SII-SWORD/CoKE huggingface dataset:
Nucleoside diphosphate kinase 7 (NDPK7)
Type: Family

The nm23-H7 nucleoside diphosphate kinase (also known as NDPk7 or NME7) consists of an N-terminal DM10 domain and two functional catalytic NDPk modules, NDPk7A and NDPk7B. The function of the DM10 domain, which also occurs in multiple copies in other proteins, is unknown. NDPk7 is predominantly expressed in testes, although appreciable amounts are also found in liver, heart, brain, ovary, small intestine and spleen . The nm23-H7 gene is located in or near the hereditary prostrate cancer susceptibility locus. Nm23-H7 may be involved in the development of colon and gastric carcinoma, the latter possibly in a type-specific manner .
NTP pyrophosphohydrolase MazG-related, YvdC (MazG-related_YvdC)
Type: Family

Members of this group are distantly related to MazG-type NTP pyrophosphohydrolase. Conserved residues of the MazG domain (at least three of the Glu residues, Asp, Lys and Arg), including those shown to be functionally important , are also conserved here. MazG protein of Thermotoga maritima has been shown to have both nucleoside triphosphate pyrophosphohydrolase and pyrophosphatase activities, while Escherichia coli MazG has only NTP pyrophosphohydrolase activity .
Coronamic acid biosynthesis thioesterase CmaT (CmaT_thioesters)
Type: Family

This group represents a coronamic acid biosynthesis thioesterase CmaT. Please see the following relevant reference: .
Uncharacterised conserved protein UCP036540 (UCP036540_AIR)
Type: Family

Members of this family belong to a large group that also contains thiamine monophosphate kinase (

), hydrogenase maturation factor HypE (

), AIR synthase, FGAM synthase (

), selenophosphate synthase (

), and other groups. In AIR synthase, the N-terminal domain forms the dimer interface of the protein and, upon dimerisation, forms the putative ATP binding domain, while the cleft formed between the N- and C-terminal domains is postulated to be a sulphate binding site . It could be speculated that similar structure-function relationship exists in members of this family; however, there is no experimental data that proves the biochemical activity.
Uncharacterised conserved protein UCP036541 (UCP036541_AIR)
Type: Family

Members of this family belong to a large group that also contains thiamine monophosphate kinase, hydrogenase maturation factor HypE (

), AIR synthase, FGAM synthase (

), selenophosphate synthetase (

), and other groups. In AIR synthase, the N-terminal domain forms the dimer interface of the protein and, upon dimerisation, forms the putative ATP binding domain, while the cleft formed between the N- and C-terminal domains is postulated to be a sulphate binding site . It could be speculated that similar structure-function relationship exists in members of this family; however, there is no experimental data that proves the biochemical activity.
Predicted bifunctional spore maturation protein, fused SpmA/SpmB (SpmA_SpmB)
Type: Family

This group contains two-domain proteins that are fusions of spore maturation protein A (SpmA) and spore maturation protein B (SpmB). SpmA and SpmB are thought to be involved in spore core dehydration in Bacillus subtilis. Spore dehydration is important for heat resistance, and for processing the spore germination protease GPR into an active form . SpmA and SpmB might be involved in import or export from the forespore, or for modification of the cortex peptidoglycan structure . SpmA and SpmB are predicted to be integral membrane proteins.

For additional information please see .
Predicted RNA-binding protein YdrC-type, Chlamydia (YdrC-type_chlamyd)
Type: Family

This group contains homologues of Escherichia coli YrdC with an additional unique short (~100 aa) C-terminal domain. In accordance with its proposed role as a translation factor, YrdC preferentially binds dsRNA, likely via a depression on the surface of the protein . However, members of both this group lack the C-terminal domain that has been shown to be essential for the regulatory (probably translational) function of the related two-domain protein SUA5 (

) .
AP180 N-terminal homology (ANTH) domain (ANTH_dom)
Type: Domain

The AP180 N-terminal homology (ANTH) domain is a membrane binding domain found in endocytotic accessory proteins, such as AP180. AP180 has been implicated in the formation of clathrin-coated pits. The ANTH domain is involved in phosphatidylinositol 4,5-bisphosphate (also known as PIP2) binding. The ANTH domain containing proteins appear to be universal elements in nucleation of clathrin coats .
ATP12, ATP synthase F1-assembly protein (ATP12_ATP_synth-F1-assembly)
Type: Family

This entry represents a group proteins from eukaryotes and bacteria that may have chaperone activity and be involved in F1 ATPase complex assembly. The eukaryotic proteins include yeast ATP12 and mammalian homologue ATPAF2 (ATP synthase mitochondrial F1 complex assembly factor 2) , which are required for assembly of the mitochondrial F1-ATPase.

