SII-SWORD/CoKE huggingface dataset:
Lambda phage tail tube protein, N-terminal (Phage_TTP_N)
Type: Domain

This entry represents the N-terminal region of the phage-tail-tube protein from a group of tailed bacteriophages and prophages from proteobacteria. Tail tube proteins (TTPs) polymerise with the assistance of the Tail-tip complex, a tape measure protein and two chaperones. Infectivity of host is delivered through the tube .
Phage tail tube protein, lambda-like (Phage_TTP_11)
Type: Family

This family represents the phage-tail-tube protein from a set of Siphoviridae from Gammaproteobacteria. Tail tube proteins polymerise with the assistance of the Tail-tip complex, a tape measure protein and two chaperones. Infectivity of host is delivered through the tube .
Hemolysin, beta-prism lectin (Hemolysin_beta-prism_lec)
Type: Domain

This β-prism lectin domain is found at the C terminus of the Vibrio cholerae cytolytic pore-forming toxin hemolysin . It binds to N-glycans with a heptasaccharide GlcNAc4Man3 core (NGA2) , but promotes self-assembly of the beta-pore-forming toxin by a carbohydrate-independent mechanism .
Uncharacterised protein YmgD (YmgD)
Type: Family

This family of proteins is found in bacteria. Proteins in this family are approximately 110 amino acids in length.
PI3K regulatory subunit p85-related , inter-SH2 domain (PI3K_P85_iSH2)
Type: Domain

This is the inter SH2 (iSH2) domain found in phosphatidylinositol 3-kinase regulatory subunit p85alpha, p85beta and p55gamma.

Phosphoinositide 3-kinases (PI3Ks) are essential for cell growth, migration, and survival. Class IA PI3Ks are heterodimers of a p110 catalytic (C) subunit and a p85-related regulatory (R) subunit . p110 is composed of an adaptor-binding domain, a Ras-binding domain, a C2 domain, a helical domain, and a kinase domain. p85 is composed of an SH3 domain, a RhoGap domain, a N-terminal SH2 (nSH2) domain, a inter SH2 (iSH2) domain, and C-terminal (cSH2) domain. There are two inhibitory interactions between p110alpha and p85 of P13K: 1) p85 nSH2 domain with the C2, helical, and kinase domains of p110alpha and 2) p85 iSH2 domain with C2 domain of p110alpha. There are three inhibitory interactions between p110beta and p85 of P13K: 1) p85 nSH2 domain with the C2, helical, and kinase domains of p110beta, 2) p85 iSH2 domain with C2 domain of p110beta, and 3) p85 cSH2 domain with the kinase domain of p110beta .
Bacteriophage CI repressor, C-terminal (Phage_CI_C)
Type: Domain

The bacteriophage lambda cI repressor is a part of a phage molecular switch which transforms the phage from lysogenic to lytic growth. The CI repressor from Enterobacteria phage phi80 is known to function as a transcriptional switch, determining whether transcription is lytic or lysogenic . It contains two domains connected by a flexible "hinge" region with a cleavage site .

This entry represents the C-terminal domain of the CI repressor, which functions in oligomer formation .
Spike glycoprotein S1, N-terminal domain, betacoronavirus-like (bCoV_S1_N)
Type: Domain

