nucleolus. In mammalian cells, the phosphorylation state of Rrn3 regulates rDNA transcription by determining the steady-state concentration of the Rrn3 .
Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, CybS (CybS)
Type: Family

This family consists of mitochondrial succinate dehydrogenase [ubiquinone] cytochrome b small subunit CybS (also known an SQR) and import inner membrane translocase subunit Tim18. Members of this subfamily are classified as Type C SQRs because they contain two transmembrane subunits and one heme group. CybS and CybL are the two transmembrane proteins of eukaryotic SQRs. They contain heme and quinone binding sites. CybS is the eukaryotic homologue of the bacterial SdhD subunit.

CybS is a membrane-anchoring subunit of succinate dehydrogenase (SDH) that is involved in complex II of the mitochondrial electron transport chain and is responsible for transferring electrons from succinate to ubiquinone (coenzyme Q) . CybS is composed of a flavoprotein catalytic subunit, an iron-sulfur protein and one or two hydrophobic transmembrane subunits . The two-electron oxidation of succinate in the flavoprotein active site is coupled to the two-electron reduction of quinone in the transmembrane subunits via electron transport through FAD and three iron-sulfur centres . The reversible reduction of quinone is an essential feature of respiration, allowing transfer of electrons between respiratory complexes. Mutations in human Complex II result in various physiological disorders including hereditary paraganglioma and pheochromocytoma tumors. The gene encoding for the SdhD subunit is classified as a tumor suppressor gene .

In Saccharomyces cerevisiae, Tim18 is a component of the TIM22 complex, a complex that mediates the import and insertion of multi-pass transmembrane proteins into the mitochondrial inner membrane. The TIM22 complex forms a twin-pore translocase that uses the membrane potential as external driving force. Its role in the complex is unclear but it may be involved in the assembly and stabilisation of the TIM22 complex .
Protein of unknown function DUF742 (DUF742)
Type: Family

This family consists of several uncharacterised Streptomyces proteins as well as one from
Mycobacterium tuberculosis. The function of these proteins is
unknown.
Vesivirus VP2 (Vesivirus_VP2)
Type: Family

This family consists of several Calicivirus VP2 proteins . VP2 is a minor capsid protein encoded by all caliciviruses. It forms a large portal-like assembly at a unique three-fold axis of symmetry, following receptor engagement. This assembly-which was not detected in undecorated virions-is formed of twelve copies of VP2, arranged with their hydrophobic N terminus pointing away from the virion surface.
Protein of unknown function DUF719 (DUF719)
Type: Family

This family consists of several eukaryotic proteins of unknown function.
Protein of unknown function DUF745 (DUF745)
Type: Family

This family consists of several uncharacterised Drosophila melanogaster proteins of unknown function.
Rhamnose/fucose mutarotase (Rham/fucose_mutarotase)
Type: Family

Mutarotases are enzymes which interconvert the alpha and beta stereoisomers of monosaccharides, enhancing the rate of their metabolism. Proteins in this entry are homologues of the rhamnose mutarotase YiiL (

) from Escherichia coli, and are often encoded in rhamnose utilisation operons. YiiL is an enzyme which interconverts the alpha and beta stereoisomers of the pyranose form of L-rhamnose . It is not required for growth on rhamnose, but allows cells to utilise this carbon source more efficiently .The structure of YiiL is distinct from other mutarotases, forming an asymmetric dimer stabilised by an intermolecular β-sheet, hydrophobic interactions and a salt bridge .

Included in this family is the L-fucose mutarotase from Xanthomonas campestris XCC4070 , but not other L-fucose mutarotases.
Macrophage colony stimulating factor-1 (MCSF-1)
Type: Family

Colony stimulating factor 1 (CSF-1) is a homodimeric polypeptide growth factor whose primary function is to regulate the survival, proliferation, differentiation, and function of cells of the mononuclear phagocytic lineage. This lineage includes mononuclear phagocytic precursors, blood monocytes, tissue macrophages, osteoclasts, and microglia of the brain, all of which possess cell surface receptors for CSF-1. The protein has also been linked with male fertility and mutations in the Csf-1 gene have been found to cause osteopetrosis and failure of tooth eruption .
Herpesvirus, Orf30 (Herpes_Orf30)
Type: Family

This entry is represented by the Human herpesvirus 8, Orf30 protein; it is a family of uncharacterised viral proteins.
Protein of unknown function DUF739 (DUF739)
Type: Family

This entry includes Bacteriophage bIL285, Orf5. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

This family contains several bacteriophage proteins. Three of the proteins in this
family have been labelled putative cro repressor proteins.
Protein OCTOPUS-like (OCTOPUS-like)
Type: Family

This family consists of several plant proteins, including protein OCTOPUS (OPS, At3g09070) and OPSL1 (At5g01170) from Arabidopsis . OPS is a membrane-associated protein that regulates phloem differentiation entry . It is a positive regulator of the brassinosteroid (BR) signaling pathway and sequesters BIN2 to the plasma membrane to promote phloem differentiation .
Per os infectivity factor 6 (PIF6)
Type: Family