Mitochondrial F1-ATPase is an oligomeric enzyme composed of five distinct subunit polypeptides. The alpha and beta subunits make up the bulk of protein mass of F1. In Saccharomyces cerevisiae both subunits are synthesised as precursors with N-terminal targeting signals that are removed upon translocation of the proteins to the matrix compartment .
Nitrogen regulatory AreA, N-terminal (AreA_N)
Type: Domain

The AreA nitrogen regulatory proteins (which are GATA type transcription factors) share a highly conserved N terminus and have

at the C terminus.
BCNT-C domain (BCNT-C)
Type: Domain

Vertebrate BCNT (named after Bucentaur) protein is found in the nucleus and cytosol. Gene duplication of the ancestral BCNT gene leads to the h-type BCNT or craniofacial development protein 1 (CFDP1) gene and the ruminant-specific p97BCNT or craniofacial development protein 2 (CFDP2) gene. The h-type BCNT proteins contain a highly conserved 82-amino acid region at the C terminus (BCNT-C) that is not present in p97BCNT. Instead ruminant p97BCNT contains a region derived from the endonuclease domain of a retrotransposable element RTE-1 .

In addition to h-type BCNT proteins, a BCNT-C domain is also found in Drosophila YETI, a protein that binds to a microtubule-based motor kinesin-1, and the yeast SWR1-complex protein 5 (SWC5) or AOR1 (actin overexpression resistant 1), a component of the SWR1 chromatin remodeling complex .

The entry represents the entire BCNT-C domain.
BRCA1-associated 2/ETP1, RRM (BRAP2/ETP1_RRM)
Type: Domain

This entry represents the RNA-binding domain (also referred to as RNA recognition motif (RRM)) of BRAP2 and its homologues.

This entry includes human BRCA1-associated protein (BRAP/BRAP2, also known as impedes mitogenic signal propagation (IMP), RING finger protein 52, or renal carcinoma antigen NY-REN-63) and its homologues from yeast ETP1. BRAP2 is a cytoplasmic protein interacting with the two functional nuclear localization signal (NLS) motifs of BRCA1, a nuclear protein linked to breast cancer. It also binds to the SV40 large T antigen NLS motif and the bipartite NLS motif found in mitosin. BRAP2 serves as a cytoplasmic retention protein and plays a role in the regulation of nuclear protein transport .

These proteins contain an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C3H2C3-type RING-H2 finger and a UBP-type zinc finger.
Mediator of RNA polymerase II transcription subunit 9 (Med9)
Type: Family

This entry represents subunit Med9 of the Mediator complex. Subunit Med9 is part of the middle module of the Mediator complex ; this associates with the core polymerase subunits to form the RNA polymerase II holoenzyme.

Med9 alternatively known as the chromosome segregation protein, CSE2 (

) is required, along with CSE1 (

) for accurate mitotic chromosome segregation in Saccharomyces cerevisiae (Baker's yeast) .

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.
CamS sex pheromone cAM373 (CamS)
Type: Family

This family includes CamS (

), from which Staphylococcus aureus sex pheromone staph-cAM373 is processed. It also includes a number of uncharacterised bacterial proteins.
Chlamydia polymorphic membrane, middle domain (Polymorphic_membr_middle)
Type: Domain

This domain is found in several Chlamydia polymorphic membrane proteins . Chlamydia pneumoniae (Chlamydophila pneumoniae) is an obligate intracellular bacterium and a common human pathogen causing infection of the upper and lower respiratory tract. This domain is found between the β-helical repeats (

) and the C-terminal

.
Spore coat protein X/V (Spore_coat_X/V)
Type: Domain

This domain is found in the Bacilli coat protein X as a tandem repeat and as a single domain in coat protein V. The proteins are found in the insoluble fraction .
Cytochrome C, Planctomycete-type (Cyt_c_Planctomycete-type)
Type: Domain

These proteins share a region of homology at their N terminus that contains the C-{CPWHF}-{CPWR}-C-H-{CFYW} motif typical of cytochrome c. They are found mainly in Planctomycetes, Verrucomicrobia and Bacteroidetes.
U3 small nucleolar RNA-associated protein 20, N-terminal (UTP20_N)
Type: Domain

