SII-SWORD/CoKE huggingface dataset:
DNA topoisomerase 3-beta, zinc ribbon domain (Zn_ribbon_TOP3B)
Type: Domain

This domain is found in human DNA topoisomerase 3-beta (TOP3B) and related proteins predominantly from animals and plants. TOP3B, a recently identified member of the topoisomerase superfamily, is essential for chromosome stability, including in cancer cells . The domain represented by this entry is predicted to adopt a zinc ribbon fold. It contains a pair of invariant CxxC sequence motifs.
DNAJC9, HTH domain (HTH_DNAJC9)
Type: Domain

This domain is found in human DnaJ homolog subfamily C member 9 (DNAJC9) and related eukaryotic proteins. DNAJC9 acts as a dual histone chaperone and heat-shock co-chaperone . This protein was shown to also assemble histones onto DNA in vitro . The domain represented in this entry has a weak similarity to helix-turn-helix (HTH) domains and it is predicted to adopt similar three helical bundle.
IP5PC-F, beta-propeller domain (Beta-prop_IP5PC_F)
Type: Domain

This entry represents the β-propeller domain found in plant inositol polyphosphate 5-phosphatases (IP5P), including Type I IP5P12/IP5PC and IP5P13/IP5PD, Type II IP5P14/IP5PE and IP5P15/IP5PF from Arabidopsis thaliana. In the case of IP5P13, the β-propeller domain interacts with the sucrose non-fermenting-1-related kinase (SnRK1.1) in order to achieve a regulatory role linking inositol, sugar and stress signalling .

IP5Ps have different functions, including the degradation of phosphoinositides in the signalling pathways of various cellular processes such as Ca2+ release, abscisic acid signalling and vesicle trafficking, among others .
IP5PC-F, immunoglobulin-like domain (Ig-like_IP5PC_F)
Type: Domain

This entry represents the immunoglobulin-like domain found in plant inositol polyphosphate 5-phosphatases Type I IP5P12/IP5PC and IP5P13/IP5PD and Type II IP5P14/IP5PE and IP5PF/IP5PF from Arabidopsis thaliana. The function of this domain is unknown.

IP5Ps have different functions, including the degradation of phosphoinositides in the signalling pathways of various cellular processes such as Ca2+ release, abscisic acid signalling and vesicle trafficking, among others .
IFT80, second beta-propeller domain (Beta-prop_IFT80_2nd)
Type: Domain

This entry represents the second β-propeller domain of the Intraflagellar transport protein 80 homolog (IFT80) from human and related proteins. IFT80 is a component of the intraflagellar transport (IFT) complex B, which is essential for the development and maintenance of motile and sensory cilia. It is required for initiation of the ciliary axoneme . It has an unique architecture consisting of two β-propellers followed by an α-solenoid structure . This β-propeller is involved in dimerisation together with the α-solenoid .
DOP1-like, C-terminal (DOP1_C)
Type: Domain

This entry represents the C-terminal region of of DOP1 (A/B) from vertebrates, DOP1 from E. nidulans and S. cerevisiae, DOP1 homolog from D. melanogaster and C. elegans ortholog (pad-1) and other homologous proteins in animals and fungi. This domain consists of TPRs repeats.

DOP1 is the founding member of the Dopey family and is required for correct cell morphology and spatiotemporal organisation of multicellular structures in the filamentous fungus Emericella nidulans (Aspergillus nidulans) . In S.cerevisiae, it is required for normal cellular morphogenesis . Loss of Dop1 activity affects endosome to Golgi transport and causes a severe perturbation of the organization of the endoplasmic reticulum; Mon2 a relative of large Arf exchange factors, recruits Dop1 to the Golgi apparatus . Dop1 homologues are found in mammals, where they may play a role in regulating membrane trafficking of cargo proteins. Together with ATP9A and MON2, it regulates SNX3 retromer-mediated endosomal sorting of WLS away from lysosomal degradation . These are long proteins consisting of tetratricopeptide (TPRs) repeats.
DOP1-like, middle TPR domain (TPR_DOP1_M)
Type: Domain

This entry represents a domain found at the middle region of DOP1 (A/B) from vertebrates, DOP1 from S.cerevisiae and E. nidulans, DOP1 homolog from D. melanogaster and other homologous proteins from animals and fungi. This domain consists of TPRs repeats.

