SII-SWORD/CoKE huggingface dataset:
YwqH-like (YwqH-like)
Type: Family

This entry represents a family of proteins from firmicutes, including Protein YwqH from Bacillus subtilis, an homologue of the polymorphic LXG toxin . This group was previously known as DUF5082.
Type VII secretion system protein EsaE (EsaE)
Type: Family

EsaE interacts with the type VII secretion system (T7SS) ATPase, EssC. It is required for efficient secretion of EsaD and at least one further T7SS substrate. It is located both in the cytoplasm and cell membrane .
Domain of unknown function DUF4716 (DUF4716)
Type: Domain

This domain is found in eukaryotes, and is approximately 60 amino acids in length.
Sperm-egg fusion protein LLCFC1 (LLCFC1)
Type: Family

LLCFC1 (also known as SOF1) and its homologues can be found in eukaryotes. They have two conserved sequence motifs: LLLL and CFNLAS. LLCFC1 is a sperm protein required for sperm-oocyte fusion in mice .
Testis-expressed sequence 29 protein (TEX29)
Type: Family

TEX29, testis-expressed sequence 29 protein, is a family of proteins found in eukaryotes. Proteins in this family are typically between 39 and 150 amino acids in length.
ATPsynthase alpha/beta subunit, barrel-sandwich domain (ATP-synth_a_Xtn)
Type: Domain

This barrel-sandwich domain is found in the alpha-beta catalytic subunit of VATA or V-type proton ATPase catalytic subunit at the N-terminal end. This domain has a circularly permuted topology compared to other barrel-sandwich domains. In VATA barrel-sandwich domain the C-terminal strand is circularly permuted and occupies the spatial position of the N-terminal strand in other hybrid domains.
ADP-ribosylation factor-like protein 17, C-terminal (ARL17_C)
Type: Domain

ADP-ribosylation factor-like protein 17 (ARL17) is a protein of unknown function found in primates. It belongs to the Arf-like (ARL) GTPases family . This entry represents the C-terminal domain of ARL17. This domain is also found in NBR2 or Neighbour of BRAC1 gene 2 .
Voltage-gated calcium channel subunit alpha, C-terminal (CAC1F_C)
Type: Domain

This entry represents the C-terminal region of voltage-gated calcium channel subunit α in higher eukaryotes. The exact function of this domain is not known. This region lies immediately downstream from the CDB motif.
Protein of unknown function DUF5080 (DUF5080)
Type: Family

This protein is believed to be involved in the type VII secretion system.
Protein of unknown function DUF5079 (DUF5079)
Type: Family

This protein is believed to be involved in the type VII secretion system.
Lipoyl synthase, N-terminal (LIAS_N)
Type: Domain

This domain is found in the N terminus of lipoyl synthases.

Lipoyl synthase is an iron-sulphur protein . It is localised to mitochondria in yeast and Arabidopsis . It generates lipoic acid, a thiol antioxidant that is linked to a specific Lys as prosthetic group for the pyruvate and alpha-ketoglutarate dehydrogenase complexes and the glycine-cleavage system.
EH domain-containing protein, N-terminal (EHD_N)
Type: Domain

This is a short domain that lies at the very N terminus of many dynamins and EF-hand domain-containing proteins.
Sin3, C-terminal (Sin3_C)
Type: Domain

This entry represents a domain found in the C-terminal of the transcriptional repressor Sin3.

Budding yeast Sin3 is a component of both the Rpd3S and Rpd3L histone deacetylase complexes . In mammals there are two Sin3 paraologues, Sin3A and Sin3B. They forms the larger Sin3L/Rpd3L and the smaller Sin3S/Rpd3S complexes, both complexes rely largely on HDAC (histone deacetylase) activity to affect transcriptional repression. Sin3A and Sin3B may partition into the Sin3L/Rpd3L and Sin3S/Rpd3S complexes, respectively .
Transmembrane protein 239 (TMEM239)
Type: Family

