SII-SWORD/CoKE huggingface dataset:
Zinc finger 512, zinc finger (ZNF512_znf-C2H2)
Type: Domain

This C2H2-type zinc finger is found in human Zinc finger protein 512 (ZNF512) (

) and related proteins primarily from chordates. The human ZNF512 contains six zinc fingers, of which three are classical type C2H2 zinc fingers and three are variant C2HC. The structure of the first pair of C2H2-C2HC zinc fingers was determined by NMR (

). The function of these domains is unknown.

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 .
DYN1, AAA+ ATPase lid domain (DYN1_lid)
Type: Domain

This entry includes dynein heavy chain (DYN1) from S.cerevisiae, which is a cytoplasmic dynein that acts as a motor for intracellular retrograde motility of vesicles and organelles along microtubules. This entry represents the AAA ATPase lid domain .
Gliding motility-associated protein GldM, first immunoglobulin-like domain (GldM_Ig-like-1)
Type: Domain

This entry represents the first immunoglobulin-like domain is found in the gliding motility-associated protein GldM from Flavobacterium johnsoniae (

) and in similar bacterial sequences. GldM is required for a type of rapid gliding motility found in certain members of the Bacteriodetes . It consist of four domains and forms a dimer with a straight rod shape (

). This domain follows the N-terminal helical domain

.
Gliding motility-associated protein GldM, second immunoglobulin-like domain (GldM_Ig-like-2)
Type: Domain

This entry represents the second immunoglobulin-like domain is found in the gliding motility-associated protein GldM from Flavobacterium johnsoniae (

) and in similar bacterial sequences. GldM is required for a type of rapid gliding motility found in certain members of the Bacteriodetes . It consist of four domains and forms a dimer with a straight rod shape (

). This domain follows the N-terminal helical domain

and the first Ig-like domain

.
Dumpy, DPY module (Dumpy_DPY)
Type: Repeat

This entry represents the DPY repeat module described in dumpy from Drosophila melanogaster (

), a gigantic extracellular matrix protein that contains epidermal growth factor (EGF) modules interspersed with DPY modules. The DPY module forms a compact fold consisting of a small N-terminal 3-10 helix packed against a double-stranded antiparallel disulphide-stabilised β-sheet motif capable of linking end-to-end with EGF modules to form a fibre .
Zinc finger protein 512, C2HC zinc finger (ZNF512_C2HC)
Type: Domain

This C2HC zinc finger is found in human ZNF512 protein (

) and other related proteins primarily from chordates. The human ZNF512 contains six zinc fingers, of which three are classical type C2H2 zinc fingers and three are variant C2HC. The structure of the first pair of C2H2-C2HC zinc fingers was determined by NMR (

). The function of these domains is unknown.

Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates . Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few . Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target.
DTX3L, KH-like domain (DTX3L_KH-like)
Type: Domain

DTX3L is a RING-domain E3 ubiquitin-protein ligase that regulates endosomal sorting of the G protein-coupled receptor CXCR4 from endosomes to lysosomes . It also regulates subcellular localisation of its partner protein, B aggressive lymphoma (BAL), by a dynamic nucleocytoplasmic trafficking mechanism . This entry represents two copies of a domain found before the Znf domain (

) in DTX3L. According to structure predictions, it seems to be related to KH domains.
RNA-binding, Nab2-type zinc finger (Znf-CCCH_2-like_3)
Type: Domain

This domain is found in nuclear polyadenylated RNA-binding 2 protein NAB2 from Saccharomyces cerevisiae (also known as Nab2p) and its homologues from yeast. Nab2p is a major family of Poly A-binding proteins whose interactions are thought to be crucial for the control of poly(A) tail length. This domain is the second of seven CCCH zinc fingers which are responsible for polyadenosine recognition. The structures of the first two independent tandem zinc fingers (TZF12 and TZF34) were determined by NMR (

,

). These four zinc fingers together may bind RNA in the 3' to 5' direction .
Huntingtin, N-terminal, HEAT repeats 1 (Htt_N_HEAT_rpt-1)
Type: Repeat

This entry represents the first region of HEAT repeats from Huntingtin (Htt), which is part of the N-terminal HEAT domain . It is separated from the rest of the domain (