DOP1 is the founding member of the Dopey family and is required for correct cell morphology and spatiotemporal organisation of multicellular structures in the filamentous fungus Emericella nidulans (Aspergillus nidulans) . In S.cerevisiae, it is required for normal cellular morphogenesis . Loss of Dop1 activity affects endosome to Golgi transport and causes a severe perturbation of the organization of the endoplasmic reticulum; Mon2 a relative of large Arf exchange factors, recruits Dop1 to the Golgi apparatus . Dop1 homologues are found in mammals, where they may play a role in regulating membrane trafficking of cargo proteins. Together with ATP9A and MON2, it regulates SNX3 retromer-mediated endosomal sorting of WLS away from lysosomal degradation . These are long proteins consisting of tetratricopeptide (TPRs) repeats.
DOP1-like, TPR domain (TPR_DOP1)
Type: Domain

This entry represents a domain found near the C-terminal end of DOP1 (A/B) from vertebrates, DOP1 homolog from Drosophila melanogaster and Caenorhabditis elegans ortholog (pad-1).

DOP1 homologues are found in mammals, where they may play a role in regulating membrane trafficking of cargo proteins. Together with ATP9A and MON2, it regulates SNX3 retromer-mediated endosomal sorting of WLS away from lysosomal degradation . These are long proteins consisting of tetratricopeptide (TPRs) repeats.
DUF1512, N-terminal domain (DUF1512_N)
Type: Domain

This domain is found at the N-terminal end of several archaeal sequences of around 370 residues in length. The function of this group of proteins is unknown.
DUF1512, C-terminal domain (DUF1512_C)
Type: Domain

This entry includes archaeal proteins of around 370 residues in length. This entry corresponds to the C-terminal domain. The function of this group of proteins is unknown. This domain shows structural similarity to peptidyl tRNA hydrolase enzymes.
Glycerol-3-phosphate acyltransferase RAM2/GPAT1-8, HAD-like domain (HAD_RAM2/GPAT1-8)
Type: Domain

This domain is found at the N-terminal of Glycerol-3 -phosphate acyltransferase RAM2 from Medicago truncatula, GPAT1-8 from Arabidopsis and related plant proteins which esterify the acyl-group from acyl-ACP to the sn-2 position of glycerol-3-phosphate, a step in cutin biosynthesis . RAM2 is involved in the production of cutin monomers, which act as plant signals that promote colonisation by arbuscular mycorrhizal fungi . GPAT1 is involved in pollen development, by being required for tapetum differentiation and male fertility. In addition to the sporophytic effect, it also exerts a gametophytic effect on pollen performance . This domain is predicted to adopt an α-β structure similarly to this found in other haloacid dehalogenase (HAD) proteins.
DUF7373, C-terminal (DUF7373_C)
Type: Domain

This domain is found C-terminal in uncharacterised proteins from actinomycetes. It is predicted to adopt a seven-stranded antiparallel β-sheet with similarity to Mog1p/PsbP-like domains. Some proteins containing this domain have a lipoprotein attachment motif at the N terminus suggesting they may be associated with the membrane. This domain is usually found in two copies that share little sequence similarity to each other.
DotM, C-terminal cytoplasmic domain (DotM_C)
Type: Domain

This entry represents the C-terminal cytoplasmic domain of DotM from Legionella pneumophila and related proteins found mainly in gammaproteobacteria. DotM is a component of Type 4B secretion (T4BS) system that translocates over 300 effectors into the host cell during infection. The DotM cytoplasmic domain adopts an α-helical structure consisting of 13 α-helices . In the membrane-embedded T4 coupling complex (T4CC), DotM makes extensive contacts with DotL and also interacts with the DotN and DotZ proteins. The DotLMNYZ components form a hetero-pentameric core of the T4CC complex from which the flexible IcmSW module protrudes . These hetero-pentameric complexes assemble and form an inner membrane channel for effectors to pass through.
DotY (DotY)
Type: Family