This family of proteins is found in mammals and includes TMEM239. It has been identified as an important host factor that facilitates African swine fever virus entry into early endosomes through the interaction with the early endosomal marker Rab5A .
Protein of unknown function DUF4718 (DUF4718)
Type: Family

This family of proteins is found in eukaryotes. Proteins in this family are typically between 130 and 224 amino acids in length.
Protein of unknown function DUF4719 (DUF4719)
Type: Family

This family of proteins is found in eukaryotes. Proteins in this family are typically between 67 and 240 amino acids in length.
Transmembrane and coiled-coil domain-containing protein 2 (TMCCDC2)
Type: Family

This family of proteins is found in mammals. Proteins in this family are approximately 180 amino acids in length.
Cysteine-rich C-terminal protein 1 (NICE-1)
Type: Family

Cysteine-rich C-terminal protein 1 (also known as NICE-1) is family of proteins found in mammals. Proteins in this family are typically between 51 and 105 amino acids in length.
Protein of unknown function DUF4720 (DUF4720)
Type: Family

This family of proteins is found in vertebrates. Proteins in this family are typically between 101 and 117 amino acids in length.
Loricrin (Loricrin)
Type: Family

Loricrin is a major keratinocyte cell envelope protein . The cornified cell envelope is a structure that replaces the plasma membrane during keratinocyte terminal differentiation. Loricrin acts as an important epidermal barrier, comprising 70% of the total protein mass of the cornified layer. Expression of Loricrin is regulated by TNF-alpha via a c-Jun N-terminal kinase-dependent pathway . Loricrin mutations cause the Vohwinkel syndrome and other congenital skin abnormalities collectively termed as loricrin keratoderma .
Homeobox protein SIX1, N-terminal SD domain (SIX1_SD)
Type: Domain

The SD domain is found N-terminal to the homeobox domain in the protein SIX1. As a transcription factor, SIX1 lacks intrinsic activation domains and thus needs to bind to the EYA family of co-factors in order to mediate transcriptional activation. The SD domain is necessary for this protein-protein interaction, binding to the C-terminal region of EYA (Eyes absent homologue proteins) .
Protein of unknown function DUF5078 (DUF5078)
Type: Family

This family of unknown function is largely found in Mycobacterium spp.
Lipin, middle domain (Lipin_mid)
Type: Domain

This is a middle domain of lipins. Overall the enzyme acts as a magnesium-dependent phosphatidate phosphatase enzyme that catalyses the conversion of phosphatidic acid to diacylglycerol during triglyceride, phosphatidylcholine and phosphatidylethanolamine biosynthesis (

) .
Glycosyl hydrolase family 36, N-terminal (Glyco_hydro_36_N)
Type: Domain

This domain is found at the N terminus of many family 36 glycoside hydrolases. It has a β-supersandwich fold .
Glycosyl hydrolase family 36, C-terminal (Glyco_hydro_36_C)
Type: Domain

This domain is found in the C terminus of many family 36 glycoside hydrolases. It has a β-sandwich structure with a Greek key motif .
Odontogenesis associated phosphoprotein (ODAPH)
Type: Family

This family is found in mammals. It includes odontogenesis associated phosphoprotein (ODAPH or in human C4orf26) which is expressed in the enamel organ of the tooth and may promote nucleation of hydroxyapatite .
Putative abortive phage resistance protein AbiGii toxin (AbiGii_2)
Type: Family

This is a family of putative type IV toxin-antitoxin system toxins. The AbiG abortive phage resistance protein affects lactococcal bacteriophages phiP335 and phiQ30 but not the other P335 phage species. AbiGii toxin appears to confer resistance to phages by a mechanism of abortive infection that acts by interfering with phage RNA synthesis . The cognate anti-toxin is found in (

).
Protein of unknown function DUF4722 (DUF4722)
Type: Family

This family of proteins is found in vertebrates. Proteins in this family are typically between 86 and 203 amino acids in length.
Putative phage abortive infection protein (PutAbiC)
Type: Family

Several members in this family have been annotated as putative phage abortive infection proteins .
Protein of unknown function DUF4723 (DUF4723)
Type: Family

This family of proteins is found in mammals. There are a number of conserved cysteines but it is unlikely to be a zinc-finger family. Proteins in this entry includes the uncharacterised protein C9orf57 from human.
Domain of unknown function DUF4724 (DUF4724)
Type: Domain

This domain is found in mammals and has a conserved KVKPL sequence motif.