) by an unstructured region. Htt is expressed in many tissues with various expression levels and is involved in a number of cellular functions. However, its exact function is not yet clear. An abnormal polyglutamine (polyQ) expansion between 1-90aa at the very N-terminal causes Huntington's disease (HD), a progressive autosomal-dominant neurodegenerative disease characterised by an uncontrolled motor movement known as chorea, cognitive disorder and depression . Htt consists of multiple HEAT repeats organised in N-terminal, bridge and C-terminal domains , which function as a scaffold that mediated interactions with binding partners.
Huntingtin, bridge (Htt_bridge)
Type: Repeat

Huntingtin (HTT) is expressed in many tissues, with various expression levels and is involved in a number of cellular functions. However, its exact function is not yet clear. An an abnormal polyglutamine (polyQ) expansion in this protein causes Huntington's disease (HD) a progressive autosomal-dominant neurodegenerative disease characterised by an uncontrolled motor movement known as chorea, cognitive disorder and depression . HTT consists of multiple HEAT repeats organised in N-terminal (formed by

and

), bridge (represented in this entry) and C-terminal domains , which function as a scaffold that mediates interactions with binding partners. This domain connects the N- and C-HEAT domains.
Huntingtin, C-terminal HEAT repeats (Htt_C-HEAT_rpt)
Type: Repeat

This entry represents the C-terminal domain of Huntingtin (Htt), which consists of HEAT repeats. Htt is expressed in many tissues with various expression levels and is involved in a number of cellular functions. However, its exact function is not yet clear. An an abnormal polyglutamine (polyQ) expansion in this protein causes Huntington's disease (HD) a progressive autosomal-dominant neurodegenerative disease characterised by an uncontrolled motor movement known as chorea, cognitive disorder and depression . HTT consists of multiple HEAT repeats organised in N-terminal (

and

), bridge (

) and C-terminal domains , which function as a scaffold that mediated interactions with binding partners. It has been suggested that the polyQ expansion in Htt alters phosphorylation status along the protein which affects its structure and function. In particular, modifications of phosphorylation in this domain induce conformational changes that impair its movement and interaction with the N-HEAT domain .
Histone-lysine N-methyltransferase PRDM9-like, C2H2 zinc finger-like (PDRM9-like_Znf-C2H2)
Type: Domain

This C2H2 zinc finger is found in human Histone-lysine N-methyltransferase PRDM9 (

) and related proteins. PRDM9 sequentially mono-, di-, and tri-methylates both 'Lys-4' (H3K4) and 'Lys-36' (H3K36) of histone H3 and is a key determinant of the localisation of meiotic recombination hot spots in humans and mice .

This zinc finger is also found in Zinc finger proteins ZNF589, ZNF875 and ZNF343 that are though to be involved in transcriptional regulation.

Members of this group of proteins are usually found in vertebrates.
Distal tail protein pb9, B domain (DTP-pb9_B-dom)
Type: Domain

This entry includes phage distal tail proteins which form a hexameric ring located at the tail tube end, such as pb9 from bacteriophage T5 . pb9 consists of two domains, A and B. This entry represents domain B which adopts an OB fold and is inserted in domain A .
Distal tail protein pb9, A domain, C-terminal (DTP-pb9_A-dom_C)
Type: Domain

This entry includes phage distal tail proteins which form a hexameric ring located at the tail tube end, such as pb9 from bacteriophage T5 . pb9 consists of two domains, A and B. Domain A adopts a split barrel fold and includes residues 1 to 82-172 to 205. This entry covers the C-terminal region of the A domain .
Distal tail protein pb9, A domain, N-terminal (DTP-pb9_A-dom_N)
Type: Domain

This entry includes phage distal tail proteins which form a hexameric ring located at the tail tube end, such as pb9 from bacteriophage T5 . pb9 consists of two domains, A and B. Domain A adopts a split barrel fold and includes residues 1 to 82-172 to 205. This entry covers the N-terminal region of the A domain . The C-terminal segment of the A domain is represented in

