SII-SWORD/CoKE huggingface dataset:
RTL1-related (RTL1-rel)
Type: Family

This family includes mammalian retrotransposon-derived proteins from the Mart family: RTL1/Mart1, PEG10/Mart2, ZCCHC5/Mart3, Zcchc16/Mart4, RGAG4/Mart5 and related retrotransposon Gag-like proteins. RTL1/Mart1 Plays an essential role in capillaries endothelial cells for the maintenance of feto-maternal interface and for development of the placenta. .
Protein of unknown function DUF4926 (DUF4926)
Type: Family

This family consists of uncharacterised proteins around 70 residues in length and is mainly found in bacteria. The function of this family is unknown.
Nucleophosmin, C-terminal (NPM1_C)
Type: Domain

This domain, approximately 50 residues in length, is mainly found in C-terminal region of nucleophosmin from animals . Nucleophosmin (also known as NPM1/B23) is a multifunctional protein that is involved in a number of cellular activities, such as ribosome maturatation and export, centrosome duplication, and response to stress stimuli . Although it shuttles rapidly between the nucleus and the cytoplasm, a large fraction of NPM1/B23 resides in the nucleoli . Mutations of the NPM1 gene has been linked to acute myeloid leukemia .
Splicing factor 1, helix-hairpin domain (SF1-HH)
Type: Domain

This helix-hairpin domain can be found in the N-terminal region of mammalian splicing factor 1 (SF1), plant splicing factor-like protein 1 and fungal branchpoint binding proteins (BBP) . These proteins are required for pre-spliceosome formation, which is the first step of pre-mRNA splicing .

SF1 forms a complex with U2AF65 through the interaction between this domain and the C-terminal U2AF homology motif domain (UHM) of U2AF65. This domain forms a secondary, hydrophobic interface with U2AF65 (UHM) to lock the orientation of the two subunits, which is essential for cooperative formation of the ternary SF1-U2AF65-RNA complex . This domain contains a highly conserved SPSP motif at its C terminus; the phosphorylation of the SPSP motif induces a disorder-to-order transition within a novel SF1/U2AF65 interface .
KHDRBS, Qua1 domain (Qua1_dom)
Type: Domain

The Qua1 domain can be found in the N-terminal region of the KHDRBS (KH-domain containing, RNA-binding, signal transduction-associated) proteins . This domain is a homodimerisation domain necessary for the function of KHDRBS1 (also known as Sam68) in alternative splicing .
Nuclear migration protein nudC (NuDC)
Type: Domain

This entry represents a domain found in nuclear migration protein nudC, which is implicated in cell division through the regulation of cytoplasmic dynein . NudC may play a role not only in mitosis and cytokinesis , but also in interkinetic nuclear migration and neuronal migration during neocortical development .
Protein of unknown function DUF4925 (DUF4925)
Type: Family

This family consists of uncharacterised proteins around 400 residues in length and is mainly found in various Bacteroides and Parabacteroides species. The function of this family is unknown.
Protein of unknown function DUF4924 (DUF4924)
Type: Family

This family consists of uncharacterised proteins around 180 residues in length and is mainly found in Bacteroides, Prevotella and Porphyromonas species. The function of this family is unknown.
Lipocalin-like domain (DUF4923) (DUF4923)
Type: Domain

Proteins containing this domain are a group of uncharacterised proteins around 200 residues in length and mainly found in Bacteroidales. Their function is unknown. This domain is distantly related to lipocalins.
Domain of unknown function DUF4921 (DUF4921)
Type: Domain

This domain can be found in a group of uncharacterised proteins around 450 residues in length. Several proteins containing this domain are predicted as galactose-1-phosphate uridylytransferases. The function of this domain is unknown.
Protein of unknown function DUF4920 (DUF4920)
Type: Family

This family consists of uncharacterised proteins around 190 residues in length and is found in bacteria. The function of this family is unknown.
Protein of unknown function DUF4919 (DUF4919)
Type: Family

This family consists of uncharacterised proteins around 230 residues in length and is mainly found in Bacteroidetes. The function of this family is unknown.
DNA glycosylase Phe SMUG2-like (Phe_SMUG2-like)
Type: Family

This protein family includes the family 3 SMUG1-like DNA glycosylase Phe SMUG2 from Pedobacter heparinus and uncharacterised proteins mainly found in bacteria. Phe SMUG2 has catalytic activity towards DNA containing uracil or hypoxanthine/xanthine .
SatD family (SatD)
Type: Family

