SII-SWORD/CoKE huggingface dataset:
Fatty acid synthase-like, central AT domain (FAS-like_AT_central)
Type: Domain

This entry includes a domain found in the central region of the acyltransferase domain (AT) from fungal type I fatty acid synthase (FAS) mainly from myco and bifidobacteria, which have secondary-structure elements and sequence homology . Mycobacterial fatty acid synthase (FAS) complex is an homohexameric multifunctional enzyme that catalyses the synthesis of fatty acid precursors of mycolic acids, the major components of the cell wall in Mycobacteria and play an important role in pathogenicity .
Abnormal cell migration protein 18-like, fibronectin type I domain (Mig18_Fn1)
Type: Domain

This entry represents a domain that structurally resembles the fibronectin type 1 repeat. This domain is found in Abnormal cell migration protein 18 (Mig-18) from Caenorhabditis elegans and other uncharacterised nematode proteins. Mig-18 is required for the directional control of distal tip cell migration during gonadogenesis, probably by recruiting fibulin fbl-1 to the gonad basement membrane .
Chitin synthase chs-1/2, N-terminal putative transporter domain (Chs-1/2_IV_N)
Type: Domain

This entry represents an N-terminal integral membrane domain found in chitin synthases chs-1/2 from C.elegans and similar sequences mainly from arthropods, nematodes and molluscs.

The Chitin Synthase Class IV family is involved in the synthesis of chitin, which is a key structural component in various biological structures. Members of this entry are essential for specific developmental processes in organisms. For instance, Chs-11 is crucial for the embryonic synthesis of chitin that forms part of the eggshell, indicating a role in protecting and structuring the embryo . On the other hand, Chs-2 appears to be involved in the synthesis of chitin within the pharynx during larval development, suggesting a function in the morphogenesis and maintenance of larval structures . The activities of the Chitin Synthase Class IV family members are indicative of their importance in the developmental stages of organisms that produce chitin as a component of their extracellular matrix or exoskeleton.
Winged helix-turn-helix domain, arthropods/nematodes (HTH_69)
Type: Domain

This entry represents a winged helix-turn-helix domain that may bind to DNA, mainly found in uncharacterised sequences from arthropods and nematodes.
Mediator complex subunit MED14, N-terminal (Med14_N)
Type: Domain

This entry represents the N-terminal domain found human Mediator of RNA polymerase II transcription subunit 14 (Med14) and its homologues.

Med14 is a component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors . Med14 along with Med17 are scaffold subunits in nucleating Mediator . The major portion of Med14 exists in the Head-Shoulder module of the Mediator and consists of nine tandem repeats (RM1 to RM9), which are arranged in an atypical right-handed helix .

Saccharomyces cerevisiae (Baker's yeast) RGR1 mediator complex subunit affects chromatin structure, transcriptional regulation of diverse genes, and sporulation. It is required for glucose repression, HO repression, RME1 repression and sporulation . This subunit is also found in higher eukaryotes and MED14 is the agreed unified nomenclature for this subunit .
Polyketide synthase extender module SpnB-like, Rossmann fold domain (SpnB-like_Rossmann)
Type: Domain

This entry represents a domain found in a group of proteins mainly from actinomycetes, including the polyketide synthase extender module SpnB from Saccharopolyspora spinosa (

) and Phenolphthiocerol synthesis polyketide synthase type I Pks15/1 from Mycobacterium bovis . This domain adopts a classical Rossmann fold .
ATP-dependent RNA helicase DDX60, PIN-like domain (PIN-like_DDX60)
Type: Domain

This domain is found N-terminal in human ATP-dependent RNA helicase DDX60 (also known as DEAD-box RNA helicase) and similar sequences from animals and fungi. This helicase binds ssRNA, dsRNA and dsDNA and can promote the binding of RIGI to dsRNA. DDX60 is non-essential in mammals but it is required for the cell fitness in kinetoplastids and trypanosomatids and plays a specific role in translation initiation in these parasites . In Trypanosoma cruzi, k-DDX60 binds both to the head and the body of the 40S ribosome subunit. It is also involved in the stabilization of the 43S PIC and the remodelling of the 43S PIC mRNA channel . This domain adopts a globular structure with a significant structural similarity to PIN domains.
Wiz, C-terminal zinc finger (Wiz_C_Znf)
Type: Domain