This entry is represented by Autographa californica nuclear polyhedrosis virus (AcMNPV) Orf68 (also known as per os infectivity factor 6, PIF6 or ac68). PIF6 is present in both the budded virus (BV) and the occluded-derived virus (ODV). The ac68 gene overlaps the lef3 gene which encodes the single-stranded DNA binding protein, and knockout experiments of ac68 have to ensure that a functional lef3 gene is present. In ac68KO experiments, viral DNA replication and BV levels were unaffected as were mortality rates if caterpillars were injected with BV directly into the hemolymph bypassing the gut. However, in oral bioassays the ac68KO occlusion bodies failed to kill larvae, indicating that PIF6 is a per os infectivity factor .
Peptidase M26, N-terminal domain (Peptidase_M26_N_dom)
Type: Domain

Over 70 metallopeptidase families have been identified to date. In these enzymes a divalent cation, which is usually zinc but may be cobalt, manganese or copper, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. In some families of co-catalytic metallopeptidases, two metal ions are observed in crystal structures ligated by five amino acids, with one amino acid ligating both metal ions. The known metal ligands are His, Glu, Asp or Lys. At least one other residue is required for catalysis, which may play an electrophilic role.

Many metalloproteases contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site . The HEXXH motif is relatively common but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases .

This entry represents a domain found in the N-terminal half of metallopeptidases belonging to MEROPS peptidase family M26. They are extracellular enzymes, which cleave mammalian IgA. They are only found in Gram-positive bacteria and are often found associated with an LPXTG-motif cell wall anchor, indicating that they may be attached to the cell wall. The family also includes the metallopeptidases ZmpB and ZmpC from Streptococcus pneumoniae. These metallopeptidases are thought to contribute to the inflammatory response to Streptococcal infection .
Peptidase M42 (Peptidase_M42)
Type: Family

These peptidases are found in Archaea and Bacteria. The example in Lactococcus lactis, PepA, aids growth on milk . Pyrococcus horikoshii contain a thermostable de-blocking aminopeptidase member of this family, which is used commercially for N-terminal protein sequencing .
Domain of unknown function DUF746 (DUF746)
Type: Domain

This is a short conserved region found in some transposons.
Tapt1 family (Tatp1)
Type: Family

This family of membrane proteins is conserved in eukaryotes. It includes Tapt1 (transmembrane anterior posterior transformation 1) and homologues. Analysis of mouse Tapt1 has shown it to be involved in patterning of the vertebrate axial skeleton . Its cellular function is not known, but defective Tapt1 disrupts Golgi morphology and trafficking, and normal primary cilium formation .

The homologues in yeast, endoplasmic reticulum membrane protein 65, and Arabidopsis, POD1, seem to be involved in protein folding in the endoplasmic reticulum .
Complex 1 LYR protein domain (Complex1_LYR_dom)
Type: Domain

Proteins containing this domain include an accessory subunit of the higher eukaryotic NADH dehydrogenase complex. In Saccharomyces cerevisiae, the Isd11 protein (

) has been shown to play a role in Fe/S cluster biogenesis in mitochondria . We have named this family LYR after a highly conserved tripeptide motif close to the N terminus of these proteins.
Proteasome maturation factor Ump1 (Ump1)
Type: Family

Ump1 is a short-lived chaperone present in the precursor form of the 20S proteasome and absent in the mature complex. Ump1 is required for the correct assembly and enzymatic activation of the proteasome. Ump1 seems to be degraded by the proteasome upon its formation .
GATA-type transcription activator, N-terminal (GATA_N)
Type: Domain

GATA transcription factors mediate cell differentiation in a diverse range of tissues. Mutations are often associated with certain congenital human disorders. The six classical vertebrate GATA proteins, GATA-1 to GATA-6, are highly homologous and have two tandem zinc fingers. The classical GATA transcription factors function as transcription activators. In lower metazoans GATA proteins carry a single canonical zinc finger. This entry represents the N-terminal domain of the family of GATA transcription activators.
Glycogen synthase kinase-3 binding protein (GSK3-bd)
Type: Family

Glycogen synthase kinase-3 (GSK-3) sequentially phosphorylates four serine residues on glycogen synthase (GS), in the sequence SxxxSxxxSxxx-SxxxS(p), by recognising and phosphorylating the first serine in the sequence motif SxxxS(P) (where S(p) represents a phosphoserine). Interaction of GSK-3 with a peptide derived from GSK-3 binding protein prevents GSK-3 interaction with Axin. This interaction thereby inhibits the Axin-dependent phosphorylation of beta-catenin by GSK-3 .
GMP phosphodiesterase, delta subunit (PDED_dom)
Type: Domain

This entry represents a domain found in GMP-PDE delta subunit and related proteins.
Portal protein Gp10 (Gp10)
Type: Family

This entry represents the upper collar protein (also known as portal protein Gp10) from various bacteriophage. The upper collar protein of Bacteriophage phi-29 is composed of twelve 36kDa subunits with 12-fold symmetry. It consists of two domains: an α-helical bundle domain and a β-barrel domain. This protein is located between the head and the tail of the bacteriophage and acts as the central component of a rotary motor that packages the genomic dsDNA into pre-formed proheads. This motor consists of the upper collar protein, surrounded by a 29-encoded, 174-base, RNA and a viral ATPase protein .