This entry represents a region of tetratricopeptide-like (TPR) repeats found towards the N-terminal of eukaryotic proteins including U3 small nucleolar RNA-associated protein 20 from yeast and the human homologue, also known as Small subunit processome component 20 homolog or DRIM (Down-Regulated In Metastasis) (

). DRIM is differentially expressed in metastatic and non-metastatic human breast carcinoma cells . Proteins of this entry are involved in processing of non-coding RNA as components of the small-subunit (SSU) processome; SSU processome is involved in the biogenesis of the 18S rRNA . UTP20 is a huge α-solenoid that functions as a scaffold .
Protein trafficking Pga2 (Trafficking_Pga2)
Type: Family

A Saccharomyces cerevisiae (Baker's yeast) member of this family (PGA2,

) is a single pass membrane protein which is implicated in protein trafficking and processing of glycosylated proteins .
Heme-binding protein Shr-like, Hb-interacting domain (Shr-like_HID)
Type: Domain

This entry represents the Hb-interacting domain (HID), which is found duplicated in Heme-binding protein Shr from Streptococcus pyogenes, a potentially lethal human pathogen, and in one to six copies in other uncharacterised bacterial proteins. Shr is a virulence factor that captures Hb and binds to the oxidized form of heme through an N-terminal region that contains two copies of this domain. HID shows a β-sandwich-type fold in which two antiparallel β-sheets are flanked by an α-helix .
Putative host cell surface-exposed lipoprotein Ltp-like, HTH region (Ltp-like_HTH)
Type: Domain

This entry represents a domain found as 1 to 5 copies in proteins from bacteria and virus, including Putative host cell surface-exposed lipoprotein from Streptococcus phage TP-J34 (Ltp,

), a superinfection exclusion protein. This domain shows a three-helix bundle belonging to the HTH superfamily .
Na(+), Li(+), K(+)/H(+) antiporter subunit A/B (UmpAB)
Type: Family

UmpAB function as a two-component Na+(Li+, K+)/H+ antiporter .
Domain of unknown function DUF1539 (DUF1539)
Type: Domain

This domain is found in a small number of Chlamydia proteins of unknown function. It occurs together with

.
Domain of unknown function DUF1540 (DUF1540)
Type: Domain

These proteins have four conserved cysteines, which is suggestive of a metal binding function. This domain may be found on its own or duplicated in the proteins.
Domain of unknown function DUF1541 (DUF1541)
Type: Domain

This domain is found in several hypothetical bacterial proteins as a tandem repeat.
Domain of unknown function DUF1542 (DUF1542)
Type: Domain

This domain is found in several cell surface proteins, such as extracellular matrix-binding protein ebh . Some members are involved in antibiotic resistance (e.g.

and

) and/or cellular adhesion (e.g.

) . In some proteins it is repeated more than fifteen times, being the most repeated domain in streptococci . This is a predominantly α-helical domain that forms a long, thin, fibre-like structure and it has been proposed to function as a stalk that helps the adhesive non-repeat region (NRR) of proteins protrude beyond the cell surface .
Domain of unknown function DUF1543 (DUF1543)
Type: Domain

This domain is found as 1-2 copies in a small family of proteins of unknown function.
TAF6, C-terminal HEAT repeat domain (TAF6_C)
Type: Domain

This is the C-terminal domain of the TAF6 subunit of the general transcription factor TFIID. The crystal structure reveals the presence of five conserved HEAT repeats. This region is necessary for the complexing together of the subunits TAF5, TAF6 and TAF9 .
Domain of unknown function DUF1547 (DUF1547)
Type: Domain

This domain appears to be found only in a small family of Chlamydia species . It is usually found repeated. This domain can be found in translocated actin-recruiting phosphoprotein (Tarp) from Chlamydia trachomatis serovar L2. Tarp appears to initiate or participate in signalling events that regulate the actin recruitment, which ultimately leads to internalization .
Domain of unknown function DUF1549 (DUF1549)
Type: Domain

The function is not known. It is found associated with

. It is also found associated with the Planctomycete cytochrome C domain

.
Putative beta barrel porin-7 (BBP7)
Type: Family

This is a family of putative β barrel porin-7 BBP7 proteins identified initially in Rhodopirellula baltica.
Protein of unknown function DUF1552 (DUF1552)
Type: Family