This family includes SatD from Streptococcus. SatD is involved in acid resistance .
Protein of unknown function DUF4917 (DUF4917)
Type: Family

This family consists of uncharacterised proteins around 340 residues in length and is mainly found in Proteobacteria. The function of this family is unknown.
Protein of unknown function DUF4916 (DUF4916)
Type: Family

This family consists of uncharacterised proteins around 175 residues in length and is mainly found in Actinobacteria. The function of this family is unknown.
Protein of unknown function DUF4914 (DUF4914)
Type: Family

This family consists of uncharacterised proteins around 630 residues in length and is found in bacteria. The function of this family is unknown.
Protein of unknown function DUF4913 (DUF4913)
Type: Family

This family consists of uncharacterised proteins around 150 residues in length and is mainly found in Actinobacteria.
Protein of unknown function DUF4912 (DUF4912)
Type: Family

This family consists of uncharacterised proteins around 160 residues in length and is mainly found in bacteria. The function of this family is unknown.
Tagaturonate/fructuronate epimerase (UxaE)
Type: Family

This family of proteins around 500 residues in length and is mainly found in various Bacteria. This entry includes T. maritima UxaE, a tagaturonate-fructuronate epimerase involved in the hexuronate catabolic network .
Protein of unknown function DUF4911 (DUF4911)
Type: Family

This family consists of uncharacterised proteins around 75 residues in length and is found in bacteria. The function of this family is unknown.
Putative GDSL-like Lipase/Acylhydrolase (Lipase_GDSL_lke)
Type: Family

This entry represents a group of putative GDSL-like Lipases/Acylhydrolases from bacteria.
Domain of unknown function DUF4910 (DUF4910)
Type: Domain

This domain is related to aminopeptidase domains, but its function is not clear.
Protein of unknown function DUF4909 (DUF4909)
Type: Family

Proteins in this family are approximately 160 amino acids in length. Several members are associated with vancomycin virulence in Staphylococcus aureus in some way . These proteins are all lipoproteins, carrying the characteristic prokaryotic membrane-attachment site at their N termini.
Protein of unknown function DUF4908 (DUF4908)
Type: Family

This is a small family of uncharacterised proteins around 260 residues in length and found in Alphaproteobacteria. The function of this family is unknown.
Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus (NSP3_NAB_bCoV)
Type: Domain

This entry represents the nucleic acid binding domain (NAB/NAR), of approximately 100 residues in length, found in the multidomain nonstructural protein NSP3 from betacoronavirus, and described as NSP3e domain. NSP3 is part of Orf1a polyproteins in SARS-CoV . It is an essential component of the replication/transcription complex .

The global domain of the NAB represents a new fold, with a parallel four-strand β-sheet holding two α-helices of three and four turns that are oriented antiparallel to the β-strands. A group of residues form a positively charged patch on the protein surface as the binding site responsible for binding affinity for nucleic acids. When binding to ssRNA, the NAB prefers sequences with repeats of three consecutive Gs, such as (GGGA)5 and (GGGA)2. A positively charged surface patch (Lys75, Lys76, Lys99, and Arg106) is involved in RNA binding .
Protein of unknown function DUF4907 (DUF4907)
Type: Family

This is a family of uncharacterised proteins around 110 residues in length and found in bacteria. The function of this family is unknown.
Domain of unknown function DUF4906 (DUF4906)
Type: Domain

This domain is found in a group of uncharacterised proteins from Bacteroidales. Its function is unknown.
Protein of unknown function DUF4905 (DUF4905)
Type: Family

This is a small family of uncharacterised proteins around 270 residues in length and found in bacteria. The function of this family is unknown.
Domain of unknown function DUF4904 (DUF4904)
Type: Domain

This domain is found in uncharacterised proteins mainly from Cyanobacteria. It is mainly composed of antiparallel β-sheets and has a cystatin-like fold, but the specific function is unknown.
Protein of unknown function DUF4903 (DUF4903)
Type: Family

This entry represents a family of uncharacterised proteins around 210 residues in length and found in Bacteroidetes. The function of this family is unknown.
Transcriptional regulator RsaM-like (RsaM-like)
Type: Family

This entry represents a family of proteins mainly found in Proteobacteria, including RsaM from Burkholderia cenocepacia (encoded by bcam1869,

) and similar proteins mainly found in Proteobacteria. RsaM is a transcriptional regulator involved in quorum sensing (QS). This protein folds into a unique domain with a five-stranded antiparallel β-sheet that wraps around two α-helices .
YcdB/YcdC, repeated domain (YcdB/YcdC_rep_domain)
Type: Domain

