SII-SWORD/CoKE huggingface dataset:
USP48 domain (USP48_dom)
Type: Domain

This entry represents a domain found towards the C-terminal of USP48 C. elegans and related sequences from nematodes. This domain is usually found in association with

.

In C.elegans, USP48 is required post-developmentally to restrict the plasticity of epidermal cells, probably by regulating gene expression .
UTP23, sensor motif region (UTP23_sensor)
Type: Domain

This entry represents the sensor motif region found in the UTP23 protein. The sensor motif is located in the C-terminal region of UTP23 and recognises the snR30-ES6 three-way junction in the 18S rRNA. This interaction is crucial for the early stages of 90S pre-ribosome assembly and 18S rRNA processing. The sensor motif is highly conserved across eukaryotes and is essential for UTP23 function. Deletion of this motif results in a substantial growth defect, highlighting its importance in ribosome biogenesis.

Utp23 share homology with PINc domain protein Fcf1. They are components of the small subunit processome (SSU) that are involved in rRNA-processing and ribosome biogenesis .
Vein, beta-barrel domain (Beta-barrel_vein)
Type: Domain

This entry includes vein protein from Drosophila, a secreted neuregulin-like EGFR ligand. It may play a role in the global proliferation of wing disc cells and the larval patterning . This entry represents a β-barrel domain found in vein, which is similar to that found in Tissue inhibitors of metalloproteinases (TIMP). Vein is an orthologue of neuregulin 1 (NRG1

). This domain, however, seems to be specific for vein proteins.
Vigilin, N-terminal KH domain (KH_Vigilin_N)
Type: Domain

This entry represents the first KH domain located at the N-terminal of Vigilin proteins.

Vigilin, also known as high-density lipoprotein-binding protein (HDL-binding protein), is a ubiquitous and highly conserved RNA-binding protein that shuttles between the nucleus and cytoplasm, presumably in association with RNA molecules. It may be involved in chromosome partitioning during mitosis, facilitation of translation and tRNA transport, and regulation of mRNA metabolism, including oestrogen-mediated stabilisation of vitellogenin mRNA. Vigilin is upregulated in response to cholesterol loading in cells and functions to protect against excessive intracellular cholesterol accumulation. It may also play a role in cellular sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin possesses a unique structure comprising 14 to 15 consecutively arranged, though non-identical, K-homology (KH) domains, which appear to mediate RNA-protein interactions .
Vps41, C-terminal RING finger (Znf_RING_Vps41)
Type: Domain

This entry represents the C-terminal RING finger domain of Vps41. Eukaryotic cells utilise conserved membrane tethering complexes like CORVET and HOPS to regulate endomembrane fusion, with each complex comprising six subunits, including unique C-terminal zinc-finger domains. Biochemical studies in human CORVET and HOPS reveal direct interaction between the zinc-containing RING domains of Vps18 and Vps41, forming a stable heterodimer. Within cells, these domains integrate into endogenous HOPS, with the Vps18 RING domain recruiting Vps41 to the core complex. However, yeast Vps41 lacks a C-terminal zinc-finger motif. In human CORVET, the analogous subunit Vps8 requires both its RING and disordered C-terminal domains for integration into endogenous complexes, suggesting distinct molecular interactions for recruiting Vps41 and Vps8 to HOPS and CORVET, respectively .

Vsp41 is a subunit of the homotypic vacuole fusion and vacuole protein sorting (HOPS) complex, which is essential for membrane docking and fusion at the Golgi-to-endosome and endosome-to-vacuole stages of protein transport . This protein interacts with Caspase-8, which plays a key role in apoptosis and development . Vsp41 consists of a β-propeller at the N-terminal (

), represented in this entry, followed by an α-solenoid (TPR-like) domain, a CHCR domain and a RING zinc finger (

).
Vps41, beta-propeller (Beta-prop_Vps41)
Type: Domain

This entry represents the N-terminal in Vsp41 proteins which contains a β-propeller.

Vsp41 is a subunit of the homotypic vacuole fusion and vacuole protein sorting (HOPS) complex, which is essential for membrane docking and fusion at the Golgi-to-endosome and endosome-to-vacuole stages of protein transport . This protein interacts with Caspase-8, which plays a key role in apoptosis and development . Vsp41 consists of a β-propeller at the N-terminal (

), represented in this entry, followed by an α-solenoid (TPR-like) domain, a CHCR domain and a RING zinc finger (

).
YKL023C-A-like (YKL023C-A-like)
Type: Family

This entry represents the small uncharacterised protein YKL023C-A from Saccharomyces cerevisiae and similar yeast sequences . This microprotein is predicted to adopt an α-helical configuration.