This entry represents the N-terminal domain of the betacoronavirus-like trimeric spike glycoprotein. The distal S1 subunit of the coronavirus spike protein is responsible for receptor binding. S1 contains two domains; an N-terminal galectin-like domain (NTD) and a receptor-binding domain (S1 RBD) also referred to as the S1 CTD or domain B. Either the S1 NTD or S1 RBD, or occasionally both, are involved in binding the host receptors. S1 NTD is located on the side of the spike trimer and mainly recognises sugar receptors . For many betacoronaviruses (bCoVs), for example mouse hepatitis virus (MHV), the RBD is located in the NTD. The structure of the MHV S1 NTD showed the same fold as human galectins (galactose-binding lectin), however it does not bind any sugar; instead, it binds to the carcinoembryonic antigen cell-adhesion molecule (CEACAM1) through protein-protein interactions . All three CEACAM21a-binding sites in MHV spikes can be fully occupied by CEACAM1a. It has been shown that CEACAM1a binding to the MHV spike weakens the interactions between S1 and S2 and facilitates the proteolysis of the spike protein and dissociation of S1 . The homologous bovine CoV (BCov) S1 NTD also possesses a galectin fold but binds to sialic acid-containing moieties on host cell membranes, as does the NTD of three other group A b-Covs, namely human CoV (HCoV) OC43, avian b-CoV, and infectious bronchitis virus (IBV) . Despite the S1 NTD of human respiratory b-CoV HKU1 being highly homologous to the NTDs of MHV and bovine CoV, it does not bind to either sugar or human CEACAMs and the RBD is found instead in the S1 RBD domain .

The bCoV NTDs contain a conserved β-sandwich core, but exhibit variant folds in the peripheral elements located in the top-ceiling region and on the lateral side. The core sandwich comprises in total sixteen anti-parallel β-strands, assembling into three (upper, middle, and lower) β-sheet layers. While showing different compositions and structures, the peripheral elements are topologically equivalent β-sandwich-core insertions, highlighting a divergent evolution process for bCoVs to form different lineages .
Proteasomal ATPase, second OB domain (Prot_ATP_ID_OB_2nd)
Type: Domain

This is the interdomain (ID) or second oligonucleotide binding (OB) domain of proteasomal ATPase .
Protein of unknown function DUF4979 (DUF4979)
Type: Family

This family consists of uncharacterised proteins around 450 residues in length and is mainly found in various Bacteroides species. The function of this protein is unknown.
FAD dependent oxidoreductase, central domain (FAO_M)
Type: Domain

This domain occurs in several FAD dependent oxidoreductases: sarcosine dehydrogenase, dimethylglycine dehydrogenase and dimethylglycine oxidase. It's function is not known.
Domain of unknown function DUF4978 (DUF4978)
Type: Domain

This domain can be found in a group of uncharacterised proteins, mainly from Bacteroides. Several proteins containing this domain are annotated as Glycoside hydrolases, but their function is not clear.
Non-structural protein NSP4, C-terminal, coronavirus (CoV_NSP4_C)
Type: Domain

This is the C-terminal domain of the coronavirus non-structural protein NSP4. NSP4 is encoded by ORF1a/1ab and proteolytically released from the pp1a/1ab polyprotein. It is a membrane-spanning protein which is thought to anchor the viral replication-transcription complex (RTC) to modified endoplasmic reticulum membranes . This predominantly α-helical domain is involved in protein-protein interactions . It has been shown that in betacoronavirus, the coexpression of NSP3 and NSP4 results in a membrane rearrangement to induce double-membrane vesicles (DMVs) and convoluted membranes (CMs), playing a critical role in SARS-CoV replication. There are two well conserved amino acid residues (H120 and F121) in NSP4 among betacoronavirus, which were demonstrated to be essential for membrane rearrangements during interaction with NSP3. This suggests that the specific details of the interaction between these two proteins varies among different coronavirus .
N-sulphoglucosamine sulphohydrolase, C-terminal (SGSH_C)
Type: Domain

This entry represents a domain found at the C-terminal end of sulfatases and alkaline phosphatases from bacteria, eukaryotes and archaea, including N-sulphoglucosamine sulphohydrolase from humans (SGSH) and Bifunctional sulfatase/alpha-L-rhamnosidase from Formosa agariphila (P36_S1_25). This domain shows a four-stranded antiparallel β-sheet, with four surrounding α-helices, followed by a C-terminal extension consisting of a small two-stranded antiparallel β-sheet .
BT1760-like, C-terminal domain (BT1760-like_C)
Type: Domain