This entry represents a domain that is generally found in two copies in YcdB and YcdC from B. subtilis. These proteins are uncharacterised. The C-terminal half of this domain appears to show similarity at the sequence level to the PEPSY domain.
Sm-like domain (Sm-like_dom)
Type: Domain

This domain, approximately 150 residues, is mainly found in several uncharacterised proteins from various Prochlorococcus and Synechococcus phages. The crystal structure of ECX21941 reveals unexpected similarity to Sm/LSm proteins, which are important RNA-binding proteins, despite no detectable sequence similarity . The specific function of this family is unknown, but the structure analysis of ECX21941 indicates nucleic acid-binding capabilities and suggests a role in RNA and/or DNA processing .
Protein of unknown function DUF4900 (DUF4900)
Type: Family

This family consists of uncharacterised proteins around 600 residues in length and is found in bacteria. The function of this family is unknown.
Protein of unknown function DUF4899 (DUF4899)
Type: Family

A small family of uncharacterised proteins around 340 residues in length and found in bacteria. The function of this family is unknown.
Protein of unknown function DUF4898 (DUF4898)
Type: Family

This entry represents a family of uncharacterised proteins around 100 residues in length and found in Sulfolobaceae. The function of this family is unknown.
Protein of unknown function DUF4897 (DUF4897)
Type: Family

This is a small family of uncharacterised proteins around 200 residues in length found in Thermotogae and Halobacteria. The function of this family is unknown.
Domain of unknown function DUF4896 (DUF4896)
Type: Domain

This domain is found in uncharacterised proteins from various Thermotoga species, many annotated as maltose ABC transporter permeases.
Protein of unknown function DUF4895 (DUF4895)
Type: Family

This entry represents a family of uncharacterised proteins around 250 residues in length and found in various Thermotoga species. The function of this family is unknown.
Protein of unknown function DUF4894 (DUF4894)
Type: Family

This entry represents a family of uncharacterised proteins around 180 residues in length and found in Thermotogae. The function of this family is unknown.
Protein of unknown function DUF4892 (DUF4892)
Type: Family

This family consists of uncharacterised proteins mainly found in Proteobacteria. This entry includes PA1624, an hypothetical periplasmic protein from Pseudomonas aeruginosa that may be a potential drug target .
Protein of unknown function DUF4893 (DUF4893)
Type: Family

This family consists of uncharacterised proteins around 200 residues in length and is mainly found in Proteobacteria. The function of this family is unknown.
Domain of unknown function DUF2172 (DUF2172)
Type: Domain

This domain, found in various hypothetical prokaryotic proteins, has no known function. It is an inserted (nested domain) within an amino-peptidase domain. The relevance of the amino-peptidase domain has not been established yet and the function of this small domain is not known.
Protein of unknown function DUF4891 (DUF4891)
Type: Family

This family consists of uncharacterised proteins around 140 residues in length and is mainly found in various Bacteroides species. The function of this family is unknown.
Protein of unknown function DUF4890 (DUF4890)
Type: Family

This family consists of uncharacterised proteins around 200 residues in length and is mainly found in various Bacteroidetes species. The function of this family is unknown.
Protein of unknown function DUF4889 (DUF4889)
Type: Family

This family consists of uncharacterised proteins around 110 residues in length and is mainly found in various Staphylococcus species. The function of this family is unknown.
Protein of unknown function DUF4888 (DUF4888)
Type: Family

This family consists of uncharacterised proteins around 190 residues in length and is mainly found in various Staphylococcus species. The function of this family is unknown.
Protein of unknown function DUF4887 (DUF4887)
Type: Family

This family consists of uncharacterised proteins around 210 residues in length and is mainly found in various Staphylococcus species. The function of this family is unknown.
Domain of unknown function DUF4886 (DUF4886)
Type: Domain

This domain is mainly found in uncharacterised proteins around 290 residues in length and is mainly found in bacteria. It has a curved central β sheet flanked by helices. The function of this domain is unknown.
Protein of unknown function DUF4885 (DUF4885)
Type: Family

This family consists of several uncharacterised proteins around 390 residues in length and is mainly found in Bacillus species. The function of this family is not clear.
Protein of unknown function DUF4884 (DUF4884)
Type: Family

This family consists of several uncharacterised proteins around 90 residues in length and is mainly found in bacteria. The function of this family is unknown.
Protein of unknown function DUF4883 (DUF4883)
Type: Family

