SII-SWORD/CoKE huggingface dataset:
STICHEL, DnaA_N-like alpha-beta domain (DnaA_N-like_STI)
Type: Domain

This domain is found in protein STICHEL (STI) from Arabidopsis thaliana and related proteins from plants and cyanobacteria. STICHEL acts as a key regulator of trichome branching through an endoreduplication-independent pathway . The domain represented by this entry is predicted to adopt a globular α/β structure with significant similarity to domains belonging to Ribosome-binding factor A, RbfA superfamily including ribosomal protein eS7. It has a significant sequence similarity to DnaA N-terminal domain. This domain is topologically very similar to KH type II domains but it lacks their characteristic KH-motif.
CGL2689-like, C-terminal domain (CGL2689-like_C)
Type: Domain

This entry represents the α-helical C-terminal domain of CGL2689 from Corynebacterium glutamicum (

,

) and similar sequences from actinomycetes. CGL2689 is a putative dehydrogenase that contain an N-terminal Rossmann domain (

). This domain is involved in dimerisation by swapping of helices along a central long α-helix axis.
Cell wall mannoprotein PIR1-like, C-terminal domain (PIR1-like_C)
Type: Domain

This entry represents a presumed domain found at the C-terminal of fungal cell wall mannoproteins, including PIR1, CIS3 and PIR5 from S.cerevisiae. These proteins are part of the outer cell wall layer, required for stability of the cell wall and for optimal growth. This domain may have a trefoil fold.
Leucine--tRNA ligase, ubiquitin-like domain (LARS1_ULD)
Type: Domain

This domain is found in human Leucine--tRNA ligase (LARS1) and related metazoan proteins. LARS1 is aminoacyl-tRNA synthetase that catalyses the specific attachment of leucine to its cognate tRNA (tRNA(Leu)) . It also mediates activation of leucine-dependent mechanistic target of rapamycin complex 1 (mTORC1). In the presence of leucine, LARS1 is translocated to the lysosome and facilitates the conversion of RagD-GTP to RagD-GDP form, resulting in mTORC1 activation .

The domain represented by this entry is predicted to adopt ubiquitin-like fold with similarity to SPN domain of SHANK3. This domain is usually found in combination with domains that are typical for Leucyl-tRNA ligases.
Tm0771-like, C-terminal domain (Tm0771-like_C)
Type: Domain

This entry represents the C-terminal domain of Tm0771 from Thermotoga maritima, a DNA polymerase III, gamma subunit-related protein. This domain consists of a five α-helix bundle (

). Members of this entry are specific to Thermotogales.
RNAP inhibitory protein/P131-like (RIP_P131-like)
Type: Family

This entry represents a family of viral proteins, including RNAP Inhibitory Protein (RIP) and its paralog, the major capsid protein (MCP) P131, both from Acidianus two-tailed virus. These proteins adopt very similar bundle structures consisting of six α-helices

. RIP factor binds inside the DNA-binding channel of RNAP, inhibiting transcription by occlusion of binding sites for nucleic acid and the transcription initiation factor TFB. MCP P131 is a building block of the viral capsid.
DD-carboxypeptidase/endopeptidase Mpg-like, N-terminal (NMB0315-like_N)
Type: Domain

This entry represents the N-terminal domain I of DD-carboxypeptidase/endopeptidase Mpg (NMB0315), an outer membrane protein of Neisseria meningitidis serogroup B and a potential candidate for a broad-spectrum vaccine against meningococcal disease. This domain tightly associates with domain III, which blocks the active site and the substrate binding groove

. It is usually found associated with

).
Dret_0059-like, sensor domain (Dret_0059-like_sensor)
Type: Domain

This entry represents a sensor domain found in prokaryotic methyl-accepting chemotaxis proteins, diguanylate-cyclase and histidine kinase receptors, including Dret_0059 from Desulfohalobium retbaense (

,

).
RhiE-like, KS-MAT linker domain (RhiE-like_linker)
Type: Domain

This entry represents a linker domain found in polyketide synthases from ascomycetes and bacteria. This domain connects the N-terminal domains with the B-domain as described in RhiE (

) .
YgxA-like, substrate binding domain (YgxA-like_substrate-bd)
Type: Domain

This entry represents the substrate binding domain of the uncharacterised protein YgxA from Bacillus subtilis and similar sequences from firmicutes. This domain consists of four-helical up-and-down bundle

.
Cell-shape determining Csd6, N-terminal dimerization domain (Csd6-like_dimerization)
Type: Domain