It is also found in some uncharacterised proteins that also contain

.
YKL065W-A-like (YKL065W-A-like)
Type: Family

This protein family includes the uncharacterised protein YKL065W-A from Saccharomyces cerevisiae, a micropeptide encoded by a small open reading frame (smORF) .
YKL104W-A (YKL104W-A)
Type: Family

This protein family includes the uncharacterised protein YKL104W-A from Saccharomyces cerevisiae, a micropeptide encoded by a small open reading frame (smORF) .
YlcJ-like (YlcJ-like)
Type: Family

This protein family includes YlcJ from Escherichia coli , a 49-residue-long sequence predicted to adopt an α-helical configuration.
YLR146W-A-like (YLR146W-A-like)
Type: Family

This protein family includes the Coiled-coil domain-containing protein YLR146W-A from Saccharomyces cerevisiae, a micropeptide encoded by a small open reading frame (smORF) whose function is unknown . This protein is predicted to adopt an α-helical structure.
YmgL-like (YmgL-like)
Type: Family

This protein family includes YmgL from Escherichia coli, a 36-residue-long sequence predicted to adopt an α-helical configuration. It is expressed at approximately equal levels during exponential growth and stationary phase in rich growth medium .
YmgM (YmgM)
Type: Family

This protein family includes YmgM from Escherichia coli , a 67-residue-long sequence with unknown function.
YmiD (YmiD)
Type: Family

This protein family includes the uncharacterised protein YmiD from Escherichia coli, a 42-residue 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. It is expressed in both exponential and stationary phases in rich media .
YmjE-like (YmjE-like)
Type: Family

This protein family includes Protein YmjE from Escherichia coli , a 54-residue-long sequence with an unknown function. It is expressed at approximately equal levels during exponential growth and the stationary phase in rich growth medium.
YncO-like (YncO-like)
Type: Family

This protein family includes Protein YncO from Escherichia coli , a 61-residue-long sequence predicted to adopt an α-helical configuration.
YneP-like (YneP-like)
Type: Family

This protein family includes Protein YneP from Escherichia coli , a 40-residue-long sequence with an unknown function and a predicted all-α-helical configuration. It has low levels of expression of YneP were detected at the stationary phase.
YnfS-like (YnfS-like)
Type: Family

This protein family includes Protein YnfS from Escherichia coli , a 29-residue-long sequence encoded in the Qin prophage. It is predicted to adopt an α-helical configuration.
YnfU-like (YnfU-like)
Type: Family

This protein family includes the putative zinc-binding protein YnfU, encoded in the Qin prophage from Escherichia coli, and similar sequences mainly from proteobacteria. YnfU is a 56-residue 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 . This peptide is predicted to show an α-β configuration.
YnhH-like (YnhH-like)
Type: Family

This protein family includes Protein YnhH from Escherichia coli, a 64-residue-long microprotein encoded by a small open reading frame (smORF) .
YodE (YodE)
Type: Family

This protein family includes Protein YodE from Escherichia coli, a 48-residue micropeptide encoded by a small open reading frame (smORF) that overlaps on the same strand with small regulatory RNA RyeG. Proteins of 50 or fewer residues long have been shown to regulate the functions of larger proteins in a variety of organisms . It is predicted to contain a β configuration.
YOMG-like, N-terminal domain (YOMG-like_N)
Type: Domain

This entry represents the N-terminal domain of SPbeta prophage-derived uncharacterised protein YomG from Bacillus subtilis (strain 168). This domain adopts a β-barrel fold and is usually found in association with a neighbour prophage endopeptidase tail domain (

).
YqeB, PH domain (PH_YqeB)
Type: Domain

This entry represents a PH domain in YqeB from Bacillus subtilis and related bacterial proteins. These proteins contain 2 transmembrane helices and a bacterial PH domain that includes an unusual α/β/β/α subdomain. The function of these proteins is unknown. They contain a C-terminal domain related to an anticodon binding domain found in cysteinyl tRNA ligases (

