SII-SWORD/CoKE huggingface dataset:
Tail assembly protein gp4-like (Tail_Gp41-like)
Type: Family

This entry includes the probable tail assembly protein gp41 from Bacteriophage Mu (Mup41 and FS-gp41) and Mu-like prophage FluMu protein gp41 from H. influenzae. Mup41 and FS-gp41 may act as a chaperone mediating the interaction between the tape measure protein (TMP) and the tail tube protein (TTP) thereby directing the polymerisation of TTP to form a tail of the correct length.
HTH-like domain, bact (HTH_73)
Type: Domain

This entry represents a domain that covers the whole length of the sequence in a group of uncharacterised bacterial proteins. Proteins in this family are approximately 80 amino acids in length. These proteins structurally resemble a HTH domain. They are often found genomically associated with likely restriction modification systems. Structure prediction suggests that these domains homodimerise and bind to the major groove of double-stranded DNA.

This domain is also found in longer uncharacterised bacterial proteins in combination with other domains, such as

.
Reversion-inducing cysteine-rich protein with Kazal, EGF-like 1 domain (EGF1_RECK)
Type: Domain

This domain is found in human Reversion-inducing cysteine-rich protein with Kazal motifs (RECK) and similar animal proteins.

RECK consists of five repeats of an uncommon domain with six cysteines (the CC domain, represented by

and two copies of

), a Frizzled-like cysteine-rich domain (Fz-like CRD,

), two epidermal growth factor-like domains (EGF-like 1,

, and 2,

), and three Kazal-like motifs (Kazal-like 1 to 3,

) .

Reck is a GPI-anchored membrane protein that negatively regulates matrix metalloproteinase-9 (MMP-9) by suppressing MMP-9 secretion and by direct inhibition of its enzymatic activity . It also regulates two other MMPs, MMP-2 and MT1-MMP, known to be involved in cancer progression . Reck and the orphan receptor Gpr124 interact to activate Wnt7a/Wnt7b signalling in CNS vascular development . Reck interacts specifically with the disordered linker region of Wnt7, which confers ligand selectivity for Wnt7 .
Reversion-inducing cysteine-rich protein with Kazal, fibronectin type I module (FnI_RECK)
Type: Domain

This domain is found in human Reversion-inducing cysteine-rich protein with Kazal motifs (RECK) and similar animal proteins.

RECK consists of five repeats of an uncommon domain with six cysteines (the CC domain, represented by

and two copies of

), a Frizzled-like cysteine-rich domain (Fz-like CRD,

), two epidermal growth factor-like domains (EGF-like 1,

, and 2,

), and three Kazal-like motifs (Kazal-like 1 to 3,

) .

Reck is a GPI-anchored membrane protein that negatively regulates matrix metalloproteinase-9 (MMP-9) by suppressing MMP-9 secretion and by direct inhibition of its enzymatic activity . It also regulates two other MMPs, MMP-2 and MT1-MMP, known to be involved in cancer progression . Reck and the orphan receptor Gpr124 interact to activate Wnt7a/Wnt7b signalling in CNS vascular development . Reck interacts specifically with the disordered linker region of Wnt7, which confers ligand selectivity for Wnt7 .
Reversion-inducing cysteine-rich protein with Kazal, CC4 domain (CC4_RECK)
Type: Domain

This domain is found in Reversion-inducing cysteine-rich protein with Kazal motifs from Mus musculus (RECK) and similar proteins from animals. This entry represents the fourth and fifth CC4 domains, each consisting of four short α-helices stabilised by three disulfide bonds .

RECK consists of five repeats of an uncommon domain with six cysteines (the CC domain, represented by

and two copies of

), a Frizzled-like cysteine-rich domain (Fz-like CRD,

), two epidermal growth factor-like domains (EGF-like 1,

, and 2,

), and three Kazal-like motifs (Kazal-like 1 to 3,

) .