This is a family of uncharacterised proteins first identified in the Planctomycete Rhodopirellula baltica.
Domain of unknown function DUF1554 (DUF1554)
Type: Domain

This is a domain that occurs in 1-2 copies in a family of proteins identified in Leptospira interrogans and other bacteria. The function of the proteins is not known.
Domain of unknown function DUF1559 (DUF1559)
Type: Domain

This is a poorly conserved central region found in a large family of paralogous proteins mainly from Planctomycetes, Verrucomicrobia, Armatimonadota and Lentisphaerae.
Protein of unknown function DUF1561 (DUF1561)
Type: Family

This is a family of uncharacterised proteins.
Protein of unknown function DUF1563 (DUF1563)
Type: Family

This family of proteins is functionally uncharacterised.
Protein of unknown function DUF1564 (DUF1564)
Type: Family

This is a family of paralogous proteins in Leptospiraceae. One of them (e.g.

) have been annotated as possible CopG-like transcriptional regulators (see

).
Domain of unknown function DUF1565 (DUF1565)
Type: Domain

These proteins share a region of homology in their N termini, and are found in several phylogenetically diverse bacteria and in the archaeon Methanosarcina acetivorans. Some of these proteins also contain characterised domains such as

(e.g.

) and

(e.g.

).
Lcl, C-terminal (Lcl_C)
Type: Domain

This domain, previously known as DUF1566, is found C-terminal in the Legionella collagen-like protein (Lcl) and related proteins mainly from bacteria. Lcl is an extracellular peripheral membrane protein that recognises sulphated glycosaminoglycans (GAGs) on the surface of eukaryotic cells, but also stimulates bacterial aggregation in response to divalent cations. This domain has a structural similarity to C-type lectins and is involved in glycan recognition .
Protein of unknown function DUF1569 (DUF1569)
Type: Family

This entry represents a family of hypothetical proteins identified in Rhodopirellula baltica and other bacteria.
Domain of unknown function DUF1570 (DUF1570)
Type: Domain

This entry represents hypothetical proteins confined to bacteria.
Protein of unknown function DUF1571 (DUF1571)
Type: Family

This is a family of paralogous proteins found in Planctomycetacia and Betaproteobacteria.
Protein of unknown function DUF1572 (DUF1572)
Type: Family

This protein represents proteins with unknown function found in several diverse bacteria.
Protein of unknown function DUF1573 (DUF1573)
Type: Family

These hypothetical proteins from bacteria, such as Rhodopirellula baltica, Bacteroides thetaiotaomicron and Porphyromonas gingivalis, share a region of conserved sequence towards their N termini.
Protein of unknown function DUF1574 (DUF1574)
Type: Family

This is a family of hypothetical proteins found in Leptospira interrogans and other bacteria.
Protein of unknown function DUF1576 (DUF1576)
Type: Family

This small family has no known function. Their sequences frequently contain conserved glycine and aromatic residues.
Protein of unknown function DUF1577 (DUF1577)
Type: Family

This is a family of hypothetical proteins found in Leptospiraceae.
Protein of unknown function DUF1579 (DUF1579)
Type: Family

This is a family of paralogous hypothetical proteins identified in Rhodopirellula baltica that also has members in Gloeobacter violaceus, Rhizobium meliloti and Agrobacterium tumefaciens, amongst others.
Protein of unknown function DUF1580 (DUF1580)
Type: Family

This is a family of short hypothetical proteins found in Rhodopirellula baltica.
Domain of unknown function DUF1583 (DUF1583)
Type: Domain

This entry represents a domain mainly found in bacterial proteins from Planctomycetia. Many of the Rhodopirellula baltica hypothetical proteins that have this domain also match

.
Protein of unknown function DUF1582 (DUF1582)
Type: Family

This is a family of hypothetical proteins found in Rhodopirellula.
Domain of unknown function DUF1585 (DUF1585)
Type: Domain

This entry represents a conserved region at the C terminus of a family of cytochrome-like proteins found in bacteria such as Rhodopirellula baltica and Solibacter usitatus. These proteins also contain

,

,

and

.
Protein of unknown function DUF1589 (DUF1589)
Type: Family

This is a family of short hypothetical proteins found in Rhodopirellula baltica.
Cellulose-binding Sde182, nucleoside hydrolase-like domain (Sde182_NH-like)
Type: Domain