This entry represents the dimerization domain found at the N terminus of Cds6 from H. pylori, a cell shape-determining protein that plays key roles in alteration of cross-linking or by trimming of peptidoglycan muropeptides. It is also involved in deglycosylation of the flagellar protein FlaA . Members of this group are specific to Campylobacterales.
CPC1/SPEF2 domain D5 (SPEF2_D5)
Type: Domain

This domain is found in the axoneme central apparatus (CA) associated proteins such as Chlamydomonas Central pair complex 1 (CPC1,

) and its mammalian orthologues Sperm flagellar protein 2 (SPEF2) . CPC1 is located at C1 microtubule. Most of the distal components of the C1b projection bind CPC1 and its correct recruitment and positioning is critical to the formation of the C1b projection, and ciliary motility in Chlamydomonas and humans . CPC1 serves as the rachis of the entire C1b arm and this domain contributes to this function . It folds into a single long α-helix.
Phosphatidylserine Lipase ABHD16, N-terminal domain (ABHD16_N)
Type: Domain

This entry represents the N-terminal domain from ABHD16 family of proteins. The ABHD16 family comprises enzymes with phosphatidylserine lipase activity, catalysing the hydrolysis of phosphatidylserine to produce lysophosphatidylserine, a signaling lipid involved in immunological and neurological processes. These enzymes exhibit specificity, showing no activity towards diacylglycerol, triacylglycerol, or lysophosphatidylserine lipase. Additionally, they possess monoacylglycerol lipase activity, with a preference for certain monoacylglycerol substrates. The family's enzymatic functions highlight its role in lipid signaling pathways and potential implications in physiological regulation.
Integrator complex subunit 7, C-terminal domain (INTS7_C)
Type: Domain

This entry represents the C-terminal domain of the Integrator complex subunit 7 (INTS7).

Integrator complex subunit 7 (INTS7) is a component of the integrator complex which is recruited to the U1 and U2 snRNA genes and mediates the snRNAs' 3' end processing. The integrator complex interacts with the C-terminal tail of the largest subunit of RNA-polymerase II to promote 3'-snRNA processing . INTS7 interacts with INTS1 and INTS2 making extensive contacts with each other, nucleating the assembly of the whole INTAC complex . In zebrafish, C. elegans and Drosophila, INTS7 has been found to be essential for normal development .
Type II methyltransferase M.Eco57I, C-terminal domain (M_Eco57I_C)
Type: Domain

This domain is found at the C-terminal of the gamma subtype methylase Type II methyltransferase M.Eco57I from Escherichia coli. This domain is predicted to adopt an α-β configuration and is often found associated with

.
Heme-regulated eIF-2-alpha kinase, helical domain (HRI2_3H)
Type: Domain

This domain is found at the N-terminal of Heme-regulated eIF-2-alpha kinase (HRI1/HRI2). This enzyme phosphorylates the alpha subunit of eukaryotic translation initiation factor 2 (EIF2S1/eIF-2-alpha) in response to various stress conditions . HRI is a key activator of the integrated stress response (ISR) required for adaptation to various stress, such as heme deficiency, oxidative stress and osmotic shock . This domain is predicted to fold into an α-helical structure consisting of three α-helices.
Cadherin-related hmr-1, C-terminal (Hmr1_C)
Type: Domain

This entry represents the C-terminal region of Cadherin-related hmr-1 from Caenorhabditis elegans and similar sequences from nematodes. Hmr-1 is a calcium-dependent cell adhesion protein required for adherens junction assembly and connecting adherens junctions to the cytoskeleton . This domain is homologous to the beta-catenin binding region of E-cadherin .
Complement regulator-acquiring surface protein 2-like (CRASP-2-like)
Type: Family

This protein family includes Complement regulator-acquiring surface protein 2 from Borreliella burgdorferi (CRASP-2, also known as CspZ,

), the causative agent of Lyme disease. CRASP-2 can bind both the major alternative pathway complement regulator factor H (CFH) and factor H-like protein 1 (CFHL-1), contributing to the resistance of the bacteria to the host's immune response. This protein consists of a single domain almost entirely formed by α-helices

. This family is specific to Borreliaceae.
Ssol_1539-like, N-teminal, second subdomain (Ssol_1539-like_N_2)
Type: Domain

This domain is found in Ssol_1539 from Saccharolobus solfataricus and similar archaeal sequences. Ssol_1539 is organised into two domains

. The N-terminal domain contains two subdomains separated by a central helix. This entry represents the second subdomain, which shows an all-α configuration .
DEAD box helicase Hera, RNA-binding domain (Hera_RBD)
Type: Domain

This entry represents the RNA binding domain found at the C-terminal end of DEAD box helicase Hera from Thermus thermophilus and similar proteins from Deinococci. This domain, which is located C-terminal to the dimerisation domain (