It is sometimes found N-terminal to (

).
Domain of unknown function DUF5077 (DUF5077)
Type: Domain

This domain is found in a group of uncharacterised proteins.
G-protein coupled receptor ligand 15 (GPR15L)
Type: Family

Protein GPR15L is a chemotactic factor and an agonistic ligand for GPR15, a G protein-coupled receptor (GPCR) that is found in lymphocytes. GPR15L is found on colon and skin, especially cervix, epithelia and squamous mucosa of the oral cavity and esophagus . GPR15L attracts GPR15-expressing T cells including lymphocytes . GPR15L is also a SUSD2 binding factor, and the interaction inhibits colon cancer cell growth and induce G1 cell cycle arrest by down-regulating cyclin D and cyclin-dependent kinase 6 . Additionally, through activation of Mas-related G protein-coupled receptors (MRGPRs) contributes to pruritogenesis by activating itch-selective sensory neurons and mast cells degranulation .
Protein of unknown function DUF4726 (DUF4726)
Type: Family

This family of proteins is found in vertebrates. Proteins in this family are typically between 40 and 110 amino acids in length.
Protein of unknown function DUF4727 (DUF4727)
Type: Family

This family of proteins is found in mammals. There are a number of conserved cysteines, but the domain is not a zinc-finger.
Late cornified envelope protein 6A (LCE6A)
Type: Family

LCE6A, late cornified envelope protein 6A, is found in mammals. It was identified in a large-scale screening experiment as being involved in the barrier function of the epidermis .
2-oxoglutarate dehydrogenase E1 component/KDG, C-terminal (ODO-1/KGD_C)
Type: Domain

This domain is found immediately C-terminal to the transketolase-like pyrimidine-binding domain (

). It is found at the C terminus of 2-oxoglutarate dehydrogenase E1 component (ODO1) and the multifunctional 2-oxoglutarate metabolism enzyme Kgd and it has been described as α/β3 domain .
Deleted in esophageal cancer 1 (DEC1)
Type: Family

DEC1 (deleted in esophageal cancer 1) has been identified as being deleted in oesophageal cancers . It is also referred to as candidate tumour suppressor CTS9.
Condensin II complex subunit H2, middle domain (H2_M)
Type: Domain

This is the middle domain of the H2 subunit of the condensin II complex, found in eukaryotes but not fungi. This region represents the disordered section of CNDH2 between the N- and the C-terminal domains.

Eukaryotes carry at least two condensin complexes, I and II, each made up of five subunits. The functions of the two complexes are collaborative but non-overlapping. CI appears to be functional in G2 phase in the cytoplasm beginning the process of chromosomal lateral compaction while the CII are concentrated in the nucleus, possibly to counteract the activity of cohesion at this stage. In prophase, CII contributes to axial shortening of chromatids while CI continues to bring about lateral chromatid compaction, during which time the sister chromatids are joined centrally by cohesins. There appears to be just one condensin complex in fungi. CI and CII each contain SMC2 and SMC4 (structural maintenance of chromosomes) subunits, then CI has non-SMC CAP-D2 (CND1), CAP-G (CND3), and CAP-H (CND2). CII has, in addition to the two SMCs, CAP-D3, CAPG2 and CAP-H2. All four of the CAP-D and CAP-G subunits have degenerate HEAT repeats, whereas the CAP-H are kleisins or SMC-interacting proteins (ie they bind directly to the SMC subunits in the complex). The SMC molecules are each long with a small hinge-like knob at the free end of a longish strand, articulating with each other at the hinge. Each strand ends in a knob-like head that binds to one or other end of the CAP-H subunit. The HEAT-repeat containing D and G subunits bind side-by-side between the ends of the H subunit. Activity of the various parts of the complex seem to be triggered by extensive phosphorylations, eg, entry of the complex, in Sch.pombe, into the nucleus during mitosis is promoted by Cdk1 phosphorylation of SMC4/Cut3; and it has been shown that Cdk1 phosphorylates CAP-D3 at Thr1415 in He-La cells thus promoting early stage chromosomal condensation by CII .
Protein of unknown function DUF4728 (DUF4728)
Type: Family