). This suggests these proteins may have a role in translation, it is predicted to be located at the plasma membrane.
YqfI-like (YqfI-like)
Type: Family

This protein family includes Protein YqfI from Escherichia coli , a 27-residues long sequence predicted to adopt an α-helical configuration.
YqgG-like (YqgG-like)
Type: Family

This protein family includes Protein YqgG from Escherichia coli, a 47-residue micropeptide encoded by a small open reading frame (smORF) found antisense to yqgC. Proteins 50 or fewer residues long have been shown to regulate the functions of larger proteins in a variety of organisms .
YqgH-like (YqgH-like)
Type: Family

This protein family includes Protein YqgH from Escherichia coli, a 27-residue 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 .
YqhI domain (YqhI_dom)
Type: Domain

This entry describes an uncharacterised domain that covers the whole length of YqhI from Escherichia coli . YqhI is a 47-residue-long protein encoded by a small open reading frame (smORF).

This domain also covers the N-terminal of uncharacterised proteins that also contain

.
YqiM (YqiM)
Type: Family

This protein family includes YqiM from Escherichia coli, a 27-residue micropeptide encoded by a small open reading frame (smORF). Proteins of 50 or fewer residues long have been shown to regulate the functions of larger proteins in a variety of organisms .
YsdD (YsdD)
Type: Family

This protein family includes YsdD from Escherichia coli , a 26-residue-long sequence. YsdD is expressed during the stationary phase.
YtiC (YtiC)
Type: Family

This protein family includes YtiC from Escherichia coli , a 33-residue-long sequence predicted to adopt an α-helical configuration.
YxiF (YxiF)
Type: Family

This entry represents the uncharacterised YxiF protein from B. subtilis [

]. It contains a β-sheet surrounded by α-helices.
YxiG (YxiG)
Type: Family

This family includes proteins related to B. subtilis YxiG. This protein forms a single compact all-β domain that is predicted to homodimerise .
Zinc finger domain-containing protein 24, C-terminal domain (ZCCHC24_C)
Type: Domain

This entry represents the C-terminal domain in ZCCHC24 protein and related eukaryotic proteins. It contains highly conserved histidine and cysteine residues in an unusual arrangement (HCCC) that are likely to coordinate zinc.

Zinc finger domain-containing protein 24 (ZCCHC24) encodes a protein containing two zinc finger domains from the Znf-CCHC and Znf-3CxxC superfamilies . This protein contains a 3CxxC-type zinc finger (

) next to the C-terminal domain (

), these subdomains are represented by

.
Zinc finger CCHC domain-containing protein 3, first RNA-binding domain (RBD_ZCCHC3_1st)
Type: Domain

This entry represents the first RNA-binding domain (RBD) found in the vertebrate Zinc finger CCHC domain-containing protein 3 (ZCCHC3). This domain is followed by the second RBD (

).

Zinc finger CCHC domain-containing protein 3 from humans (ZCCHC3) is a zinc-finger protein that acts as a co-sensor of cGAS in innate immune response to cytosolic dsDNA and DNA virus . It has been shown to bind DNA and RNA in the cytoplasm and acts by promoting recognition of viral nucleic acids by virus sensors, such as DDX58/RIG-I, IFIH1/MDA5 and CGAS . Members of this family are found in eukaryotes.
Zinc finger CCHC domain-containing protein 3, second RNA-binding domain (RBD_ZCCHC3_2nd)
Type: Domain

This entry represents the second RNA-binding domain (RBD) found in vertebrate Zinc finger CCHC domain-containing protein 3 (ZCCHC3). This domain is preceded by the first RBD (

).

Zinc finger CCHC domain-containing protein 3 from humans (ZCCHC3) is a zinc-finger protein that acts as a co-sensor of cGAS in innate immune response to cytosolic dsDNA and DNA virus . It has been shown to bind DNA and RNA in the cytoplasm and acts by promoting recognition of viral nucleic acids by virus sensors, such as DDX58/RIG-I, IFIH1/MDA5 and CGAS . Members of this family are found in eukaryotes.
YKFC, SH3b2 domain (SH3_YKFC_2nd)
Type: Domain

This entry represents the second of two N-terminal bacterial SH3 (SH3b2) domains found in bacterial dipeptidyl-peptidases VI such as Gamma-D-glutamyl-L-lysine dipeptidyl-peptidase (YKFC). YKFC consist of three domains (