), is responsible for binding of Hera to 23S rRNA. It consists of a central four-stranded β-sheet, flanked by an α-helix, and a long loop connecting β-strands 3 and 4 that replaces helix α2 present in the canonical RNA recognition motif (RRM)

.
VtrC-like (VtrC-like)
Type: Family

This entry represents a family of proteins specific to Vibrionaceae, including the Vibrio parahaemolyticus VtrC protein, which shows a lipocalin-like β-barrel configuration . VtrC, along with VtrA and VtrB, are required for activating the virulence type III secretion system 2 in response to bile salts. The VtrA/VtrC complex activates VtrB in the presence of bile salts. The crystal structure of the periplasmic domains of the VtrA/VtrC heterodimer reveals a β-barrel with a hydrophobic inner chamber

.
BCE_2095-like, N-terminal domain (BCE_2095-like_N)
Type: Domain

This is the N-terminal domain found in a group of uncharacterised bacterial proteins which have a Phospholipase/carboxylesterase/thioesterase domain (

) at the C-terminal, including BCE_2095 from Bacillus cereus whose structure was determined (

,

). This domain consists of armadillo (ARM) repeats.
TcaA, second domain (TcaA_2nd)
Type: Domain

This entry represents the second domain of the TcaA proteins. TcaA plays a major role in decreasing resistance to glycopeptide antibiotics .
TcaA, 4th domain (TcaA_4th)
Type: Domain

This entry represents the fourth domain of the TcaA proteins that adopt an Ig-like fold. TcaA plays a major role in decreasing resistance to glycopeptide antibiotics . In the uncharacterised membrane protein YvbJ, thi entry covers the third and fourth domains.
TarS, C-terminal domain 2 (TarS_C2)
Type: Domain

This entry represents the C-terminal domain 2 (C2) of TarS from Staphylococcus aureus.

Beta-glycosyltransferase TarS is an enzyme responsible for the glycosylation of wall teichoic acid polymers of the S. aureus cell wall, a process that has been shown to be specifically responsible for methicillin resistance in MRSA. It contains a trimerisation domain composed of tandem carbohydrate binding motifs.The two C-terminally localised regions composed of a series of β-sheets participate in an extensive trimerisation interface and they assume an immunoglobulin-like fold. It is suggested that both carbohydrate binding domains may be involved in polyRboP binding, however unlike pullulanase, the CBMs of TarS are involved in the formation of an extensive trimerisation interface .
TPL/SMU1, LisH-like dimerisation domain (TPL_SMU1_LisH-like)
Type: Domain

This entry represents a highly conserved domain containing a lissencephaly homologous (LisH) dimerisation motif found at the N-terminal end of a group of eukaryotic proteins, including Protein TOPLESS from Arabidopsis thaliana (TPL, ) and human WD40 repeat-containing protein SMU1 . TPL is a transcriptional corepressor required for ovule development . It may repress the expression of root-promoting genes in the top half of the embryo to allow proper differentiation of the shoot pole during the transition stage of embryogenesis . SMU1 is involved in pre-mRNA splicing as a component of the spliceosome . Most members of this group also contain

towards the C-terminal.
Histone-lysine methyltransferase SETD7, N-terminal (SETD7_N)
Type: Domain

This entry includes histone-lysine N-methyltransferase SETD7 (also known as SET7/9) which specifically monomethylate Lys-4 of histone H3, creating a specific tag for epigenetic transcriptional activation . This entry represents the N-terminal region, which consists of MORN repeats.

This entry represents histone-lysine N-methyltransferase SETD7 (also known as SET7/9) (

), which contains a SET domain . This enzyme specifically monomethylate Lys-4 of histone H3, thereby creating a specific tag for epigenetic transcriptional activation. Methylation of lysine residues in the N-terminal tails of histones is thought to represent an important component of the mechanism that regulates chromatin structure. As such SETD7 plays a central role in the transcriptional activation of genes such as collagenase and insulin. It is recruited by IPF1/PDX-1 to the insulin promoter, leading to activate transcription . SETD7 also has methyltransferase activity toward non-histone proteins, including TAF10 and p53/TP53. SETD7 monomethylates Lys-189 of TAF10, which increases the affinity of TAF10 for RNA polymerase II. SETD7 monomethylates Lys-372 of p53/TP53, which stabilises p53/TP53 and increases p53/TP53-mediated transcriptional activation .
EST1-like, DNA-binding domain (EST1-like_DNA_bind)
Type: Domain