This entry represent the type 4 apparatus protein DotY from Legionella pneumophila and related proteins from gammaproteobacteria. DotY is a component of Type 4B secretion (T4BS) system that translocates over 300 effectors into the host cell during infection. This protein is part of a subcomplex which recruits effector proteins and delivers them to the core transmembrane subcomplex . In the membrane-embedded T4 coupling complex (T4CC), DotY makes extensive contacts with DotZ. The DotLMNYZ components form a hetero-pentameric core of the T4CC complex from which the flexible IcmSW module protrudes . These hetero-pentameric complexes assemble and form an inner membrane channel for effectors to pass through. DotY and DotZ play a role in effector translocation and optimise secretion by modulating the delivery trajectory of the IcmSW module .
Guanine nucleotide exchange factor DBS-like, spectrin-like (Spectrin_DBS)
Type: Domain

This spectrin-like domain is found in human Guanine nucleotide exchange factor DBS (MCF2L) and similar sequences mainly found in animals. MCF2L catalyses guanine nucleotide exchange on RHOA and CDC42, and thereby contributes to the regulation of RHOA and CDC42 signalling pathways .
GTF3C1, extended winged-helix domain (eWH_GTF3C1)
Type: Domain

This is the extended winged-helix domain (eWH) of human General transcription factor 3C polypeptide 1 (GTF3C1), a component of TFIIIC that initiates transcription complex assembly on tRNA and is required for transcription of 5S rRNA and other stable nuclear and cytoplasmic RNAs.
Guanine-nucleotide exchange factor YEL1, PH domain (PH_GEF_YEL1)
Type: Domain

This entry represents a PH domain found in the YEL1 family proteins. The YEL1 family comprises guanine-nucleotide exchange factors (GEFs) for ARF3, a small GTPase involved in vesicle transport and actin cytoskeleton organisation. Members of the YEL1 family are essential for the correct localisation of ARF3 to specific cellular sites, such as the bud neck and tip in yeast. They play a crucial role in the polarisation of actin patches, which are important for processes like endocytosis and cell shape determination . The conserved function across different species suggests a fundamental role in cellular dynamics related to membrane trafficking and cytoskeletal arrangements.
Half a barrel domain (HAB_dom)
Type: Domain

This entry represents a region found in proteins possibly related to plasmid partitioning. This domain is composed of two copies of this region each of which forms three strands of a 6-stranded β-barrel. This entry is named the HAB region for Half A Barrel. The β-barrel is capped at one end by two short β-strands, one from each region and at the other end of the barrel by a pair of longer α-helices, again one contributed by each subunit.
L-lysine 4-chlorinase BesD/L-lysine 5-chlorinase HalB-like (BesD/HalB-like)
Type: Family

This entry represents L-lysine 4-chlorinase BesD, L-lysine 5-chlorinase HalB, ornithine halogenase HalD and related proteins . BesD is involved in the biosynthesis of terminal alkyne-containing amino acids such as L-propargylglycine (Pra) and L-beta-ethynylserine, that are produced as antibiotics by S.cattleya . It catalyses the chlorination of L-lysine at the C4 position, leading to the production of 4-chloro-L-lysine. In addition to ornithine, HalD chlorinates lysine but with slower rate. This preference of HalD for ornithine is due to a narrower active site pocket. These enzymes are structurally very similar and adopt a typical cupin-like fold.
HD-CE (HD-CE)
Type: Domain

This entry represents an HD-like domain predicted to act as effector in multiples antiviral immunity system by targeting nucleotides .
Head completion protein (HCP)
Type: Family

This entry represents the Head completion protein (HCP) found in T5-like bacteriophages . HCP forms dodecameric ring assembly and is a component of the bacteriophage neck. It holds the portal protein PrtP dodecameric ring and connects with the trimeric layer of the tail tube via contacts with the tail completion (TCP) hexameric ring . HCP makes contacts with DNA. HCP consists of two domains. The first domain folds into an α-helical bundle composed of N- and C-terminal helices whereas the second domain adopts a β-sandwich .
Utp10/HEAT1, HEAT-repeats domain (HEAT_Utp10/HEAT1)
Type: Domain

This entry represents a HEAT-repeats domain found in HEATR1, Utp10 and similar eukaryotic proteins.