This domain is found at the C-terminal end of BT1760 from Bacteroides thetaiotaomicron (

) and similar bacterial proteins that predominantly belong to the glycoside hydrolase family 32 (GH32,

). BT1760 is a endo-levanase. This protein requires its C-terminal β-sandwich domain to fold and function correctly. This domain shows two facing β-sheets consisting of seven and eight antiparallel β-strands displayed in such a way a concave surface is formed on the top sheet at the same side of the protein which harbours the active centre .
Protein FecR, C-terminal (FecR_C)
Type: Domain

FecARI are responsible for induction of the ferric citrate uptake system. When the inducer, ferric citrate, binds FecA, which is also responsible for transport of ferric citrate across the outer membrane, a signal is transmitted across the outer membrane to the cytoplasmic membrane protein FecR. FecR transmits the signal across the cytoplasmic membrane and activates the sigma-70 family protein FecI. The periplasmic N terminus of FecA interacts with the periplasmic C-terminal portion of FecR .
Domain of unknown function DUF4973 (DUF4973)
Type: Domain

This domain is found in uncharacterised proteins around 340 residues in length, mainly from Bacteroides and Prevotella species.
Protein of unknown function DUF4972 (DUF4972)
Type: Family

This family consists of uncharacterised proteins around 490 residues in length from various Bacteroides specie. The function of this protein is unknown.
Protein of unknown function DUF4971 (DUF4971)
Type: Family

This small family consists of uncharacterised proteins mainly found in various Bacteroides species. The function of this protein is unknown.
Domain of unknown function DUF4969 (DUF4969)
Type: Domain

This domain is found in several uncharacterised proteins. Its function is unknown.
Glutaminase A, central domain (GtaA_central)
Type: Domain

This domain is centrally located in Glutaminase A (GtaA), an enzyme from Aspergillus oryzae that catalyses the hydrolysis of glutamine to glutamic acid and plays a key role in nitrogen metabolism . The function of this domain, previously known as DUF4965, is unknown. It is predicted to adopt a mainly α-helical configuration. Members of this group of proteins are mainly found in fungi and bacteria.
Domain of unknown function DUF4964 (DUF4964)
Type: Domain

This domain is found at the N terminus of several proteins annotated as glutaminases , but its function is unknown.
Na+/H+ antiporter, budding yeast (Nha1)
Type: Family

This entry represents a group of fungal Na+/H+ antiporters from budding yeasts, including Nha1 from S. cerevisiae. Nha1 is involved in sodium and potassium efflux through the plasma membrane. It plays a role in the homeostatic regulation of the plasma membrane potential .
Heparinase II, N-terminal (HepII_N)
Type: Domain

This domain can be found in the N terminus of dermatan-sulfate epimerase from mammals, and heparinase II from bacteria .
YbgF, trimerisation domain (YbgF_tri)
Type: Domain

This is the N-terminal domain of the YbgF protein. YbgF binds to TolA. This domain mediates trimerisation .
MukB, hinge domain (MukB_hinge)
Type: Domain

The hinge domain of chromosome partition protein MukB is responsible for dimerisation and is also involved in protein-DNA interactions and conformational flexibility .
Pestivirus envelope glycoprotein E2 (Pestivirus_E2)
Type: Domain

Pestiviruses have an outer lipid envelope bearing two glycoproteins, E1 and E2, required for cell entry . This entry represent the E2 protein, which consists of two Ig-like domains followed by an elongated β-stranded domain with a new fold .
Protein of unknown function DUF4961 (DUF4961)
Type: Family

This small family consists of several uncharacterised proteins around 350 residues in length and is mainly found in various Bacteroidetes species. The function of this protein is unknown.
Cytochrome c-type biogenesis protein CcmF, C-terminal (CcmF_C)
Type: Domain

This entry represents the C-terminal region of CcmF, one of the cytochrome c-type biogenesis proteins. This domain may deliver reductant to haem on CcmE .
ABC transporter Uup, C-terminal (ABC_tran_C)
Type: Domain