Reck is a GPI-anchored membrane protein that negatively regulates matrix metalloproteinase-9 (MMP-9) by suppressing MMP-9 secretion and by direct inhibition of its enzymatic activity . It also regulates two other MMPs, MMP-2 and MT1-MMP, known to be involved in cancer progression . Reck and the orphan receptor Gpr124 interact to activate Wnt7a/Wnt7b signalling in CNS vascular development . Reck interacts specifically with the disordered linker region of Wnt7, which confers ligand selectivity for Wnt7 .
Reversion-inducing cysteine-rich protein with Kazal, frizzled-like domain (FZ_RECK)
Type: Domain

This entry includes human Reversion-inducing cysteine-rich protein with Kazal motifs (RECK) and similar animal proteins. This entry represents a frizzled-like domain which contains ten conserved cysteine residues.

RECK consists of five repeats of an uncommon domain with six cysteines (the CC domain, represented by

and two copies of

), a Frizzled-like cysteine-rich domain (Fz-like CRD,

), two epidermal growth factor-like domains (EGF-like 1,

, and 2,

), and three Kazal-like motifs (Kazal-like 1 to 3,

) .

Reck is a GPI-anchored membrane protein that negatively regulates matrix metalloproteinase-9 (MMP-9) by suppressing MMP-9 secretion and by direct inhibition of its enzymatic activity . It also regulates two other MMPs, MMP-2 and MT1-MMP, known to be involved in cancer progression . Reck and the orphan receptor Gpr124 interact to activate Wnt7a/Wnt7b signalling in CNS vascular development . Reck interacts specifically with the disordered linker region of Wnt7, which confers ligand selectivity for Wnt7 .
RUNKEL, ARM-repeat domain (ARM_RUK)
Type: Domain

This is the C-terminal domain of Serine/threonine-protein kinase RUNKEL from Arabidopsis thaliana and related plant sequences. It consists of ARM repeats. RUNKEL is an essential protein that regulates phragmoplast microtubule organisation during cell plate expansion in cytokinesis during cell division, both somatic and syncytial .
Serine/threonine-protein kinase ULK4/RUNKEL, HEAT repeats (HEAT_ULK4_RUNKEL)
Type: Domain

This region of HEAT repeats is found in human Serine/threonine-protein kinase ULK4, Serine/threonine-protein kinase RUNKEL from Arabidopsis thaliana and similar sequences mainly found in animals and plants. ULK4 may be involved in the remodelling of cytoskeletal components and in the regulation of neurite branching and elongation, as well as cell motility. In humans, ULK4 gene has been proposed to be a rare susceptibility risk factor for a range of psychiatric diseases including schizophrenia . RUNKEL is an essential protein that regulates phragmoplast microtubule organisation during cell plate expansion in cytokinesis during cell division, both somatic and syncytial. It may not have kinase activity .
Phage ProQ RNA-binding domain, C-terminal-like (Phage_ProQ_C-like)
Type: Family

This entry represents a family of uncharacterised phage and bacterial proteins. Structurally the proteins include an N-terminal β-barrel domain that shows some structural similarity to the C-terminal domain of the ProQ RNA-binding domain. That domain has been described as being similar to the Tudor domains.
SAMD1-like, small helical domain (SAMD1-like_SHD)
Type: Domain

This domain is found in the human Sterile alpha motif domain-containing protein 1 (SAMD1) and its homologues from vertebrates. SAMD1 directly recognises and binds unmethylated CpG-containing DNA via simultaneous interactions with both the major and the minor groove . SAMD1 acts as a transcriptional repressor and chromatin regulator .
Repressor Rok, winged helix domain (WH_Rok)
Type: Domain

This entry represents the C-terminal domain of repressor Rok from Bacillus subtilis, a repressor of comK, the master regulator of competence development. It is a xenogeneic silencer that binds the DNA minor groove, with preference towards DNA sequences harbouring AACTA, TACTA, and flexible multiple TpA steps . This domain shows a typical winged helix fold, with a novel DNA recognition mechanism different from other winged helix proteins or xenogeneic silencers. Members of this group of proteins are found in tailed bacteriophages and bacterial prophages.
GH3 domain-containing protein, N-terminal domain (GH3_N)
Type: Domain