This entry represents a Rossmann-related domain found in bacterial and fungal proteins, including Cellulose-binding protein from Saccharophagus degradans (

). This protein, which seems to have capacity to bind plant carbohydrates, contain carbohydrate-binding modules (CBMs) together with a C-terminal domain of unknown function that is organised into two subdomains. This entry represents the N-terminal region of this C-terminal domain. It adopts an α/β configuration with a central β-sheet of eight β-strands surrounded by 12 α-helices and shows structural similarity to some ribonucleoside hydrolases (NH) .
Putative beta-barrel porin-2, OmpL-like bbp2 (BBP2)
Type: Family

BBP2 is a family of putative porin proteins that are likely to be outer membrane β-barrel proteins porins.
Protein of unknown function DUF1598 (DUF1598)
Type: Family

This is a family of Planctomycetales hypothetical proteins of about 500 amino acids in length.
Translation initiation factor 2, alpha subunit (TIF_2_asu)
Type: Family

In Eukaryota and Archaea, translation initiation factor 2 (eIF2/aIF2), which contains three subunits (alpha, beta and gamma), is pivotal for binding of charged initiator tRNA to the small ribosomal subunit. This entry represents the alpha subunit of both eukaryota and archaeal translation initiator factor 2.
EMI domain (EMI_domain)
Type: Domain

The EMI domain, first named after its presence in proteins of the EMILIN family, is a small cysteine-rich module of around 75 amino acids. The EMI domain is most often found at the N terminus of metazoan extracellular proteins that are forming or are compatible with multimer formation . It is found in association with other domains, such as C1q, laminin-type EGF-like, collagen-like, FN3, WAP, ZP or FAS1 . It has been suggested that the EMI domain could be a protein-protein interaction module, as the EMI domain of EMILIN-1 was found to interact with the C1q domain of EMILIN-2 .
Flagellar hook protein FlgE, D2 domain (FlgE_D2)
Type: Domain

This domain is found in several bacterial FlgE flagellar hook proteins . The flagellar hook is a short, curved, extracellular structure located between the basal body and the filament .
Non-structural protein NS3-like, DEAD-box helicase, flavivirus (Flavi_DEAD)
Type: Domain

The non-structural protein NS3 from flavivirus is a bifunctional protein that contains an N-terminal protease (

) and a C-terminal helicase domains that plays an essential role in viral polyprotein processing and genome replication. The N-terminal domain is a chymotrypsin-like serine protease, which is responsible for most of the maturation cleavages of the polyprotein precursor in the cytosolic side of the endoplasmic reticulum membrane. The C-terminal domain, is a helicase belonging to superfamily 2 (SF2) that unwinds the dsRNA and removes the gamma-phosphate at the 5'-RNA prior to RNA cap addition .

This entry represents the DEAD-box domain from flavivirus NS3 helicase domain. This domain is also found in a group of potyviruses, which are plant viruses, such as Zucchini yellow mosaic virus, Plum pox potyvirus and Tobacco etch virus.
GLUG (GLUG)
Type: Domain

This domain is found in the IgA1-specific metalloendopeptidases, which attach to the cell wall peptidoglycan by an amide bond . IgA1 protease selectively cleaves human IgA1 and is likely to be a pathogenicity factor in some pathogens including Giardia spp . This domain is also found in various other contexts, including with

. It is named GLUG after the mostly conserved G-L-any-G motif.

The IgA1-specific metalloendopeptidases belong to MEROPS peptidase family M26, clan MA(E).
Protein HIRA-like, C-terminal (HIRA-like_C)
Type: Domain

This entry represents a domain found at the C-terminal end of the HIRA proteins, which mediates homooligomerization .

The Hira proteins are found in a range of eukaryotes and are implicated in the assembly of repressive chromatin, including Hir1/2 from yeast and the orthologue from human, HIRA (also known as TUP1-like enhancer of split protein 1). These proteins contain a WD40 repeat (

) at the N-terminal a central B domain and a C domain at the C-terminal .

HIRA/Hir1/2 cooperate with ASF1A to promote replication-independent chromatin assembly. It is also required for the periodic repression of histone gene transcription during the cell cycle and for the formation of senescence-associated heterochromatin foci (SAHF) and efficient senescence-associated cell cycle exit . Human HIRA is associated with the the DiGeorge syndrome, a developmental disorder .