Proteins in this family are mainly from arthropods, and they are functionally uncharacterised.
Partial cleavage stimulation factor domain (Partial_CstF)
Type: Domain

This domain occurs in proteins from apicomplexan parasites. Currently (as of 2012), little is known about the function of this domain. However, it is homologous to the amino-terminal part of the cleavage stimulation factor, which is thought to be involved with mRNA maturation in mammals .
Coilin, N-terminal domain (Coilin_N)
Type: Domain

Coilin is a nuclear phosphoprotein that serves as an assembly centre in Cajal bodies (CBs) and has a role in small nuclear ribonucleoprotein (snRNP) biogenesis, involved in the modification and assembly of nucleoplasmic snRNPs . Coilin also acts to repress polymerase I activity in response to cisplatin-induced DNA damage, which could indicate a link between the DNA damage response and the inhibition of rRNA synthesis .

Conservation at the amino acid level is highest within coilin's N- and C-termini. The first N-terminal 92-amino acid domain have been shown to self-interact and to be essential for proper targeting of coilin to CBs .
Dimethlysulfonioproprionate lyase (DMSP_lyase)
Type: Family

There are different ways in which different lineages of bacteria release dimethyl sulfide (DMS) during dimethlysulfonioproprionate (DMSP) catabolism, a phenotype termed Ddd+. Different gene products, including DddD, DddL, DddP and DddQ, have been found in various marine bacteria which can confer a Ddd+ phenotype to Escherichia coli .

This family includes DddQ , DddL and DddY . They are dimethlysulfonioproprionate lyases that break down DMSP, releasing DMS.
Extended EGL-27 and MTA1 homology domain (EELM2)
Type: Domain

EELM2, the extended EGL-27 and MTA1 homology domain, occurs in proteins from apicomplexan parasites. Part of the EELM2 domain is homologous to the ELM2 domain, but is 'extended' in that its boundaries (the region of conservation) are longer than in the ELM2 domain. Currently (as of 2012), little is known about the function of this domain. However, some proteins that contain an EELM2 domain also contain a PHD finger domain, which is thought to be involved in chromatin remodelling. This suggests an associated role for the EELM2 domain .
Protein glycosylation ligase domain (PglL_A)
Type: Domain

This pilin glycosylation ligase domain found in Gram-negative bacteria . PglL O-oligosaccharyltransferases differ from WaaL O-antigen ligases,

, in its substrate-specificity. PglL O-oligosaccharyltransferases (O-OTase) transfer oligosaccharide to serine or threonine in a protein. A further indication that the genes identified by this domain are PglL rather than WaaL homologues is that they are not located within lipopolysaccharide biosynthetic loci . The specific pilin glycosylation ligases are a subset of the more general bacterial protein o-oligosaccharyltransferases .
Beta-glucuronidase, C-terminal (GlcAase_C)
Type: Domain

This domain is found at the C terminus of beta-glucuronidase. Its function is not yet known . Beta-glucuronidase hydrolyses beta-glucuronosyl and 4-O-methyl-beta-glucuronosyl residues of arabinogalactan-protein .
Fanconi anaemia group A protein, N-terminal domain (Fanconi_A_N)
Type: Domain

This entry represents the N-terminal domain of FANCA.