Proteins in this entry contain an armadillo-type fold, and a BP28, C-terminal domain. It includes HEAT repeat -containing protein 1 (HEATR1) from human and its orthologues from fungi, U3 small nucleolar RNA-associated protein 10 (Utp10), which is a HEAT-repeat containing protein involved in nucleolar processing of pre-18S ribosomal RNA . Utp10 is also involved in 40S ribosome maturation . HEATR1 is a ribosome biogenesis factor required for recruitment of Myc to nucleoli . It is involved in nucleolar processing of pre-18S ribosomal RNA and it is required for optimal pre-ribosomal RNA transcription by RNA polymerase I . HEATR1 plays a role in neuronal-lineage cell proliferation .
Helicase SEN1, beta-barrel domain (SEN1_barrel)
Type: Domain

This domain is found in the yeast Helicase SEN1 and related proteins from fungi and some uncharacterised plant sequences. SEN1 is an ATP-dependent 5'->3' DNA/RNA helicase required for the expression and maturation of diverse classes of non-protein-coding RNAs like precursor tRNAs, rRNAs and small nuclear (snRNA) and nucleolar (snoRNA) RNAs. The Nrd1-Nab3-Sen1 (NNS) complex mediates termination of RNA Polymerase II transcription on snoRNAs as well as on several short protein-coding genes . This domain folds into a β-barrel that has a structural similarity to alanine racemase C-terminal domain.
Hemicentin/VWA7, galactose-binding domain-like (GBD_Hemicentin/VWA7)
Type: Domain

This entry represents a galactose-binding domain-like found in Hemicentin and Willebrand factor A domain-containing protein 7 (VWA7).

HMCN1 is involved in transforming growth factor beta-mediated rearrangement of the podocyte cytoskeleton which includes reduction of F-actin fibres and broadening, flattening and elongation of podocytes . HMCN1 is also implicated in the organisation of the basement membrane and may contribute to cleavage furrow maturation during cytokinesis in embryos .

VWA7 is found in the major histocompatibility complex class III region and it is likely implicated in lung cancers
Capsid protein Vp24 (Vp24_capsid)
Type: Domain

This entry represents the capsid Vp24 protein from apple-latent spherical virus (ALSV) and related picorna-like plant viruses. This protein is encoded in a polyprotein that is cleaved into three proteins, Vp25, Vp20 and Vp24 which all have jellyroll fold and form one protomer; 60 copies of this unit compose one virion. Vp25, Vp20 and Vp24 contribute to capsid stabilisation . Vp24 form a pentameric protrusion around a fivefold axis, and the protrusion sits on a base of Vp25 and Vp20. Vp24 is more loosely held and is supported by Vp25 and Vp20 .
Capsid protein Vp25 (Vp25_capsid)
Type: Domain

This entry represents the capsid Vp24 protein from apple-latent spherical virus (ALSV) and related picorna-like plant viruses. This protein is encoded in a polyprotein that is cleaved into three capsid proteins, Vp25, Vp20 and Vp24, which all have jellyroll folds and form one protomer; 60 copies of this unit compose one virion. Vp25, Vp20 and Vp24 contribute to capsid stabilisation . Vp25 has two extra β-sheets (β1 and β2) comparing to Vp20 and Vp24. Vp25 and Vp20 form more extensive interactions with their neighbours and likely form a rigid capsid frame that supports the looser Vp24 protrusions .
Card1, hinge domain (HTH_Card1)
Type: Domain

This is the hinge domain found in a set of bacterial proteins, including Card1 (cyclic-oligoadenylate-activated single-stranded ribonuclease and single-stranded deoxyribonuclease 1) from Treponema succinifaciens (