This domain is found at the N-terminal end of human GH domain-containing protein and similar sequences from mammals. This domain is frequently found associated with

and

.
Protein jagged-1/2, predicted ferredoxin-like domain (JAG1_1/2_dom)
Type: Domain

This domain is found in human Protein jagged-1/2 (JAG1, JAG2) and similar proteins from vertebrates. JAG1 is involved in the mediation of Notch signalling. This domain is predicted to show a ferredoxin-like fold.
ZMYND8, coiled-coil (ZMYND8_CC)
Type: Domain

This entry represents a coiled-coil domain that is predicted to self associate to form a dimeric arrangement found in human and fly MYND-type zinc finger-containing chromatin reader ZMYND8 and similar animal proteins. The coiled coil is adjacent to a MYND zinc finger and is similar to that found in ZMYND11 .

The ZMYND8 family comprises chromatin readers that recognise specific histone modifications to regulate transcription. Members of this group of proteins play roles in neuronal development, transcriptional repression, DNA damage repair, and transcription elongation. They interact with histones through domains such as the bromo domain, MYND-type zinc finger domain, and PWWP domain. These interactions enable them to recognise dual histone signatures, recruit chromatin remodelling complexes, and influence gene expression relevant to cellular differentiation and cancer progression .
Zinc beta-ribbon domain, plants (Zn_ribbon_pln)
Type: Domain

This domain is found in a group of uncharacterised proteins from plants. It is predicted to adopt a zinc β-ribbon fold and contains a pair of highly conserved CxxC sequence motifs. This domain is frequently found in combination with

.
Protocadherin-15 domain (PCDH15_12th_dom)
Type: Domain

This domain is found in human Protocadherin-15 (PCDH15), a calcium-dependent cell-adhesion protein that is essential for maintenance of normal retinal and cochlear function. This domain is predicted to adopt an α-β configuration. It is found C-terminal to several copies of

.
VIN3-like, C-terminal domain (VIN3-like_C)
Type: Domain

This domain is found at the C-terminal end of Protein Vernalization Insensitive 3 from Arabidopsis thaliana (VIN3) and similar plant sequences, including VIN3-like protein 1/2/3 . VIN3 plays a central role in vernalization by mediating the initial transcriptional repression of the homeotic gene FLC, a floral repressor, after a cold treatment. This domain, predicted to adopt an all-α structure, is often found associated with

and

.
Thrombospondin type-1 domain-containing protein 7A/ 7B, C-terminal TSP1 domain (TSP1_TSH7A-B_C)
Type: Domain

This entry represents the C-terminal Thrombospondin type-1 (TSP1) domain of Thrombospondin type-1 domain-containing protein 7A and 7B from vertebrates. THSD7A is a neural protein that affects endothelial migration and vascular patterning during development . THSD7A is a membrane-associated N-glycoprotein with a soluble form, the latter promotes endothelial cell migration during angiogenesis via a FAK-dependent mechanism which implies that it may be a novel neuroangiogenic factor . THSD7A has been associated with membranous nephropathy .
Argonaute protein hrde-1/Nuclear RNAi defective-3 protein-like, N-terminal domain (HRDE1/NRDE-3-like_N)
Type: Domain

This domain is found at the N-terminal of Argonaute protein hrde-1 (HRDE1, also known as C16C10.3) and nuclear RNAi defective-3 protein (NRDE-3) from Caenorhabditis elegans and relates sequences from nematodes. This domain is predicted to adopt an α/β configuration.

HRDE1 is an argonaute protein which is involved in the endogenous small interfering RNA (endo-siRNA) pathway and is required for RNA-mediated gene silencing (RNAi) in the germline . It plays a key role in transgenerational epigenetic inheritance and germline immortality .