), the N-terminal SH3b1 (

), SH3b2 and a C-terminal NlpC/P60 (

). The active site is located at the SH3b1-NlpC/P60 interface, whereas the SH3b2 domain is distal to it .
YhiY (YhiY)
Type: Family

This protein family includes Protein YhiY from Escherichia coli, a 37-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 .
YecU-like (YecU)
Type: Family

This protein family includes Protein YecU from Escherichia coli , a 58-residues long protein encoded by a small open reading frame (smORF).
YbjQ-like domain (YbjQ-like_dom)
Type: Domain

This is a domain found C-terminal in a group of eukaryotic proteins. This domain is predicted to adopt a YbjQ-like fold.
YBR230W-A (YBR230W-A)
Type: Family

This protein family includes the uncharacterised protein YBR230W-A from Saccharomyces cerevisiae, a micropeptide encoded by a small open reading frame (smORF) .
YBR126W-A (YBR126W-A)
Type: Family

This protein family includes the uncharacterised protein YBR126W-A from Saccharomyces cerevisiae, a micropeptide encoded by a small open reading frame (smORF) . YBR126W-A is predicted to adopt an α-helical structure.
YbgU (YbgU)
Type: Family

This protein family includes the uncharacterised protein YbgU from Escherichia coli and similar sequences from gammaproteobacteria. YbgU is a 35-residues micropeptide encoded by a small open reading frame (smORF) that overlaps another smORF, ybgV, on the same strand in another reading frame. Proteins 50 or fewer residues-long have been shown to regulate the functions of larger proteins in a variety of organisms .
T4 y05I-like putative transcription factor, N-terminal domain (T4_y05I_N)
Type: Domain

This entry represents the N-terminal domain of family of uncharacterised phage protein that includes T4 y05I protein

. The family also includes homologues from T2 and T6 phage among others. These proteins contain two domains. These domains appear to be related to those found in the eukaryotic PurA transcription factor. This N-terminal presumably single stranded DNA binding domain contains two copies of a PurA-like repeat. The C-terminal domain

contains a single copy that may mediate dimerisation in an analogous fashion to PurA.
T4 y05I-like putative transcription factor, C-terminal domain (T4_y05I_C)
Type: Domain

This entry represents the C-terminal domain of a family of uncharacterised phage proteins that includes T4 y05I protein

. The family also includes homologues from T2 and T6 phage, among others. These proteins contain two domains. These domains appear to be related to those found in the eukaryotic PurA transcription factor. This N-terminal, presumably single-stranded DNA-binding domain contains two copies of a PurA-like repeat. The C-terminal domain contains a single copy that may analogously mediate dimerisation to PurA.
XPB-like, C-terminal domain (XPB_C)
Type: Domain

This domain is found at the C-terminal end of TFIIH basal transcription factor complex helicase/translocase XPB subunit from Trypanosoma brucei and related proteins from similar species. This domain is predicted to adopt an α/β configuration. This domain is found next to

and appears to be unique in XBP in Trypanosoma.

XPB, also known as Ssl2, Ercc3, RepB, Rad25 or haywire, is a core subunit of the eukaryotic basal transcription factor complex TFIIH, which plays a dual role in transcription and DNA repair . It is involved in nucleotide excision repair of DNA and in RNA transcription by RNA polymerase II . TFIIH is a multiprotein complex composed of a 7-subunit core, including XPB, p62, p52, p44, p34 and TTDA, associated with a 3-subunit CDK-activating kinase module consisting of MAT1, cyclin H and Cdk7 . XPB functions by opening DNA either around the RNA transcription start site or at sites of DNA damage . It is also required for spliced leader RNA gene transcription by RNA polymerase II, where TFIIH plays an essential role in transcription initiation . Once the pre-initiation complex has been established, TFIIH is necessary for promoter opening and promoter escape, processes that depend on the ATPase activity of XPB .
RCD1, WWE domain (WWE_RCD1)
Type: Domain

This entry represents a WWE domain found in a family of plant proteins, which includes probable inactive ADP-ribosyltransferases that are involved in the regulation of oxidative stress, hormonal and developmental responses in Arabidopsis thaliana. Members of the family, such as SRO1 and RCD1, may regulate stress-responsive genes and play distinct roles in plant development. While they are characterised as inactive due to their inability to bind NAD in vitro, they still contribute to critical processes such as embryogenesis, vegetative and reproductive development, and abiotic stress responses. The family highlights a functional partnership between its members in managing plant responses to environmental challenges.
SEC23-DDH2, WWE domain (WWE_SEC23-DDH2)
Type: Domain

This entry represents a WWE domain found in the PA-PLA1 proteins including SEC23-interacting protein (Sec23ip) and Triacylglycerol hydrolase DDHD2 (DDHD2).