This entry represents a C2H2 type zinc finger found at the C-terminal end of human Protein Wiz and similar sequences from vertebrates. Wiz interacts with the a SET-domain histone methyltransferases G9a and GLP independently and plays a major role in G9a/GLP heterodimer formation and stabilisation . This domain is also found in Zinc finger protein 644 (ZNF644). Similarly to Wiz, ZNF644 is a core subunit of the G9a/GLP complex . Both proteins contain multiple zinc finger motifs that recognise consensus DNA sequences, target G9a and GLP to the chromatin and mediate the G9a/GLP complex-dependent H3K9 methylation as well as gene repression .
Enhanced disease resistance 4-like, N-terminal domain (EDR4-like_N)
Type: Domain

This domain is found at the N-terminal end of Protein Enhanced disease resistance 4 from Arabidopsis thaliana (EDR4), which plays a negative role in salicylic acid (SA)-mediated resistance to powdery mildew , and similar plant proteins. This domain is predicted to adopt an all-β structure.
YEATS domain-containing protein 2, three-helical bundle domain (YEATS2_3HBD)
Type: Domain

This domain is found in human YEATS domain-containing protein 2 (YEATS2) and related proteins from animals and fungi. YEATS2 is a chromatin reader component of the ATAC complex, a complex with histone acetyltransferase activity on histones H3 and H4 . It specifically recognises and binds histone H3 crotonylated at 'Lys-27' (H3K27cr) . The domain represented by this entry is predicted to adopt a globular structure consisting of a bundle of three α-helices. This domain contains two semi-conserved sequence motifs: YX(5)GKRR and WCRXHGYTP. The function of this domain is unknown.
Carbamoyltransferase, Kae1-like domain, second subdomain (HypF_C_2)
Type: Domain

This domain is found at the C-terminal of Carbamoyltransferase from Caldanaerobacter subterraneus (HypF,

) and similar prokaryotic sequences. HypF is involved in the biosynthesis of the nitrile group as a precursor of the cyano groups of hydrogenases. HypF consists of four domains: the acylphosphatase domain (

), the Zn finger-like domain (

), the YrdC-like domain (

) and the Kae1 (kinase-associated endopeptidase 1)-like domain, which is composed of two α-β subdomains (

and this entry) .
YEATS domain (YEATS_dom)
Type: Domain

This domain is found in the YEATS family, named after `YNK7', `ENL', `AF-9', and `TFIIF small subunit'. It folds into a β-sandwich with a C2-like topology . YEATS domain is an acetyllysine-binding domain that binds strongly to histone H3K9 acetylation and, to a lesser extent, H3K27 and H3K18 acetylation. This domain utilises a serine-lined aromatic 'sandwiching' cage for acetyllysine readout .

This family is named after YEATS (Yaf9, ENL, AF9, Taf14, and Sas5), an evolutionarily conserved module present in 4 proteins (ENL, AF9, GAS41, and YEATS2) in humans and 3 proteins (Sas5, Taf14, and Yaf9) in yeast. These proteins are found in major chromatin-remodeling and histone acetyl-transferase (HAT) complexes and implicated in regulation of chromatin structure, histone acetylation and deposition, gene transcription and DNA damage response. The YEATS domain, which as previously shown is found in a number of chromatin-associated proteins, has recently been shown to have the capacity to bind histone lysine acetylation . The ability of the YEATS domains of human AF9 and yeast Taf14 to recognise the histone mark H3K9ac, have shown that these proteins are members of the family of acetyllysine readers .
Presequence protease, mitochondrial-type, C-terminal domain (PreP_C)
Type: Domain

Human presequence protease, mitochondrial (PreP) is a protease that degrades targeting peptides as well as other unstructured peptides in mitochondria . This entry represents the C-terminal domain of PreP and similar proteins from eukaryotes and bacteria.
Cj1289-like, C-terminal domain (Cj1289-like_C)
Type: Domain

This domain is found at the C-terminal of the possible periplasmic protein

from Campylobacter jejuni (Cj1289) and similar sequences mainly found in epsilonproteobacteria. This domain is normally associated to

. It shows an α-β configuration. Its specific function is unknown.
Ribonuclease J, beta-CASP domain (RNase_J_b_CASP)
Type: Domain

This domain is found in Ribonuclease J from Thermus thermophilus (RNaseJ) and similar prokaryotic proteins . RNaseJ is an RNase that has endonuclease and possibly 5'-3' exonuclease activity. It is probably involved in maturation of rRNA and in some organisms also mRNA maturation and/or decay. This protein shows three globular domains: the beta-lactamase core (formed by two separate regions,

and

), the beta-CASP (this entry) and the C-terminal domain (

). This domain consists of a central five-stranded parallel β-sheet that is surrounded by five α-helices .
Arabinosidase BT_3657-like, N-terminal (BT_3657-like_N)
Type: Domain

This domain is found at the N terminus of BT_3657 from Bacteroides thetaiotaomicron (

) and similar bacterial sequences. BT_3657 has been reported to be an arabinosidase .
RECK, EGF-like 2 domain (EGF2_RECK_dom)
Type: Domain

This domain is found in human Reversion-inducing cysteine-rich protein with Kazal motifs (RECK) and similar proteins mainly from vertebrates. RECK is a membrane-anchored glycoprotein that plays a role in Wnt7-specific responses in the central nervous system angiogenesis and in the blood-brain barrier regulation . This domain is usually found in association with several copies of

.