Fanconi anemia (FA) is a human disorder characterised by cancer susceptibility and cellular sensitivity to DNA crosslinks and other damages. The FA complex repairs the interstrand cross-linking (ICL) lesions and coordinates activities of the downstream DNA repair pathway including nucleotide excision repair, translesion synthesis, and homologous recombination. It is required for the monoubiquitylation of FANCD2 and FANCI heterodimer. The FA core complex consists of FANCA, FANCB, FANCC, FANCE, FANCF, FANCG, FANCL, FANCM, FANCT (UBET2), FAAP100 and FAAP24 .
Carbamoyltransferase, C-terminal (Carbam_trans_C)
Type: Domain

This domain is found in NodU from Rhizobium, CmcH from Nocardia lactamdurans and the bifunctional carbamoyltransferase TobZ from Streptoalloteichus tenebrarius. NodU, a Rhizobium nodulation protein involved in the synthesis of nodulation factors, has 6-O-carbamoyltransferase-like activity . CmcH is involved in cephamycin (antibiotic) biosynthesis and has 3-hydroxymethylcephem carbamoyltransferase activity (

). TobZ functions as an ATP carbamoyltransferase and tobramycin carbamoyltransferase . These proteins contain two domains, this is the smaller, C-terminal domain.
IMS import disulfide relay-system, CHCH-CHCH-like Cx9C (CX9C)
Type: Domain

CX9C is the first half of a twin Cx9C motif in eukaryotic proteins. The function of this motif is to import nuclear-encoded mitochondrial intermembrane-space-proteins into the IMS (intermembrane space), as these latter lack a mitochondrial targeting sequence. The Cx9C proteins have a disulfide-bonded α-hairpin conformation. Cx9C-containing proteins are thus putative substrates for the Mia40-dependent thiol-disulfide exchange mechanism that carries out an oxidative folding process resulting in the proteins being trapped in the IMS .
Domain of unknown function DUF4729 (DUF4729)
Type: Domain

This domain is functionally uncharacterised and is present in insects. Proteins with this domain typically consist of 238 to 666 amino acids. This domain is predicted to be structurally similar to TRAF-like domains (

) .
Dynein attachment factor, N-terminal (Dynein_attach_N)
Type: Domain

This entry represents the N terminus of a dynein arm attachment factor (known as coiled-coil domain-containing protein 103, CCDC103) which is required for dynein arm assembly and cilia motility .
Transcription activator MBF2 (MBF2)
Type: Family

MBF2 activates transcription via its interaction with TFIIA . In Bombyx mori, it has been found to form a complex with MBF1 and the DNA-binding regulator FTZ-F1 .
RNA exonuclease 1 homolog-like domain (REXO1-like_dom)
Type: Domain

This domain of unknown function is found in RNA exonuclease 1 homolog (also known as elongin A binding-protein 1) and similar proteins such as exonuclease GOR from mammals and pqe-1 from C.elegans. Pqe-1 is a putative RNA exonuclease which protects neurons from the toxic effects of expanded poly-Q disease proteins . It is unclear if this is through participation in the pathogenic mechanism underlying poly-Q-induced neurodegeneration or if it is by acting as a genetic modifier of the age of onset or progression of neurodegeneration . Pqe-1 regulates gene expression in neurons .
Condensin-2 complex subunit H2, C-terminal (CNDH2_C)
Type: Domain

This entry represents the C-terminal winged Helix-Turn-Helix domain of the H2 subunit of the condensin II complex (Ncaph2), found in eukaryotes but not fungi.

Condensin complexes are involved in the restructuring and maintenance of chromatin. Eukaryotes possess two condensins (condensin I and condensin II), each composed of structural maintenance of chromosomes proteins SMC2 and SMC4, with three additional non-SMC condensin-associated proteins (Ncaps) unique to each condensin (condensin I - Ncaph, Ncapd2, and Ncapg; condensin II - Ncaph2, Ncapd3, and Ncapg2) .
JMY/WHAMM, middle domain (JMY/WHAMM)
Type: Domain

JMY (junction-mediating and -regulatory protein) and WHAMM (WASP homologue-associated protein with actin, membranes and microtubules) are two nucleation-promoting factors (NPFs) with similar domain architecture. JMY was originally identified as a transcriptional co-factor in the p53-response to DNA damage. Aside from this nuclear function, JMY is involved in cytoskeleton remodelling and trans-Golgi transport . WHAMM binds microtubules and is involved in ER to cis-Golgi transport . JMY and WHAMM show similar localisation and could be involved in similar processes .
Condensin-2 complex subunit H2 (Ncaph2)
Type: Family