This domain is found at the C terminus of ATP-binding cassette (ABC) transporters such as Uup from Escherichia coli. Uup is a member of the REG subfamily of class II ABC ATPases. It comprises two nucleotide-binding domains (NBD), separated by a 75-residue linker, and a C-terminal domain (CTD). CTD has a coiled coil structure with an atypical 3(10)-helix in the α-hairpin region and is involved in DNA binding .
Peptidase family U32, C-terminal (Peptidase_U32_C)
Type: Domain

This domain is found at the C terminus of many members of peptidase family U32 (

) .
Domain of unknown function DUF4960 (DUF4960)
Type: Domain

This domain is mainly found in proteins from Bacteroides and Prevotella species. The function of this domain is unknown.
Domain of unknown function DUF4959 (DUF4959)
Type: Domain

This domain is found in a group of uncharacterised proteins around 400 residues in length and is mainly found in various Bacteroides, Pedobacter and Parabacteroides species.
Sigma 54 modulation/S30EA ribosomal protein, C-terminal (Ribosom_S30AE_C)
Type: Domain

This domain often occurs at the C terminus of the ribosomal protein S30Ae/sigma 54 modulation protein (

).
Surface glycan binding protein BT4661-like (BT4661-like)
Type: Family

This entry represents a family of proteins mainly found in Bacteroides, including the putative surface glycan binding protein (SGBP) BT4661 from Bacteroides thetaiotaomicron (

). This protein seem to play a role in the bacterial degrading apparatus of the host glycosaminoglycans heparin (Hep) and heparan sulfate (HS). It shows six discrete domains that adopt an Ig-like fold arranged in an extended, curved conformation .
Domain of unknown function DUF4957 (DUF4957)
Type: Domain

This domain is found in a group of uncharacterised proteins around 150 residues in length and is mainly found in various Bacteroidetes species. The function of this domain is unknown.
Protein of unknown function DUF4956 (DUF4956)
Type: Family

This family consists of uncharacterised proteins around 220 residues in length. The function of this protein is unknown.
Domain of unknown function DUF4955 (DUF4955)
Type: Domain

This domain is found in a group of uncharacterised proteins around 850 residues in length and is mainly found in various Bacteroides species. The function of this domain is unknown.
Protein of unknown function DUF4954 (DUF4954)
Type: Family

This family consists of uncharacterised proteins around 660 residues in length and is mainly found in various Bacteroides, Prevotella and Treponema species. The function of this protein is unknown.
EcxA, zinc-binding (EcxA_zinc-bd)
Type: Domain

This domain is found in a group of bacterial proteins, including EcxA from Escherichia coli (

), one of the two components of the metalloprotease AB5 Toxin EcxAB, which functions as an endopeptidase. This region carries the highly characteristic met-zincin motif HExxHxxGxxH, the extended zinc-binding domain of metallopeptidases .
Oberon, coiled-coil region (Oberon_CC)
Type: Domain

This entry represents the coiled-coil region of Oberon proteins from plants. Oberon is necessary for maintenance and/or establishment of both the shoot and root apical meristems in Arabidopsis. Most Oberon proteins carry a PHD finger domain and this coiled-coil domain . Oberon proteins mediate the TMO7 (the direct target of transcription factor Monopteros) expression through modification of, or binding to, chromatin at the TMO7 locus. TMO7 stands for the target of Monopteros 7 (or Auxin response factor 7) .
Transmembrane protein 100 (TMEM100)
Type: Family

Transmembrane protein 100 (TMEM100) is a two-transmembrane protein highly conserved in vertebrates. It acts as an ALK1 receptor signalling-dependent protein during endothelial differentiation and vascular morphogenesis, and regulates TRPA1-TRPV1 complex that mediates pain signals in dorsal root ganglia neurons .
Protein of unknown function DUF4952 (DUF4952)
Type: Family