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

],

,

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

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

, and EGF-like 2, represented by this entry), and three Kazal-like motifs (Kazal-like 1 to 3, [

]) .
Protein arginine N-methyltransferase domain (PRMT_dom)
Type: Domain

This entry represents a domain found C-terminal in Protein arginine N-methyltransferase 1 and twice in Protein arginine N-methyltransferase 7. This domain is also found in histone-arginine methyltransferases CARM1 and CARMER. CARM1 methylates (mono- and asymmetric dimethylation) the guanidino nitrogens of arginyl residues in several proteins involved in DNA packaging, transcription regulation, pre-mRNA splicing, and mRNA stability . This domain shows a β-barrel structure and is involved in oligomerization.

Protein arginine methyltransferases (PRMTs) are enzymes that transfer methyl groups to the arginine residues of histones and other proteins. Arginine methylation is an important posttranslational modification process that plays functional roles in transcriptional control, splicing, DNA repair, and signaling .
LFE_1968-like (LFE_1968-like)
Type: Family

This protein family includes a group of uncharacterised prokaryotic proteins that adopt an α/β structures with similarity to haem iron utilisation proteins, such as LFE_1968 from Leptospirillum ferrooxidans (

).
AlkA-like, TATA-box binding protein-like domain (AlkA-like_TBP-like)
Type: Domain

This entry represents a TATA-box binding protein (TBP)-like domain present at the N-terminal end of AlkA from Archaeoglobus fulgidus (

). AlkA is a glycosylase involved in base excision repair, capable of repairing mutagenic lesions such as N1-methyladenine (m1A) and N3-methylcytosine (m3C) found in DNA .
Neopullulanase-like, C-terminal domain (Neopullulanase-like_C)
Type: Domain

This entry represents the C-terminal all-β domain found in (Neo)pullulanase (

) from Thermus thermophilus (

) and similar bacterial sequences.
Interleukin-18-binding protein-like domain (IL18BP-like_dom)
Type: Domain

This entry represents a domain found in human Interleukin-18-binding protein (IL18BP, ) and similar sequences from vertebrates and virus. IL18BP is unique among the diverse family of mammalian and poxvirus IL18BPs in that it uses a bivalent binding mode and a unique set of interacting residues for binding IL18 . It binds to the same surface of IL18 used by other IL18BPs, suggesting that all IL18BPs use a conserved inhibitory mechanism by blocking a putative receptor-binding site on IL18. This domain adopts a typical Ig-like fold.
Thiolase, C-terminal domain 2 (Thiolase_C_2)
Type: Domain

This domain is found C-terminal in a group of thiolases from all cellular organisms that are not included in

. Thiolases are essential CoA-dependent enzymes in lipid metabolism. This domain folds into a four-stranded antiparallel β-sheet with α-helices packed on one side

.
Transcriptional adapter 2-alpha/beta-like domain (TADA2A_B-like_dom)
Type: Domain

This domain is found in human Transcriptional adapter 2-alpha (TADA2A), Transcriptional adapter 2-beta (TADA2B) and similar eukaryotic proteins. TADA2A is a component of the ATAC complex that plays a role in chromatin remodelling . TADA2B differs both biochemically and functionally from TADA2A. TADA2B interacts selectively, but not stably, with the Gcn5-containing histone acetylation complex TFTC/STAGA. In addition, TADA2B interacts with Baf57 (a component of the human Swi/Snf complex) and can coordinate the targeting of both histone acetylation and chromatin remodelling activities . This domain is predicted to adopt an α/β structure.
Protein zer-1 homolog-like, C-terminal domain (ZER1-like_C)
Type: Domain