.
DTX3L, alpha/beta domain (DTX3L_a/b_dom)
Type: Domain

DTX3L is a RING-domain E3 ubiquitin-protein ligase that regulates endosomal sorting of the G protein-coupled receptor CXCR4 from endosomes to lysosomes . It also regulates subcellular localisation of its partner protein, B aggressive lymphoma (BAL), by a dynamic nucleocytoplasmic trafficking mechanism . This entry represents a domain found towards the N-terminal of DTX3L, whose function is unknown. According to structure predictions (AlphaFold), it may adopt a β-α-β-β-α conformation, similar to Smr domains.
TOPLESS, zinc finger domain (Topless_Znf)
Type: Domain

This is the zinc finger domain of TOPLESS and TOPLESS-related proteins. TOPLESS are tetrameric plant transcriptional co-repressors that belong to the conserved Tup1/Groucho/TLE (transducin-like enhancer of split) family . The function of this zinc finger is unclear.
Zap1-like, C2H2 zinc finger 1 (Zap1-like_Znf1)
Type: Domain

Zap1 transcription factor (

) controls the expression of genes that regulate zinc homeostasis in Saccharomyces cerevisiae. Zap1 contains seven classical C2H2 zinc fingers. This domain corresponds to zinc finger 1 (Znf1) which together with zinc finger 2 (Znf2) has been shown to be a responsive transcriptional activator. Both zinc fingers interact cooperatively to stabilise the Zn-binding .

This zinc finger is also found in pH-response transcription factor pacC/RIM101 (

) that mediates regulation of both acid- and alkaline-expressed genes in response to ambient pH .

Proteins containing this domain are primarily found in fungi and eumetazoa.
YqgU-like, 6-bladed beta-propeller domain (YqgU_beta-prop)
Type: Domain

This entry represents a β-propeller domain found in YqgU from B. subtilis (

) and related bacterial proteins. The proteins containing this domain usually possess an N-terminal lipid attachment motif suggesting they are lipoproteins. The function of this domain is unknown.
NOA1/YqeH-like, C-terminal domain (NOA1/YqeH-like_C)
Type: Domain

This entry is found at the C terminus of Nitric oxide-associated protein 1 (NOA1) from animals and rice, BPG2 from Arabidopsis and YqeH from B. subtilis. YqeH is an orthologue of NOA1. This domain folds into a β-sandwich structure with significant similarity to proteins members of the RsmA/CsrA translational regulators family that bind to RNA (

). The residues for RNA recognition in these proteins are conserved in members of this entry, suggesting that these may be involved in nucleic acid recognition .
Oxidoreductase DRL-like, catalytic domain (DRL_cat)
Type: Domain

This domain is found in DRL (deoxyxylulose-5-phosphate reductoisomerase-like) from Brucella abortus (

) and other bacterial putative oxidoreductases and homoserine dehydrogenases. DRL is involved in isoprenoid biosynthesis. This protein is organised into three structural domains: N-terminal, central and C-terminal. This is the central, catalytic domain which shows an α/β fold with a central four-stranded mixed β-sheet. The active site lid is formed by a protrusion made of two antiparallel helices connected by a short loop .
YqbF, C-terminal domain (YqbF_HeH)
Type: Domain

This entry represents the C-terminal domain of the uncharacterised protein YqbF from Bacillus subtilis and related bacterial proteins. This domain folds into a three helical bundle (

). It contains a bi-helical motif named helix-extension-helix (HeH) motif which is linked to DNA-binding and other diverse functions .
mRNA capping enzyme catalytic subunit, GTase, NTPase domain (MCEL_GT_NTPase)
Type: Domain

mRNA-capping enzyme catalytic subunit from Vaccinia virus (MCEL, also known as mRNA-capping enzyme D1 subunit) catalyses the hydrolysis of the 5' triphosphate end of the pre-mRNA, the capping of the resulting diphosphate RNA end with GMP and the methylation of the GpppN cap [1-3]. It consists of an N-terminal RNA triphosphatase (TPase)-guanylyltransferase (GTase) module, and a C-terminal guanine-N7-methyltransferase (MTase) module (

) . The N-terminal module comprises a TPase domain (

), followed by the GTase at the C-terminal, which consists of the nucleotidyltransferase (NTPase, this entry) and OB fold (