This family consists of several uncharacterised proteins around 150 residues in length and is mainly found in various Leptospira, Pseudomonas and Stenotrophomonas species. The function of this family is unknown.
Protein of unknown function DUF4951 (DUF4951)
Type: Family

This family consists of several uncharacterised proteins around 125 residues in length and is mainly found in various Acinetobacter baumannii species. The function of this family is unknown.
Domain of unknown function DUF4950 (DUF4950)
Type: Domain

This domain is found in several uncharacterised proteins around 250 residues in length mainly from Enterococcus species. Its function is unknown.
Protein of unknown function DUF4949 (DUF4949)
Type: Family

This small family consists of uncharacterised proteins around 140 residues in length and is found mainly in Legionella neumophila and other Legionella species. The function of this family is unknown.
Protein of unknown function DUF4948 (DUF4948)
Type: Family

This small family consists of uncharacterised proteins around 200 residues in length and is mainly found in Bacteroidales. The function of this family is unknown.
Protein of unknown function DUF4947 (DUF4947)
Type: Family

This small family consists of uncharacterised proteins around 220 residues in length and is mainly found in various Streptococcus species. The function of this family is unknown.
Protein of unknown function DUF4946 (DUF4946)
Type: Family

This small family consists of uncharacterised proteins around 180 residues in length and is mainly found in various Pseudomonas species. The function of this family is unknown.
Protein of unknown function DUF4945 (DUF4945)
Type: Family

This small family consists of uncharacterised proteins around 140 residues in length and is mainly found in various Bacteroides species, specially in Bacteroides fragilis. The function of this family is unknown.
Protein of unknown function DUF4944 (DUF4944)
Type: Family

This family consists of uncharacterised proteins around 160 residues in length and is mainly found in various Bacillus species, specially in Bacillus subtilis. The function of this family is unknown.
Protein of unknown function DUF4943 (DUF4943)
Type: Family

This small family consists of several uncharacterised proteins around 170 residues in length and is mainly found in various Bacteroides species. The function of this family is unknown.
Protein of unknown function DUF4941 (DUF4941)
Type: Family

This family consists of several uncharacterised proteins around 300 residues in length and is mainly found in various Thermotoga species. The function of this family is unknown.
Protein of unknown function DUF4940 (DUF4940)
Type: Family

This family consists of several uncharacterised proteins around 250 residues in length and is mainly found in various Thermotoga species. The function of this family is unknown.
Domain of unknown function DUF4939 (DUF4939)
Type: Domain

This domain is found in some members of the Mart (mammalian retrotransposon-derived) family, including LDOC1/Mart7, LDOC1L/Mart6, RTL1/Mart1, PEG10/Mart2, FAM127/Cxx1/Mart8, ZCCHC5/Mart3 and RGAG4/Mart5 . Its function is not known.
PBP-dependent ABC transporters TM subunit, N-terminal (TM_PBP2_N)
Type: Domain

This domain is found in putative transmembrane subunits (TM) from Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs, such maltose transport permease MalF. It is mainly found in Actinobacteria and Thermotoga species. The function of this domain is unknown.
HTH-type transcriptional repressor, C-terminal (BscR_C)
Type: Domain

This entry represents a domain found in the C-terminal region of some HTH-type transcriptional repressors, such as Bm3R1 from Bacillus megaterium and BscR from Bacillus subtilis .
Acin1, RNSP1-SAP18 binding (RSB) motif (RSB_motif)
Type: Conserved_site

The RSB motif on the Acinus (also known as Acin1) protein is the core around which the ASAP complex is built. The apoptosis and splicing-associated protein complex, ASAP, is made up of three proteins, SAP18 (Sin3-associated protein of 18kDa), RNA-binding protein S1 (RNPS1) and apoptotic chromatin inducer in the nucleus (Acinus). The ASAP complex appears to be an assembly of proteins at the interface between transcription, splicing and nonsense-mediated mRNA decay (NMD), acting as a hub in the network of protein-interactions that regulate gene-expression .
UCP032676, C2H2 type zinc-finger domain (UCP032676_Znf-C2H2)
Type: Domain