), a protein that is part of type III CRISPR-Cas immune response system. This protein consists of a CARF (CRISPR-associated Rossmann fold) domain at the N-terminal end, an helical hinge domain and a C-terminal endonuclease domain (

) .
CARF-associated, helix-turn-helix domain (CARF-assoc_HTH)
Type: Domain

This entry represents a presumed helix-turn-helix (HTH) domain found at the C terminus of a group of CARF-containing archaeal proteins. This domain is found associated with

.
Hfq-like (Phage_Hfq)
Type: Domain

This entry includes phage proteins that contain a central Hfq-like domain. This suggests that this protein may have an RNA binding function. AlphaFold prediction suggests a confident homohexameric structure. This entry represents a hypothetical protein found in several mycobacteriophages, including Bxz1, Mangeria, Derek, DrPhinkDaddy, Phusco and Jedediah.
Krimper, first tudor domain (Tudor_krimper_1st)
Type: Domain

This entry represents the first Tudor domain found in Protein krimper (also known as Tudor domain-containing protein krimp) from Drosophila melanogaster and similar fly proteins. Krimper is required for ping-pong piRNA amplification and is capable of both self-interactions and binding of the two PIWI proteins: Aub and Ago3 . The ping-pong cycle is a process where the degradation of complementary target mRNA by PIWI proteins can trigger the generation of new RNA guides for the repression of transposable elements proliferation . This domain is found in a region of the protein involved in the interaction and binding to Ago3, but not Aub .
Histidine N-acetyltransferase, C-terminal (Hisat_C)
Type: Domain

This entry represents the C-terminal domain of Histidine N-acetyltransferase HISAT from ectothermic vertebrates and the orthologue from human, NAT16. HISAT is responsible for the N-acetyl-histidine (NAH) synthesis, which is a major constituent of brain and lens of ectothermic vertebrates . NAT16, unlike fish HISAT, has only trace enzyme activity for NAH synthesis.
Histone acetyltransferase p300/CREBBP, PHD domain (PHD_P300)
Type: Domain

This domain is found in human Histone acetyltransferase p300 (EP300), Histone lysine acetyltransferase CREBBP and similar animal proteins. EP300 functions as a histone acetyltransferase and regulates transcription via chromatin remodelling . Histone lysine acetyltransferase CREBBP acetylates histones, giving a specific tag for transcriptional activation . It mediates acetylation of histone H3 at 'Lys-18' and 'Lys-27' (H3K18ac and H3K27ac, respectively) . CREBBP also acetylates non-histone proteins, like DDX21, FBL, IRF2, MAFG, NCOA3, POLR1E/PAF53 and FOXO1 .

This entry represents the PHD domain, which forms a module with the bromodomain (

) and the RING domain (

) that associates intimately with the HAT domain (

) through numerous conserved contacts .
KRIT1, ARM-repeats domain (ARM_KRIT1)
Type: Domain

KRIT1, also known as CCM1, a Rap1-binding protein, is expressed in endothelial cells where it is present in cell-cell junctions and associated with junctional proteins . Together with CCM2/MGC4607 and CCM3/PDCD10, KRIT1 constitutes a set of proteins whose mutations are found in cerebral cavernous malformations, characterised by cerebral hemorrhages and vascular malformations in the central nervous system. KRIT-1 localization is mediated by its FERM domain . This entry represents an ARM-repeats domain found in the central region of KRIT1.
HVO_2525, N-terminal (HVO_2525_N)
Type: Domain

This domain is found at the N-terminal of the predicted transcription regulator HVO_2525 (

) from Haloferax volcanii and similar archaeal proteins. This domain is predicted to adopt an α-β structure. It is often found associated with

.
DpnD, N-terminal domain (DpnD_N)
Type: Domain

This entry represents a presumed domain found at the N-terminal of DpnD protein from Streptococcus pneumoniae and similar sequences from bacteria. These proteins are functionally uncharacterised. This domain is predicted to be all helical.
HMPTM, N-terminal zinc ribbon domain (Zn_ribbon_HMPTM)
Type: Domain