) domains . The TPase and GTase modules stabilise their active conformations and their contacts also clamp the NTase and OB fold.
mRNA-capping enzyme catalytic subunit, GTase, OB fold (MCEL_GT_OB)
Type: Domain

mRNA-capping enzyme catalytic subunit from Vaccinia virus (MCEL, also known as mRNA-capping enzyme D1 subunit) catalyses the hydrolysis of the 5' triphosphate end of the pre-mRNA, the capping of the resulting diphosphate RNA end with GMP and the methylation of the GpppN cap . It consists of an N-terminal RNA triphosphatase (TPase)-guanylyltransferase (GTase) module and a C-terminal guanine-N7-methyltransferase (MTase) module (

) . The N-terminal module comprises a TPase domain (

), followed by the GTase at the C-terminal, which consists of the nucleotidyltransferase (NTPase,

) and OB fold (represented in this entry) domains . This domain contains an essential motif (RxxK) for GTase activity.
YpoC-like (YpoC)
Type: Domain

This entry represents the structural domain of the uncharacterised protein YpoC (

) from Bacillus subtilis and related proteins primarily found in Bacillota. They are predicted to adopt a globular structure consisting mainly of α-helices.
YobI-like, P-loop NTPase (YobI-NTPase)
Type: Domain

This entry represents a domain found at the N-terminal of uncharacterized membrane protein YobI (

) and related bacterial proteins. This domain is a P-loop NTPase and probably involved in antiviral immunity in bacteria. Members of this entry have a pair of transmembrane helices inserted into the P-loop NTPase domain .
Methylcrotonyl-CoA carboxylase, alpha-subunit, BT domain (MCC_alpha_BT)
Type: Domain

This entry represents a domain found in the Biotin-dependent 3-methylcrotonyl-coenzyme A carboxylase alpha1 subunit (AccA1) from Mycobacterium tuberculosis, the biotin-containing alpha subunit of 3-methylcrotonyl-CoA carboxylase (MCC) from Pseudomonas aeruginosa and in similar bacterial proteins. AccA1 is a component of a biotin-dependent acyl-CoA carboxylase complex. This subunit catalyses the ATP-dependent carboxylation of the biotin carried by the biotin carboxyl carrier (BCC) domain, resulting in the formation of carboxyl biotin . 3-Methylcrotonyl-CoA carboxylase (MCC) is essential for the metabolism of leucine, and is also involved in terpenoid metabolism . The alpha subunit contains the N-terminal biotin carboxylase (BC), the C-terminal biotin carboxyl carrier protein (BCCP) domains, and a domain that mediates BC-CT interactions (BT domain, this entry). This domain shows a central α-helix surrounded by a seven-stranded, highly-twisted anti-parallel β-sheet, with an overall structure that has great similarity with the β-barrel of the BT domain of the human MCC .
MASE9 (MASE9)
Type: Domain

This entry represents the membrane-associated sensor domain 9 (MASE9), which has been found in combination with HD-GYP (

), GGDEF (

) and EAL (

) domains, or in MASE9-HD-GYP-GAF-GGDEF domain architecture . It has 8 predicted transmembrane (TM) segments of which two are likely to form an intramembrane hairpin. It has several charged residues in the hydrophobic core of the membrane, that, in addition to the poor conservation of the short periplasmic segments, suggests that ligand binding and/or protein-protein interactions by MASE9 may occur within the membrane .
MASE8 (MASE8)
Type: Domain

This entry represents the membrane-associated sensor domain MASE8 , which is found in association with GGDEF domain (

), histidine sensor kinases and adenylate cyclase output domain (

). This domain is widespread among various classes of proteobacteria and is also found in other phyla.
Adenylate cyclase, MASE7 (MASE7)
Type: Domain

This entry represents an integral membrane sensor domain (MASE7) that is found at the N-terminal end of Adenylate cyclase from Mycobacterium tuberculosis (Cya) and similar proteins mainly found in actinomycetes and proteobacteria. This domain is often found in association with GGDEF domain (

), histidine sensor kinases and adenylate cyclase output domain (

).
YNCE-like beta-propeller (YNCE-like_beta-prop)
Type: Domain

This entry includes bacterial YncE proteins which adopts a β-propeller structure (the so-called YVTN β-propeller) . This domain is known to bind DNA. The structures of YncE in the free form and complexed with DNA revealed that the surface region of YncE corresponding to the 'canonical' substrate-binding site forms essential contacts with DNA (

) .