This entry represents a C2H2 type zinc-finger domain found in a group of uncharacterised proteins known as UCP032676.
Protein of unknown function DUF4938 (DUF4938)
Type: Family

A small family consists of several uncharacterised proteins around 300 residues in length and is mainly found in Chloroflexia. The function of this family is unknown.
Domain of unknown function DUF4937 (DUF4937)
Type: Domain

This domain can be found in a group of uncharacterised proteins around 120 residues in length and is found in bacteria.
Protein of unknown function DUF4936 (DUF4936)
Type: Family

This family consists of uncharacterised proteins around 100 residues in length and is mainly found in Betaproteobacteria. The function of this family is unknown.
PIN domain (DUF4935) (DUF4935)
Type: Domain

This domain is found on the N-terminal region of uncharacterised proteins. It shows homology to other PIN-like families and contains several acidic residues critical for chelating metal ions that are conserved in other PIN-like domains .
Domain of unknown function DUF4934 (DUF4934)
Type: Domain

This domain can be found in a group of uncharacterised proteins around 400 residues in length and is mainly found in Bacteroidales. The function of this domain is unknown.
Protein of unknown function DUF4933 (DUF4933)
Type: Family

This family consists of uncharacterised proteins around 450 residues in length and is mainly found in Bacteroidales species. Their function is unknown.
Protein of unknown function DUF4932 (DUF4932)
Type: Family

This family consists of uncharacterised proteins around 460 residues in length and is found in bacteria and archaea. Their function is unknown.
Protein of unknown function DUF4930 (DUF4930)
Type: Family

This is a family of uncharacterised proteins around 150 residues in length and found mainly in Staphylococcus. The function of this family is unknown.
Protein of unknown function DUF4929 (DUF4929)
Type: Family

This family consists of uncharacterised proteins around 400 residues in length and is mainly found in Bacteroides and Prevotella species. The function of this family is unknown.
DAMP1, SANT/Myb-like domain (DAMP1_SANT-like)
Type: Domain

This domain, approximately 90 residues, is mainly found in DNA methyltransferase 1-associated protein 1 (DAMP1), which plays an important role in development and maintenance of genome integrity in various mammalian species . It mainly consists of tandem repeats of three α-helices that are arranged in a helix-turn-helix motif and shows a structural similarity with SANT domain and Myb DNA-binding domain, indicating it contains a putative DNA-binding site .
Protein of unknown function DUF4928 (DUF4928)
Type: Family

This family consists of uncharacterised proteins around 330 residues in length and is found in bacteria. The function of this family is unknown.
Nuclear receptor coactivator 2/3, DUF4927 (NCOA2/3_DUF4927)
Type: Domain

This entry represents a domain found in Nuclear receptor coactivators 2/3 (NCOA2/3), which are ligand-dependent transcription factors . NCOA2 is a transcriptional coactivator for steroid receptors and nuclear receptors. It functions as a coactivator of the steroid binding domain (AF-2) but not of the modulating N-terminal domain (AF-1) . Together with NCOA1, it is required to control energy balance between white and brown adipose tissues . NCOA3 is overexpressed in a fraction of breast cancers and has been linked to prognosis and tamoxifen resistance .
Aprataxin, C2HE/C2H2/C2HC zinc finger (Znf-C2HE)
Type: Domain

This is an unusual zinc-binding domain found in fungi, plants and metazoa. It is often found at the C terminus of HIT-domain-containing proteins (

). In fungi the fourth ligand is a Glu, in plants it is Cys and in metazoans it is usually a His. The fourth ligand is often mutated in neurogenerative disease-states .

This domain can be found in Aprataxin, a DNA-binding protein involved in single-strand and double-strand DNA break repair, and base excision repair .