This entry represents a DNA/RNA binding domain found in a group of worm sequences, such as

from C.elegans , which are related to Est1A from human (SMG6), defined as 14-3-3-like proteins involved in nonsense-mediated mRNA decay (NMD) pathway.
HphA, N-terminal heme-binding domain (HphA_N)
Type: Domain

HphA (heme scavenger) is a secreted hemophore that binds and acquires heme from hemoglobin. It consists of two domains: N-terminal heme binding domain (this entry) and C-terminal β-barrel that is related to domains members of the Outer membrane β-barrel superfamily. The N-terminal domain has a clamp-like structure consisting of six antiparallel β-strands and an α-helix. Two histidines located on loops coordinate the heme .
HphA, C-terminal domain (HphA_C)
Type: Domain

HphA (heme scavenger) is a secreted hemophore that binds and acquires heme from hemoglobin. It consists of two domains: N-terminal heme binding domain and C-terminal β-barrel (this entry) that is related to domains members of the Outer membrane β-barrel superfamily .
Headcase, N-terminal (HECA_N)
Type: Domain

This domain is found towards the N-terminal of Drosophila headcase protein and the human headcase protein homologue. Drosophila headcase protein is involved in dendrite pruning and is a branching inhibitor during tracheal development . It also promotes cell survival and niche maintenance in the Drosophila testis . Human headcase protein may play an important role in human carcinogenesis and it could be considered as an interesting therapeutic agent against Wnt-dependent tumor progression .
F1F0 ATP synthase subunit ASA5 (ASA5)
Type: Family

This entry represents the homologues of mitochondrial F1F0 ATP synthase subunit ASA5. F0 has six transmembrane helices and four long, membrane-intrinsic helices, which form the two helical hairpins of the conserved alpha subunit. Of the six transmembrane helices, two belong to ASA6 and one each to ASA5, ASA8, ASA9, and ASA10 .
Pyrroloquinoline quinone-dependent pyranose dehydrogenase, beta-propeller domain (Beta-prop_PDH)
Type: Domain

This entry includes homologues of the AA12 (Auxilliary activities family 12) enzyme from Trichoderma reesei (TrAA12,

,

) , and pyrroloquinoline quinone-dependent pyranose dehydrogenases. TrAA12 is a monodomain protein that adopts six-bladed β-propeller structure. AA12 shows similarities to the global active-site architecture of bacterial glucose dehydrogenases, suggesting their common evolutionary origin.

Pyrroloquinoline quinone-dependent pyranose dehydrogenases catalyse the oxidation of various sugars including L-galactose, L-gulose, D-talose, D-arabinose, D-lyxose, L-fucose and D-glucosone and show significant activity toward the reverse-chair conformation of pyranoses . In this proteins, this entry corresponds to the central domain.
NrS-1 polymerase-like, head domain (NrSPol-like_head)
Type: Domain

This entry represents the head domain found in NrS-1 polymerase (NrSPol) from Nitratiruptor phage NrS-1, the first known phage that can infect epsilonproteobacteria, one of the predominant primary producers in the deep-sea hydrothermal vent ecosystems. NrS-1 polymerase is a multidomain enzyme and is a key component of the phage replisome . This domain, together with the helicase (

) and tail (

) domains, is responsible for the DNA activity in this protein. It has a novel α/β fold .
NrS-1 polymerase-like, tail domain (NrSPol-like_tail)
Type: Domain

This entry represents the C-terminal tail domain found in NrS-1 polymerase (NrSPol) from Nitratiruptor phage NrS-1, the first known phage that can infect epsilonproteobacteria, one of the predominant primary producers in the deep-sea hydrothermal vent ecosystems. NrS-1 polymerase is a multidomain enzyme and is a key component of the phage replisome . This domain, together with the head (

) and helicase (

) domains, is responsible for the DNA activity in this protein. It has a novel α/β fold . The tail domain is important for the hexamer assembly and polymerization activity of NrS-1 polymerase .
Cys/Met metabolism enzyme, pyridoxal-phosphate attachment site (Cys_met_metab_PP)
Type: Conserved_site

This entry represents a conserved site which contains a lysine residue located in the central section of these enzymes to which the pyridoxal-P group is attached. The sequence around this residue is highly conserved.

A number of pyridoxal-dependent enzymes involved in the metabolism of cysteine, homocysteine and methionine have been shown to be evolutionary related. These enzymes are proteins of about 400 amino-acid residues. The pyridoxal-P group is attached to a lysine residue located in the central section of these enzymes.

One of these enzymes is the sulfhydrylase FUB7 from fungi such as Gibberella and Fusarium. The gene is part of a cluster that mediates the biosynthesis of fusaric acid, a mycotoxin with low to moderate toxicity to animals and humans, but with high phytotoxic properties .