NRDE-3 transports small interfering RNAs (siRNAs) from the cytoplasm to the nucleus. It is required for RNA interference (RNAi) in nuclei and also for exogenous RNAi-induced H3K27 methylation .
Activating signal cointegrator 1, third domain (TRIP4_3rd_dom)
Type: Domain

This entry represents a presumed domain found in Activating signal cointegrator 1 (TRIP4, also known as ASC-1) from human and related sequences from animals and some plant species. The function of this domain is unknown.

TRIP4 is the orthologue of yeast RQT4 and is part of the RQC trigger (RQT) complex that activates the ribosome quality control (RQC) pathway, a pathway that degrades nascent peptide chains during problematic translation . TRIP4 has also been described as a transcription coactivator which associates with nuclear receptors and transcriptional coactivators including EP300, CREBBP and NCOA1, and basal transcription factors like TBP and TFIIA to facilitate nuclear receptors-mediated transcription .
Activating signal cointegrator 1, N-terminal (TRI4_N)
Type: Domain

This entry represents a presumed domain found at the N-terminal of Activating signal cointegrator 1 (TRIP4, also known as ASC-1) from human and related animal sequences. The function of this domain is unknown. According to structure predictions, this domain may adopt a four helical bundle fold.

TRIP4 is the orthologue of yeast RQT4 and is part of the RQC trigger (RQT) complex that activates the ribosome quality control (RQC) pathway, a pathway that degrades nascent peptide chains during problematic translation . TRIP4 has also been described as a transcription coactivator which associates with nuclear receptors and transcriptional coactivators including EP300, CREBBP and NCOA1, and basal transcription factors like TBP and TFIIA to facilitate nuclear receptors-mediated transcription .
Peroxisomal ATPase PEX6, fourth domain (PEX6_4th_dom)
Type: Domain

This domain is found in the yeast Peroxisomal ATPase PEX6 and related fungal proteins. PEX6 is a component of the PEX1-PEX6 AAA ATPase complex, a protein dislocase complex that mediates the ATP-dependent extraction of the PEX5 receptor from peroxisomal membranes, an essential step for PEX5 recycling . The domain represented in this entry is predicted to adopt a globular structure with some topological similarity to AAA ATPase p97.
SLA1-like, PH domain-like (PH_SLA1)
Type: Domain

This domain is found in Actin cytoskeleton-regulatory complex protein SLA1 from Saccharomyces cerevisiae and similar proteins from ascomycetes. SLA1 is a component of the PAN1 actin cytoskeleton-regulatory complex required for the internalisation of endosomes during actin-coupled endocytosis . This domain is predicted to adopt a PH domain-like fold.
Arabinofuranosyltransferase D, third carbohydrate binding module (CBM_AftD)
Type: Domain

This is the third carbohydrate binding module (CBM) found in Arabinofuranosyltransferase D from Mycolicibacterium smegmatis (AftD, also known as Alpha-(1->3)-arabinofuranosyltransferase) and similar proteins from actinomycetes. The membrane embedded portion of AftD contains a typical GT-C glycosyltransferase domain (

); the periplasmic portion is made up of five distinct domains: a domain of mixed α/β folds, three CBMs and one structural β-sandwich domain . This domain shows a β-sandwich fold.
Asd-4/GZF3-like, helical region (Asd-4/GZF3_helical)
Type: Domain

This entry represents a helical region found in GATA type zinc finger protein asd-4 from Neurospora crassa (Asd-4), transcriptional regulator GZF3 from Candida albicans and similar fungal proteins. Asd-4 is a transcriptional regulator that functions in sexual development. GZF3 is transcription factor involved in response to fluconazole, LiCl, and copper.
Phage zinc binding protein, tailed bacteriophages (Phage_zn_bind)
Type: Family