This entry represents the C-terminal domain of human Protein zer-1 homolog (ZER1) and similar animal proteins including Protein SERAC1 from Danio rerio. ZER1 serves as substrate adapter subunit in the E3 ubiquitin ligase complex ZYG11B-CUL2-Elongin BC. This protein functions to target substrates bearing N-terminal degrons for proteasomal degradation with the first four residues of substrates being the key recognition elements. SERAC1 plays an important role in the phosphatidylglycerol remodelling that is essential for both mitochondrial function and intracellular cholesterol trafficking . This domain consists of armadillo repeats .
Membrane-bound transcription factor site-1 protease-like, N-terminal domain (MBTP1_N)
Type: Domain

This entry represents a domain found N-terminal in a family of membrane bound serine proteases from animals and plants, including the human member Membrane-bound transcription factor site-1 protease (MBTP1) . Members of this family are involved in regulated intramembrane proteolysis (RIP) of various substrates, playing a crucial role in cellular signalling and regulation. These proteases cleave after hydrophobic or small residues, with a preference for Arg or Lys at the P4 position. They are responsible for the proteolytic activation of sterol regulatory element-binding proteins (SREBPs), cyclic AMP-dependent transcription factors (ATF6 and ATF6B), and other factors like BDNF, GNPTAB, and FAM20C. This activation process is essential for lipid homeostasis, lysosome biogenesis, osteoblast differentiation, and ER stress response. Additionally, they regulate M6P-dependent trafficking of lysosomal enzymes and are involved in collagen trafficking through the activation of CREB3L2/BBF2H7 .
tRNA-intron endonuclease SEN2-like, N-terminal domain (SEN2-like_N)
Type: Domain

This entry represents the N-terminal domain of tRNA-intron endonuclease from Aeropyrum pernix (

, ) and similar archaeal sequences.
PSV hypothetical protein ORF131-like domain (PSV_ORF131-like_dom)
Type: Domain

This domain is found in the uncharacterised protein

from Pyrobaculum spherical virus (PSV), also known as ORF131, and similar sequences from virus and archaeal prophagues. It adopts a two-layered α-β configuration .
Phage DNA Adenine Methylase-like domain 2 (DAM-like-phage2)
Type: Domain

This domain, which is found in a group of proteins from bacteroidetes, has been characterised as part of a nucleic acid modifying system in certain phages. This system may modify tRNAs that are encoded adjacent to the system on the genome. These tRNAs are then possibly packaged into the viral head, to render them resistant to host restriction .
Phage G20C small terminase, C-terminal domain (TerS_C)
Type: Domain

This domain is found at the C-terminal of terminase small subunit (TerS) from Thermus phage G20c, which oligomerises into a nonamer that binds DNA, stimulates terminase large subunit ATPase activity, and inhibits TerL nuclease activity. TerS is organised into an N-terminal helix-turn-helix (HTH) motif (

) followed by an oligomerisation domain consisting of two antiparallel helices (this entry) that pack against the oligomerisation domain helices of the neighbouring subunit, forming a helical barrel .
ZW10, C-terminal helical domain (ZW10_C_2)
Type: Domain

This entry represents the last of the α-helical repeat domains of Zw10 protein. Zw10 protein, in the context of the conserved Rod-Zwilch-Zw10 (RZZ) complex, is required for correct metaphase check-pointing during mitosis and it is also important in vesicle transport between Golgi and ER as part of a second complex together with the conserved conserved RINT1/Tip20p and NAG/Sec39p proteins . Zw10 is the metazoan homologue of yeast Dsl1, both included in the complexes associated with tethering containing helical rods (CATCHR) family, sharing structural features .
Alpha-1,3-glucanase, catalytic domain, D2 (Agl_cat_D2)
Type: Domain

This entry represents a domain found at the C-terminal end of a group of Alpha-1,3-glucanases, including the members from from Paenibacillus glycanilyticus and Niallia circulans (Bacillus circulans) . This domain, found C-terminal in the catalytic domain, folds into a right-handed β-helix fold .
Iron hydrogenase 1-like, iron-sulfur centre-binding domain (Fe_hydrogense_Fe-S_bd)
Type: Domain

This entry represents a Fe-S centre binding domain found in iron hydrogenases mainly from Clostridium species .
Glycoside Hydrolase Family 113 (GH113)
Type: Family

This family includes Endo-beta-1,4-mannanase from Alicyclobacillus acidocaldarius and similar bacterial sequences that belong to the Glycoside Hydrolase Family 113 (GH113) . It shows a (β/α)8-barrel fold .
Transketolase-like, C-terminal domain (Transketolase-like_C_2)
Type: Domain

This entry represents a C-terminal domain found in transketolase and transketolase-like enzymes , such as pyruvate dehydrogenase E1 component from Escherichia coli (OPD1) .
L-gulonolactone oxidase 2-like, C-terminal domain (GULLO2-like_C)
Type: Domain