Pyridoxal phosphate is the active form of vitamin B6 (pyridoxine or pyridoxal). Pyridoxal 5'-phosphate (PLP) is a versatile catalyst, acting as a coenzyme in a multitude of reactions, including decarboxylation, deamination and transamination . PLP-dependent enzymes are primarily involved in the biosynthesis of amino acids and amino acid-derived metabolites, but they are also found in the biosynthetic pathways of amino sugars and in the synthesis or catabolism of neurotransmitters; pyridoxal phosphate can also inhibit DNA polymerases and several steroid receptors . Inadequate levels of pyridoxal phosphate in the brain can cause neurological dysfunction, particularly epilepsy .

PLP enzymes exist in their resting state as a Schiff base, the aldehyde group of PLP forming a linkage with the ε-amino group of an active site lysine residue on the enzyme. The α-amino group of the substrate displaces the lysine ε-amino group, in the process forming a new aldimine with the substrate. This aldimine is the common central intermediate for all PLP-catalysed reactions, enzymatic and non-enzymatic .
Epi-isozizaene synthase (IsozizSyn)
Type: Family

This entry represents Epi-isozizaene synthase and related sequences. It catalyses the cyclization of farnesyl diphosphate (FPP) to the sesquiterpene epi-isozizaene .
Pesticidal crystal protein Cry1Aa, domain IV (Pest_crys_Cry1Aa_dom-IV)
Type: Domain

This entry represents a domain found in the protoxin portion of insecticidal proteins (parasporins, or Cry proteins) such as Cry1Aa from Bacillus thuringiensis (Bt) and related proteins. These proteins contain a proteolytically labile protoxin segment (in the C-terminal region) and a three-domain toxic core at the N-terminal (domains I-III). This entry describes domain IV, one of the four protoxin domains (domains IV-VII). Domains IV and VI are α-helical bundles that resemble structural/interaction domains such as spectrin

or bacterial fibrinogen-binding complement inhibitor. The structure of full length Cry1Aa was determined

.
ApeI dehydratase-like (ApeI-like)
Type: Domain

This entry represents a domain found in ApeI dehydratase (

) and its homologues. This enzyme forms a heterodimer with ApeP that carries out dehydratation in APE biosynthesis. Both subunits in this complex adopt a typical hotdog fold comprising six antiparallel β-strands and a central α-helix . The domain represented by this entry is found either stand alone or in combination with other domains mainly in proteobacteria.
NACHT N-terminal Helical domain 1 (NNH1)
Type: Domain

This entry represents an α-helical domain found at the N-terminualof bacterial NACHT conflict systems . This position is frequently occupied by an effector domain.
SCP160-like, KH domain (SCP160-like_KH)
Type: Domain

This entry represents a KH domain found in SCP160 from S.cerevisiae and similar fungal sequences. SCP160 is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which, in S.cerevisiae, enclose the duplicated chromosomes. This domain is typically found in RNA-binding proteins along with many other KH domains belonging to

.
Protein root UVB sensitive/RUS domain (UVB_sens_RUS_dom)
Type: Domain

This domain is found in a group of root UVB sensitive plant proteins and their eukaryotic RUS homologues.

In plants, this domain plays a role in auxin-transport, plant growth and development and appears to be expressed by all cells in the plant as well as in plastids. This group of proteins has been shown to play a role in vitamin B6 photo-protection and homoeostasis in plants .

This domain is predicted to adopt a similar structure to other major facilitator superfamily (MFS) membrane transporters, consisting of several transmembrane helices.
Mal s 1 allergenic protein-like (Mala_s_1-like)
Type: Family

This protein family includes Mal s 1 allergenic protein from the yeast Malassezia sympodialis (Mala s 1), which forms a relatively compact cup-like β-propeller consisting of six blades each with four antiparallel β-strands .
RSC4, Ig-like domain (RSC4_Ig-like)
Type: Domain

The RSC4 family includes components of the RSC chromatin remodeling complex, which plays a crucial role in the regulation of transcription and the positioning of nucleosomes. Members of the RSC4 family are particularly important for the control of genes associated with membrane and organelle development, thereby influencing cellular structure and function. This protein contains two N-terminal bromodomains followed by this C-terminal Ig-like domain.

This entry includes RSC4 from S.pombe and closely related fungal sequences.
SPT2 homolog, N-terminal (SPT2_N)
Type: Domain

This entry represents an N-terminal conserved region found in the SPT2 homologues from animals. SPT2 is a histone chaperone that stabilises pre-existing histone tetramers and regulates replication-independent histone exchange on chromatin .