This entry represents a group of small uncharacterised tailed bacteriophage proteins with a domain that covers the whole length of the protein. Structure prediction shows that this domain adopts a four stranded β-meander fold and is likely zinc binding, with an N-terminal conserved CXXC motif and more central CXXXXC motif providing the zing binding residues.
Smacovirus capsid protein (Smaco_capsid)
Type: Family

This entry represents probable capsid proteins found mainly in smacoviruses, a family of small, circular single-stranded DNA viruses. This capsid protein is typically around 300-400 amino acids in length. Smacoviruses have been identified in the fecal matter of a variety of mammals, including humans, non-human primates, pigs, and other domestic and wild animals. The viruses are currently not known to be associated with any disease.
RYYR-CCHC domain (RYYR-CCHC)
Type: Domain

This domain is found in uncharacterised proteins from nematodes. It is named after its conserved sequence motifs. It contains a semi-conserved RxY(x)nYR motif and two invariant CxxC and HxxxC motifs. This domain is predicted to adopt a globular structure with significant similarity to FLYWCH-type zinc finger, in particular

. It is quite likely that this domain is a zinc-finger, given the strict conservation of the cysteine and histidine residues. However, this potential zinc-finger has a distinct pattern of the zinc coordinating residues compared to the FLYWCH-type zinc fingers.
YdgV (YdgV)
Type: Family

This protein family includes YdgV from Escherichia coli and similar sequences from gammaproteobacteria. YdgV is a 33-residues micropeptide encoded by a small open reading frame (smORF). Proteins 50 or fewer residues-long have been shown to regulate the functions of larger proteins in a variety of organisms .
Phage tail termination protein, tailed bacteriophages (Phage_tail_terminator_2)
Type: Family

This entry represents probable phage tail terminator proteins found in some bacteriophages that infect Actinobacteria. These proteins are likely located in the tail region and act as a terminator or cap the end of the tail. They are around 130-170 amino acids in length.
Gp90-like protein, tailed bacteriophages (Gp90-like)
Type: Family

This family represents the Gp90-like protein from Synechococcus phages. Sequences in the family are typically around 110 residues in length. Gp90 homologues are found in a variety of different tailed bacteriophages. The function of Gp90 is currently unknown.
Phage tail assembly chaperone, tailed bacteriophages (Phage_TAC_17)
Type: Family

This family represents proteins found in tailed bacteriophages with structural similarity to the phage tail assembly chaperone proteins.
Phage tail chaperone protein-like (Phage_TAC_19)
Type: Family

This entry represents a family of proteins structurally similar to phage tail chaperone proteins and found in viruses and bacteria. The family contains proteins between 50-164 amino acids in length. Phage tail chaperone proteins play a role in the assembly of the phage tail apparatus.
Type III Secretion system protein OrgC (OrgC)
Type: Family

This entry represents the type III Secretion system protein OrgC from Salmonella Typhimurium and related proteins from proteobacteria. OrgC is a protein encoded within the T3SS gene cluster that is secreted by the T3SS. It interacts with the needle filament subunit PrgI and accelerates its polymerization into filaments in vitro . OrgC structure consists of an array of four α-helices.
SpoVR-like, C-terminal (SpoVR-like_C)
Type: Domain

This entry represents a presumed domain found at the C-terminal of Stage V sporulation protein R from Bacillus subtilis (SpoVR), the uncharacterised protein YcgB from E.coli and related sequences from proteobacteria. SpoVR appears to be involved in spore cortex formation. This region may adopt a fold consisting of four β-strands and an α-helix.
Fimbrial adhesin MrpH, N-terminal domain (MrpH_N)
Type: Domain

This entry represents the N-terminal domain of fimbrial adhesin MrpH and related proteins from bacteria. This protein is associated with strain virulence and is involved in surface adherence, biofilm formation and autoaggregation, essential for bladder and kidney colonization . This domain binds to surface receptor and coordinates one Zn2+ necessary for attachment and biofilm formation