Condensin complexes are involved in the restructuring and maintenance of chromatin. Eukaryotes possess two condensins: condensin I and condensin II. Each complex is composed of structural maintenance of chromosomes protein SMC2 and SMC4, with three additional non-SMC condensin-associated proteins (Ncaps) unique to each condensin (condensin I - Ncaph, Ncapd2, and Ncapg; condensin II - Ncaph2, Ncapd3, and Ncapg2) .

This entry includes condensin-2 subunit 2 (Ncaph2) and Kle-2 from C. elegans. Ncaph2 may play a role in lineage-specific role in T-cell development .
Cell division control protein 4, dimerisation domain (Cdc4_D)
Type: Domain

This is the dimerisation domain (D domain) of fungal cell division control protein 4 (Cdc4) . Budding yeast Cdc4 is a substrate recognition component of a SCF (SKP1-CUL1-F-box protein) E3 ubiquitin-protein ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins .
Serine-rich and transmembrane domain-containing protein (SERTM)
Type: Family

This family of uncharacterised proteins is found in chordates. Proteins in this family are approximately 100 amino acids in length.
Protein of unknown function DUF4730 (DUF4730)
Type: Family

This family of proteins is found in eukaryotes. Proteins in this family are approximately 60 amino acids in length.
Small outer capsid protein (Soc)
Type: Family

Small outer capsid protein stabilises T4 capsids after the majority of the capsid assembly stages, and helps to stabilise T4 against high temperatures and pH extremes by binding the capsid surface at interfaces between Gp23 hexameric capsomers .
Small integral membrane protein 1 (SMIM1)
Type: Family

SMIM1 is a small integral membrane protein that regulates red blood cell formation . The Vel blood group antigen is expressed on the red blood cells of most individuals. SMIM1 has been shown to encode the Vel blood group antigen .
Vps53, C-terminal (Vps53_C)
Type: Domain

This entry represents the C-terminal domain of fungal vacuolar protein sorting-associated protein 53 (Vps53), a component of the Golgi-associated retrograde complex (GARP). Budding yeast Vps53 is involved in retrograde transport from early and late endosomes to late Golgi by linking the vesicle through the t-SNARE Tgl1 to the Golgi, leading to the membrane fusion between late Golgi and endosomal vesicles . This domain has a fold consisting of an α-helical bundle known as the CATCHR fold (complexes associated with tethering containing helical rods) which is shared by proteins of other tethering complexes, namely exocyst, COG and Dsl1 .
Protein of unknown function DUF4732 (DUF4732)
Type: Family

This family of proteins is found in eukaryotes. Proteins in this family are typically between 107 and 201 amino acids in length.
Transmembrane protein 232 (TMEM232)
Type: Family

This family of proteins is found in eukaryotes. The function is not known.
Protein Frey (Frey)
Type: Family

This family represents Frey proteins, which are key regulators for male fertility expressed transiently in round spermatids where it recruits IZUMO1 at the endoplasmic reticulum (ER) membrane and coordinates the oolemmal binding multimeric complex (IZUMO1 complex) assembly. Upon complete assembly of the IZUMO1 complex, its ER retention is released, facilitating IZUMO1 complex export to the acrosome . Frey interacts with SPPL2C, which inhibits its intramembrane protease activity directly accessing the catalytic centre of an I-CLiP .
Cell division control protein 13, N-terminal (Cdc13_N)
Type: Domain

This domain is found in the N-terminal of fungal cell division control protein 13 (Cdc13), which is a single-stranded telomere binding protein required for telomere length regulation and genome stability. This domain contains an OB fold (known as OB1), which has weak affinity for long single-strand telomere DNA and is involved in Cdc13 dimerisation and recruitment of Pol alpha-primase to the telomeres for C-strand synthesis .