This domain is found at the C-terminal end of L-gulonolactone oxidase from Arabidopsis thaliana (GULLO2) and similar plant proteins. This enzyme catalyses the oxidation of L-gulono-1,4-lactone to ascorbic acid . This short domain is predicted to contain a β-hairpin and have structural similarity with omega toxins.
Tetracyclin repressor SMU_134-like, C-terminal domain (SMU_134-like_C)
Type: Domain

This domain is found at the C-terminal of Transcriptional regulator SMU_134 (

) from Streptococcus mutans and similar sequences from firmicutes. It is normally found associated with

. This domain shows an all-α configuration.
Formimidoylglutamate deiminase, N-terminal domain (HutF-like_N)
Type: Domain

This entry represents a small domain found at the N-terminal end of Formimidoylglutamate deiminase from Pseudomonas aeruginosa (also known as N-formimino-L-Glutamate Iminohydrolase, HutF,

,

), N-acetylgalactosamine-6-phosphate deacetylasefrom Escherichia coli (AgaA) and similar proteins predominantly found in proteobacteria. This domain shows an all-β structure. HutF catalyses the hydrolysis of N-formimino-L-glutamate to N-formyl-L-glutamate and ammonia . AgaA catalyses the deacetylation of N-acetyl-D-galactosamine 6-phosphate to D-galactosamine 6-phosphate. Can probably also catalyze the deacetylation of N-acetyl-D-glucosamine 6-phosphate to D-glucosamine 6-phosphate .
Flagellar biosynthesis protein FlhF, N domain (FlhF_N)
Type: Domain

This domain is found in Flagellar biosynthesis protein FlhF from Bacillus subtilis, a protein that is necessary for flagellar biosynthesis. FlhF contains a basic N-terminal domain followed by the conserved NG domain, which can be divided into two segments: the N domain (this entry) and the G domain (

) .
Response regulator protein ChxR, N-terminal domain (ChxR_N)
Type: Domain

This domain is found at the N-terminal of the response regulator protein ChxR from Chlamydia trachomatis (

). ChxR is organised into a receiver domain, represented in this entry, and a C-terminal effector domain (

). Dimerisation occurs through the receiver domain. It shows an α-β configuration .
DdMyo7, FERM domain (DdMyo7_FERM)
Type: Domain

This entry represents the C-terminal FERM domain found in Myo7 from Dictyostelium discoideum , a protein that is essential for the extension of filopodia, plasma membrane protrusions filled with parallel bundles of F-actin similarly as metazoan Myo10, which suggests a high degree of functional conservation throughout evolution.
PilE-like, C-terminal (PilE-like_C)
Type: Domain

This domain is found at the C-terminal of Type IV pili fiber building block protein from Francisella tularensis (PilE), which adopts the canonical Type IVa pilin fold, with an helix embedded in a four-stranded anti-parallel β-sheet .
Vanadium-dependent haloperoxidase NapH1-like, second helical-bundle domain (NapH1-like_2nd)
Type: Domain

This domain is found in Vanadium-dependent haloperoxidase NapH1 from Streptomyces sp. (

) and similar bacterial sequences. Nahp1 that catalyse stereospecific chlorofunctionalisation reactions on naphthoquinone-based meroterpeneoids . This enzyme contain two similar helical domains composed of five α-helices. This domain harbours the catalytic residues.
RET, cysteine rich domain (RET_CRD)
Type: Domain

RET is a single transmembrane-spanning receptor tyrosine kinase (RTK) that plays critical roles in the development of vertebrates. Structural analysis indicate that the ligand-binding RET ectodomain (RET-ECD) contains four consecutive cadherin-like domains (CLD1-CLD4) followed by a membrane-proximal cysteine-rich domain (CRD, represented by this entry) .
ALK/LTK-like, glycine-rich domain (ALK/LTK-like_GRD)
Type: Domain

This entry represents the glycine-rich domain (GRD) from the Anaplastic lymphoma kinase (ALK), the closely related leukocyte tyrosine kinase (LTK) and similar proteins. ALK and LTK have been recently deorphanized receptor tyrosine kinases . They are involved in neural development, cancer and autoimmune diseases. ALK activity is associated with learning and memory, and controls energy expenditure. Inhibition of ALK can prevent diet-induced obesity .

This is an extracellular domain that regulates receptor activity by binding to activating peptides. This domain consists of fourteen long polyglycine type II (pGII) helices tightly packed into a honeycomb-like lattice .

This entry also includes sequences from Trichomonas vaginalis and some uncharacterised bacterial sequences.