.
Fimbrial adhesin MrpH, C-terminal domain (MrpH_C)
Type: Domain

This entry represents the C-terminal domain of fimbrial adhesin MrpH and related proteins from bacteria. MrpH is associated to strain virulence and is involved in surface adherence, biofilm formation and autoaggregation, essential for bladder and kidney colonization . This domain attaches to bacterial fimbrial tip .
ULTRAPETALA1/2, SAND domain (ULT1/2_SAND)
Type: Domain

This domain is found in the family of ULTRAPETALA proteins ULT1/2 from Arabidopsis thaliana and related plant proteins. This domain is predicted to adopt a globular structure with significant similarity to SAND domains. It also contains several highly conserved cysteine residues that could be involved in metal coordination.

ULT1/2 are putative transcription factors that act as regulators of cell accumulation in shoot and floral meristems . They also act as antirepressors that counteract EMBRYONIC FLOWER1 (EMF1) action through modulation of histone marks on target genes and thus regulating their transcriptional activities .
ULTRAPETALA1/2, zinc finger domain (ULT1/2_Znf)
Type: Domain

This domain is found C-terminal in the family of ULTRAPETALA proteins ULT1/2 from Arabidopsis thaliana and related plant proteins. This domain contains several highly conserved cysteine and histidine residues that could be involved in metal coordination. In the core part, this domain shares similarity with CW-type zinc finger domains ([

]) but it has additional clusters of conserved residues indicating the presence of four putative metal-binding sites.

ULT1/2 are putative transcription factors that act as regulators of cell accumulation in shoot and floral meristems . They also act as antirepressors that counteract EMBRYONIC FLOWER1 (EMF1) action through modulation of histone marks on target genes and thus regulating their transcriptional activities .
EGF-like domain-containing protein ComC, LRR domain (LRR_ComC)
Type: Domain

This entry represents the N-terminal region of EGF-like domain containing protein ComC from Dictyostelium discoideum and similar sequences from amoebas and some plant species. ComC regulates aggregation, inhibiting lagC and activating lagD expression . The function of this domain, which is predicted to consist of leucine-rich repeats (LRR), is unknown.
EGF-like domain-containing protein ComC, first beta-sandwich (B-sand_ComC_1st)
Type: Domain

This entry represents the first β-sandwich domain found in EGF-like domain containing protein ComC from amoebas. This protein regulates aggregation, inhibiting lagC and activating lagD expression . The function of this domain is unknown.
EGF-like domain-containing protein ComC, second beta-sandwich (B-sand_ComC_2nd)
Type: Domain

This entry represents the second β-sandwich domain found in EGF-like domain containing protein ComC from amoebas. This protein regulates aggregation, inhibiting lagC and activating lagD expression . The function of this domain is unknown.
Endo-beta-N-acetylglucosaminidase EndoS/F2-like, TIM-barrel domain (EndoS_F2-like_TIM-barrel)
Type: Domain

This entry represents the TIM barrel domain found in Endo-beta-N-acetylglucosaminidase EndoS from Streptococcus spp., Endo-beta-N-acetylglucosaminidase F2 from Elizabethkingia meningoseptica and similar bacterial proteins. This domain binds to complex-type N-glycans and has an enzymatic activity .

EndoS is a secreted protein that catalyses the hydrolysis of the N-linked oligosaccharides on opsonising immunoglobulin G , thus contributing to immune response evasion and increased survival of the bacteria in patients .
F54D1.6-like, C-terminal Sushi-like domain (F54D1_6-like_C)
Type: Domain

This domain is found towards the C-terminal end of the uncharacterised protein F54D1.6 from Caenorhabditis elegans and similar sequences from worms. It is often found associated to

. This domain has a detectable similarity to Sushi domains and is predicted to adopt a similar structure.
F54D1.6-like, Ig-like domain (F54D1_6-like_Ig-like)
Type: Domain

This is an immunoglobulin-like domain of the uncharacterised protein F54D1.6 from Caenorhabditis elegans and similar worm sequences. It is often found associated to

.