This family consists of several uncharacterised proteins around 160 residues in length and is mainly found in Clostridium species. The function of this family is unknown.
Protein of unknown function DUF4882 (DUF4882)
Type: Family

This entry represents a family of several uncharacterised proteins around 325 residues in length and is mainly found in various Acinetobacter species. The function of this family is unknown.
Protein of unknown function DUF4881 (DUF4881)
Type: Family

This small family consists of several uncharacterised proteins around 200 residues in length and is mainly found in Desulfovibrio species. The function of this protein is unknown.
UCP01524, winged helix-turn-helix domain (UCP01524_HTH)
Type: Domain

This domain is an example of a circularly permuted winged helix-turn-helix domain. This domain is found at the very C terminus of UCP01524, which is structurally similar to M28-peptidases but lacking one of the key zinc-binding residues.
FecR, N-terminal (FecR_N)
Type: Domain

This domain can be found in the N-terminal region of the FecR protein, a transmembrane signal transduction protein involved in Fe2+ dicitrate sensing . The function of this domain is not clear.
Protein of unknown function DUF4879 (DUF4879)
Type: Family

This entry represents a family of bacterial proteins with phage origin, exemplified by protein SPBc2p013 from Bacillus phage SPBc2. This entry also includes SPbeta prophage-derived uncharacterised protein YolA from Bacillus subtilis. The function of this family is not clear.
Peptidase M64, N-terminal (M64_N)
Type: Domain

This domain is found at the N terminus of IgA Peptidase M64, a family of highly selective metallo-endopeptidases, in this case for IgA, the major class of immunoglobulin in human mucosal secretions. This protein is produced by Clostridium ramosum, a member of the normal flora in the human intestine which is very rarely associated with disease. It has been suggested that this peptidases enable these bacteria to escape specific immune defence on mucosal surfaces . Its function is unknown.
GxGYxYP putative glycoside hydrolase, first N-terminal domain (GxGYxYP_N_1st)
Type: Domain

This entry represents a domain that is found repeated in three copies per protein and is likely to be involved in binding the bacterial cell wall. This domain can be found in the N-terminal region of a group of proteins that carry a characteristic sequence motif, GxGYxYP, and are putative glycoside hydrolases. This domain corresponds to the first one and it is found in association with

.
Protein of unknown function DUF4876 (DUF4876)
Type: Family

This entry represents a group of uncharacterised proteins from bacteria. Proteins in this entry contain a conserved NNS sequence motif.
Adenylate cyclase, N-terminal (AC_N)
Type: Domain

This entry represents the N-terminal extracellular region and the first transmembrane 5-6 pass region of adenylate cyclase .
Mon2/Sec7/BIG1-like, dimerisation and cyclophilin-binding domain (DCB_dom)
Type: Domain

This is the N-terminal domain of Mon2-, Sec7- and BIG1-like proteins, the dimerisation and cyclophilin-binding domain (DCB) . The N terminus of Mon2 (Ysl2) binds to Arf-Like small GTPase Arl1, and shows homology to brefeldin A-inhibited guanine-exchange factor (BIG) domains . Mon2 and BIG1-like proteins play an important role in membrane traffic and Golgi homeostasis . This domain is sufficient for targeting BIG1 to the Golgi.
P-type ATPase, C-terminal (P_typ_ATPase_c)
Type: Domain

This domain is found at the C terminus of a number of phospholipid-translocating ATPases from eukaryotes. It is involved in intracellular trafficking and it seems that it also plays a role in their enzymatic activities .
P-type ATPase, N-terminal (P-type_ATPase_N)
Type: Domain

This domain is found at the N terminus of a number of phospholipid-translocating ATPases in eukaryotes. It plays a key role in specific subcellular localization of these ATPases to endosomal compartments .
Peptidase M16, middle/third domain (Peptidase_M16_M)
Type: Domain

This is the third domain of some M16 peptidases, such as insulin-degrading-enzyme in eukaryotes or protease 3 from bacteria . Insulin-degrading enzymes - insulysin - are zinc metallopeptidases that metabolise several bioactive peptides, including insulin and the amyloid-β-peptide. The tertiary structure of insulin-degrading enzymes resembles a clamshell composed of four structurally similar domains arranged to enclose a large central chamber. Substrates must enter the chamber, and it is likely that a hinge-like conformational change allows substrate binding and product release. Triphosphates are found to dock between the inner surfaces of the non-catalytic domains three and four .
ThiJ/PfpI family-like (ThiJ-like)
Type: Family