This domain is found in 7,8-dihydro-6-hydroxymethylpterin dimethyltransferase (HMPTM) and related proteins from bacteria and archaea. HMPTM is involved in catalysing the methylation at C-7 and C-9 of 7,8-dihydro-6-hydroxymethylpterin, a common intermediate in both folate and MPT biosynthesis . The domain represented by this entry is predicted to adopt a zinc β-ribbon fold. It contains three invariant cysteines and one histidine arranged in two CxxC and CxxH sequence motifs.
Fervidolysin/DR_A0283-like, Ig-like domain (Ig_Fls_DR_A0283-like)
Type: Domain

This domain with an immunoglobulin (Ig)-like fold is found in Fervidolysin (Fls) from Fervidobacterium pennivorans, in the probable subtilase-type serine protease DR_A0283 from Deinococcus radiodurans and similar sequences from terrabacteria and thermotogota. Fls is a protease able to degrade keratin into peptides. It is responsible for keratinolysis by F.pennivorans, which allows this bacterium to grow on native feathers .
Rcc01698-like, C-terminal domain (Rcc01698_C)
Type: Domain

This domain is found in proteins mainly from alphaproteobacteria, such as Rcc01698 (

) from Rhodobacter capsulatus and in some phage species . Alphaproteobacteria produce phage-like particles called gene transfer agents (GTAs) that mediate lateral gene exchange. Rcc01698 (

) has been designated as megatron/g15 in , and described as a multidomain protein that forms the core of the RcGTA baseplate, together with the hub (Rcc01696, g13) proteins, which is decorated with tail fibres. This entry represents the fibre-binding domain .
DUF6688, C-terminal domain (DUF6688_C)
Type: Domain

This entry represents a group of bacterial proteins that is functionally uncharacterised. Proteins in this family are typically between 360 and 412 amino acids in length. This entry corresponds to the C-terminal domain, which is predicted to be α-helical.
Hsr-9, Tudor domain (SH3_Hsr9)
Type: Domain

This entry represents the tandem Tudor domains of Hsr-9 (also known as TP53-binding protein 1) from C. elegans and similar proteins mainly from nematodes. Hsr-9 may have a role in DNA double-strand break repair following gamma-irradiation .
HVO_0513-like, N-terminal (HVO_0513_N)
Type: Domain

This domain is found at the N-terminal of the predicted transcription regulator HVO_0513 (

) from Haloferax volcanii and similar archaeal proteins. This domain is predicted to adopt an α-β structure. It is often found associated with

.
DUF7108, C-terminal domain (DUF7108_C)
Type: Domain

This domain is found at the C-terminal end of the uncharacterised protein HVO_0731 from Haloferax volcanii (

) and similar proteins from halobacteria. It is predicted to adopt an all-α structure. The function of this domain is unknown.
Dynamin-like GTPase MGM1-like, lipid interacting stalk (LIS_MGM1)
Type: Domain

This is the lipid-interacting stalk (LIS) domain of Dynamin-like GTPase MGM1, mitochondrial from Saccharomyces cerevisiae and similar fungal sequences. MGM1 is essential for normal mitochondrial morphology by mediating fusion of the mitochondrial inner membranes. This domain has been shown to be implicated in lipid binding with several key lysine residues .
Dynein axonemal assembly factor 11-like, CS domain (CS_DNAAF11_C)
Type: Domain

This domain is found at the C-terminal end of human Dynein axonemal assembly factor 11 (DNAAF11), TilB from Drosophila melanogaster and similar tilB family proteins mainly found in animals. DNAAF11 is involved in dynein arm assembly. It is important for expression and transporting outer dynein arm (ODA) proteins from the cytoplasm to the cilia . TilB is required for cilia structures in Johnston's sensory organ. It plays a role in motility of cilia and flagella . This domain is predicted to fold into a β-sandwich domain and shows structural similarity to the CS domain (

).