This domain is also found in hydrazine synthase subunit beta which is a component of the hydrazine synthase complex that catalyses the condensation of nitric oxide with ammonium to form hydrazine .
DraIII-like (DraIII-like)
Type: Family

This protein family includes DraIII from Deinococcus radiophilus, a type IIP restriction endonuclease that recognises a gapped double-stranded DNA sequence and nicks creating a double strand break with a three base 3' overhang. DraIII adopts a homodimeric configuration. Each monomer shows a ββα-metal fold in the C terminus, where the HNH active site is located. It also has two zinc and one magnesium-binding sites .
MASE6 (MASE6)
Type: Domain

This entry represents a predicted integral membrane sensory domain (MASE6) , which has been observed in association with GGDEF domain (

) and histidine sensor kinases.
MASE12 (MASE12)
Type: Domain

This is the membrane-associated sensor domain 12 (MASE12), found (predicted) in c-di-GMP phosphodiesterases and histidine kinases . This domain has conserved aromatic residues in the transmembrane segments, which suggests that its ligand could be a molecule with one or more aromatic rings .
MASE11 (MASE11)
Type: Domain

This entry represents the membrane-associated sensor domain 11 (MASE11), a predicted transmembrane domain that has been found in association with HD-GYP (

), PAS (

), GAF (

), GGDEF (

) and EAL (

) domains. It is also present in sensor histidine kinases with various domain architectures .
Yme1-like, N-terminal domain (Yme1-like_N)
Type: Domain

This domain is found at the N-terminal of a group of proteins predominantly from fungi. This entry includes the mitochondrial inner membrane i-AAA protease supercomplex subunit YME1 from Saccharomyces cerevisiae (

) and its homologue from S.pombe. YME1 subunit is required for mitochondrial inner membrane protein turnover. This domain adopts a tetratricopeptide repeat fold (

) .
DPAGT1, insertion domain (DPAGT1_ins)
Type: Domain

DPAGT1 catalyses the initial step of dolichol-linked oligosaccharide biosynthesis in N-linked protein glycosylation pathway. This is the insertion domain of animal DPAGT1, a feature absent in prokaryotic counterparts . It referred to as CL9 in ; it adopts a mixed α/β fold and it forms part of the substrate recognition site in human DPAGT1 .
Cyclic di-GMP phosphodiesterase VC_1295-like, MASE10 (MASE10)
Type: Domain

This entry represents the membrane-associated sensor domain 10 (MASE10) found at the N-terminal end of Cyclic di-GMP phosphodiesterase VC_1295 from Vibrio cholerae (CDPD1), which has been reported to catalyse the hydrolysis of cyclic diguanylate (c-di-GMP) to GMP in vitro and increase motility and decrease biofilm formation in vivo .

MASE10 has conserved Cys, Ser and Trp residues in the periplasmic loop, conserved aromatic residues and four charged (Arg, Asp, Lys, and another Asp) residues in the predicted transmembrane segments, suggesting specific interaction with its small molecule or protein ligands . It has been found in c-di-GMP phosphodiesterases, adenylate/guanylate cyclases and Ser/Thr protein phosphatases of the PP2C family, in which MASE10 is followed by the signal-transducing HAMP domain .
DUF1846, C-terminal (DUF1846_C)
Type: Domain

This is the C-terminal domain found in the uncharacterised protein family DUF1846 (also known as UPF0371). It has a cytidine deaminase-like fold (PDB:

).
DosC, CZB-like middle domain (DosC_2nd)
Type: Domain

This entry represents the middle (Mid) domain of DosC proteins, an oxygen-regulated diguanylate cyclase .
Ribosome-associated protein quality control protein P2, N-terminal domain (RqcP2_N)
Type: Domain

This entry represents a domain found at the N-terminal of the B. subtilis Ribosome-associated protein quality control protein P2 (RqcP2, also known as YlmH) and related bacterial proteins. RqcP2 is a component of the ribosome quality control system (RQC), a ribosome-associated complex that mediates the extraction of incompletely synthesized nascent chains from stalled ribosomes and their subsequent degradation . The function of this domain is unknown.
Deoxynucleotide monophosphate kinase (DNMK)
Type: Family

This entry includes deoxynucleotide monophosphate kinases from phages, which act on dGMP, dTMP and 5-hydroxymethyl-dCMP while excluding dCMP and dAMP .