This is a family of fungal and bacterial ThiJ/PfpI-like uncharacterised proteins. Their function is not clear.
Gef2/Nod1 domain (Gef2/Nod1_dom)
Type: Domain

This domain can be found in Gef2 and Nod1 from S. pombe. Nod1 co-localises with Gef2 - RhoGEF - in the contractile ring and its precursor cortical nodes. Nod1 and Gef2 interact through this C-terminal region of each, this interaction being important for their localisation .
Surface antigen domain (Anti_2)
Type: Domain

This is a domain found in a group of surface proteins from several Proteobacteria species.
Pilus assembly protein, E-set like domain (Pilus_assem_E-set-like_dom)
Type: Domain

This is a conserved domain on fimbrial outer membrane usher proteins like TcfC or CooC or PapC . It is an immunoglobulin like E-set domain.
Putative phage holin-like (Phage_holin-like)
Type: Family

This entry includes a group of putative holins found in bacteriophages from the Caudovirales order. However, proteins in this entry are mostly from Proteobacteria. Their function is not clear.
Putative bacterial porin (Porin_5)
Type: Family

This entry includes a group of putative bacterial porins. Their function is not clear.
Tex protein, YqgF-like domain (Tex_YqgF)
Type: Domain

This is the YqgF-like domain of the bacterial Tex protein, which is involved in transcriptional processes .
AMP-activated protein kinase, glycogen-binding domain (AMPK1_CBM)
Type: Domain

This domain can be found in AMP-activated protein kinases and CRP1/MDG1 family members. The surface of this domain reveals a carbohydrate-binding pocket .
DNA mismatch repair protein Msh2, ATP-binding cassette domain (Msh2_ATP-bd)
Type: Domain

This entry represents the DNA mismatch repair protein Msh2 (homologous to bacterial MutS) from eukaryotes. Msh2-Msh6 complex recognises base pair mismatches and small insertion/deletions in DNA and initiates repair . Human Msh2-Msh6 complex has been shown to regulate BLM helicase in response to the damaged DNA forks during double-stranded break repair .

Mismatch repair (MMR) is one of five major DNA repair pathways. The mismatch repair system recognises and repairs mispaired or unpaired nucleotides that result from errors in DNA replication. The most extensively studied general MMR system is the MutHLS pathway of the bacterium Escherichia coli. In the first step of the MutHLS pathway, the MutS protein (in the form of a dimer) binds to the site of a mismatch in double-stranded DNA. Through a complex interaction between MutS, MutL and MutH, a section of the newly replicated DNA strand (and thus the strand with the replication error) at the location of the mismatch bound by MutS is targeted for removal . Homologues of MutS have been found in many species including eukaryotes, Archaea and other bacteria, and together these proteins have been grouped into the MutS family.

This entry represents the ATP-binding cassette domain of Msh2.
Transcription factor HES-7, basic helix-loop-helix-orange domain (HES-7_bHLH-O)
Type: Domain

HES-7 is a bHLH-type repressor that is both a direct target of the Notch signalling pathway, and part of a negative feedback mechanism required to attenuate Notch signalling . It can bind to its own promoter, thereby inhibiting its own transcription. In mouse its 3'UTR is essential for somite segmentation clock . Mutations in the HES-7 gene cause spondylocostal dysostosis, an inherited disorder characterised by the presence of extensive hemivertebrae, truncal shortening and abnormally aligned ribs .

This entry represents the basic helix-loop-helix-orange (bHLH-O) domain of HES-7.
Neurogenin-2, basic helix-loop-helix domain (Ngn-2_bHLH)
Type: Domain

Neurogenin-2 (Ngn-2) is a basic helix-loop-helix transcription factor that is involved in neuronal differentiation . It is required for sensory neurogenesis . Interestingly, ectopic expression of the neural Ngn-2 is sufficient to induce rapid and efficient differentiation of embryonic stem cells (ESCs) into mature glutamatergic neurons .

This entry represents the basic helix-loop-helix (bHLH) domain of Ngn-2.
Neurogenin-3, basic helix-loop-helix domain (Ngn3_bHLH)
Type: Domain

Neurogenin-3 (Ngn3) is a basic helix-loop-helix transcription factor. Mouse Ngn3 is critical for the development of the endocrine cells of the islets . It is also involved in the neuritogenic actions of oestradiol in developing hippocampal neurones .

This entry represents the basic helix-loop-helix (bHLH) domain of Ngn3.