Sec23ip plays a role in the organisation of endoplasmic reticulum exit sites. Specifically binds to phosphatidylinositol 3-phosphate (PI3P), phosphatidylinositol 4-phosphate (PI4P) and phosphatidylinositol 5-phosphate (PI5P). However, current evidence indicates that it does not exhibit actual phospholipase activity .

DDHD2 functions as a diacylglycerol (DAG) and triacylglycerol (TAG) lipase, playing a critical role in maintaining lipid homeostasis in the central nervous system . It acts in concert with PNPLA2/ATGL in neuronal TAG catabolism by hydrolysing sn-1,3 DAG downstream of PNPLA2/ATGL. In vitro studies show that DDH2 also exhibits phospholipase activity, preferentially hydrolysing phosphatidic acids such as 1,2-dioleoyl-sn-phosphatidic acid, as well as phosphatidylcholine and phosphatidylethanolamine. Additionally, it specifically binds to phosphoinositides, including phosphatidylinositol 3-phosphate (PI3P), PI4P, PI5P, and possibly PI(4,5)P2. This lipid-binding activity suggests a role in the maintenance of endoplasmic reticulum and Golgi structures, potentially influencing vesicular transport between the Golgi apparatus and the plasma membrane.

PA-PLA1 proteins are involved in various cellular processes related to membrane lipid metabolism and organelle structure maintenance. These proteins exhibit phospholipase activity, preferentially hydrolysing phosphatidic acid and phosphatidylethanolamine. They also have specific lipid-binding capabilities, interacting with phosphatidylinositol phosphates such as PI(3)P, PI(4)P, and PI(5)P. This binding is crucial for their role in organising endoplasmic reticulum exit sites and may influence transport between the Golgi apparatus and plasma membrane. The function of these proteins is essential for maintaining the integrity of the endoplasmic reticulum and Golgi structures, which are critical for proper cellular function .
C20G8.02-like, WWE domain (WWE_C20G8.02)
Type: Domain

This entry represents a set of WWE domains found in fungal proteins, such as Probable phospholipase C20G8.02 that likely have a phospholipase activity. This domain is usually found associated with

.
WW domain, fungi (WW_fungi)
Type: Domain

This entry represents a set of WW domains that are found in a large family of fungal RasGEF domain-containing proteins. This domain is found close to the N-terminal of the proteins adjacent to an SH3 domain

.
ZNF142, C2H2 zinc finger 13 (Znf_C2H2_ZNF142_13th)
Type: Domain

This entry represents the 13th C2H2 zinc finger in human ZNF142 and related proteins. In mice ZNF142 and related proteins, this domain can be found in a different position.

Zinc finger protein 142 (ZNF142) plays a role in nervous system development. It is thought to be involved in transcriptional regulation. This proteins is predicted to contain multiple C2H2 zinc fingers which may be involved in DNA or RNA binding .

C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short β-hairpin and an α-helix (β/β/α structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 . C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes . Transcription factors usually contain several Znf's (each with a conserved β/β/α structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short α-helix in the Znf, the Znf spanning 3-4 bases of the DNA . C2H2 zinc fingers can also bind to RNA and protein targets .
ZNF142, C2H2 zinc finger 21/23 (Znf_C2H2_ZN142_21/23)
Type: Domain

This entry represents the 21st and 23rd C2H2 zinc finger in human ZNF142 and related proteins. In mice ZNF142 and related proteins, this domain can be found in a different position.

Zinc finger protein 142 (ZNF142) plays a role in nervous system development. It is thought to be involved in transcriptional regulation. This proteins is predicted to contain multiple C2H2 zinc fingers which may be involved in DNA or RNA binding .

C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short β-hairpin and an α-helix (β/β/α structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 . C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes . Transcription factors usually contain several Znf's (each with a conserved β/β/α structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short α-helix in the Znf, the Znf spanning 3-4 bases of the DNA . C2H2 zinc fingers can also bind to RNA and protein targets .