SII-SWORD/CoKE huggingface dataset:
Transcription factor IIIC subunit Tfc1/Sfc1 (TF_IIIC_Tfc1/Sfc1)
Type: Family

Transcription factor IIIC (TFIIIC) is a multisubunit DNA binding factor that serves as a dynamic platform for assembly of pre-initiation complexes on class III genes. This entry represents subunit Tfc1/Sfc1 (also known as the tau 95 subunit) which holds a key position in TFIIIC, exerting both upstream and downstream influence on the TFIIIC-DNA complex by rendering the complex more stable . Once bound to tDNA-intragenic promoter elements, TFIIIC directs the assembly of TFIIIB on the DNA, which in turn recruits the RNA polymerase III (pol III) and activates multiple rounds of transcription.
Atg6, BARA domain (Atg6_BARA)
Type: Domain

In yeast, 15 Atg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells . Atg6/Vps30 has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway . This entry is the β-α repeated, autophagy-specific (BARA) domain .
Ribonuclease H2 subunit B (RNase_H2_suB)
Type: Family

Ribonuclease H2B is one of the three proteins of the eukaryotic RNase H2 complex that is required for nucleic acid binding and hydrolysis. It is a non catalytic subunit.

RNase H is classified into two families, type I (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type II (prokaryotic RNase HII and HIII, and eukaryotic RNase H2/HII). RNase H endonucleolytically hydrolyzes an RNA strand when it is annealed to a complementary DNA strand in the presence of divalent cations, in DNA replication and repair. The enzyme can be found in bacteria, archaea, and eukaryotes. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite a lack of evidence for homology from sequence comparisons, type I and type II RNase H share a common fold and similar steric configurations of the four acidic active-site residues, suggesting identical or very similar catalytic mechanisms.

Eukaryotic RNase HII is active during replication and is believed to play a role in removal of Okazaki fragment primers and single ribonucleotides in DNA-DNA duplexes. Eukaryotic RNase HII is functional when it forms a complex with RNase H2B and RNase H2C proteins. It is speculated that the two accessory subunits are required for correct folding of the catalytic subunit of RNase HII. Mutations in the three subunits of human RNase HII cause neurological disorder .
Gamma tubulin complex component, C-terminal (GCP_C)
Type: Domain

This is the C-terminal domain found in components of the gamma-tubulin complex proteins (GCPs). Family members include spindle pole body (SBP) components such as Spc97 and Spc98 which function as the microtubule-organizing centre in yeast . Furthermore, family members such as human GCP4 (gamma-tubulin complex component 4) have been structurally elucidated (

). Structure-based sequence analysis revealed the existence of an exposed surface area conserved in all human GCPs and in GCP4 orthologues. This area is located in the C-terminal domain of GCP4, which was confirmed in vitro to bind directly to gamma-tubulin. Sequence alignment of human GCPs based on the GCP4 structure helped delineate conserved regions in the N- and C-terminal domains .
Vacuolar import/degradation Vid27 (Vid27)
Type: Family

Vid27 is a cytoplasmic protein of unknown function, possibly regulates import of fructose-1,6-bisphosphatase into Vacuolar Import and Degradation (Vid) vesicles and is not essential for proteasome-dependent degradation of fructose-1,6-bisphosphatase (FBPase) .
MJ1316 RNA cyclic group end recognition domain (MJ1316)
Type: Domain

This MJ1316 domain appears to be an RNA repair domain predicted to be involved specifically in the recognition of RNA 3' ends with 2'-3' cyclic phosphate groups . It is found in UPF0248 proteins and Leukocyte receptor cluster member 9.
Gasdermin, pore forming domain (Gasdermin_pore)
Type: Domain

The N-terminal domain of Gasdermins can bind membrane lipids, phosphoinositides and cardiolipin, and exhibits membrane-disrupting cytotoxicity. It was shown to be able to lyse phosphoinositide/cardiolipin-containing liposomes and form pores on membranes . This entry represents the pore forming domain of gasdermin.
Protein EARLY FLOWERING 4 (EARLY_FLOWERING_4)
Type: Family

Protein EARLY FLOWERING 4 is a component of the central CCA1/LHY-TOC1 feedback loop in the circadian clock that promotes clock accuracy and is required for sustained rhythms in the absence of daily light/dark cycles .
BAP29/BAP31, transmembrane domain (BAP29/BAP31_N)
Type: Domain

The mammalian B-cell receptor-associated proteins of 29 and 31kDa (BAP29 and BAP31) are integral membrane proteins with a role in endoplasmic reticulum (ER) quality control and sorting . BAP31 is also involved in apoptosis . Saccharomyces cerevisiae possesses three homologues of BAP31 known as Yet1, Yet2, and Yet3 .

These proteins are predicted to have three transmembrane segments with a cytoplasmic, coiled-coil C-terminal domain . This entry represents the transmembrane region.
Inositol 1,3,4-trisphosphate 5/6-kinase, ATP-grasp domain (InsP(3)kin_ATP-grasp)
Type: Domain

This entry represents the ATP-grasp domain. Proteins containing this domain include several inositol 1, 3, 4-trisphosphate 5/6-kinase proteins. Inositol 1,3,4-trisphosphate is at a branch point in inositol phosphate metabolism. It is dephosphorylated by specific phosphatases to either inositol 3,4-bisphosphate or inositol 1,3-bisphosphate. Alternatively, it is phosphorylated to inositol 1,3,4,6-tetrakisphosphate or inositol 1,3,4,5-tetrakisphosphate by inositol trisphosphate 5/6-kinase .
CtsR, N-terminal HTH domain (CtsR_N)
Type: Domain

This family consists of several Firmicute transcriptional repressor of class III stress genes (CtsR) proteins. CtsR of L. monocytogenes negatively regulates the clpC, clpP and clpE genes belonging to the CtsR regulon . This entry is the N-terminal HTH domain.
NF-kappa-B-activating protein (NKAP)
Type: Family

Nkap is a highly conserved protein which functions as a transcriptional repressor on Notch target genes. It is required for T cell development and acquisition of functional competency , in transcriptional repression and maintenance and survival of adult hematopoietic stem cells , it also plays a role in RNA splicing and processing . MSA2, the Nkap human orthologue in Arabidopsis thaliana, is involved in rRNA synthesis . Nkap is a key regulator of mitosis, and its dysregulation might contribute to tumorigenesis by causing chromosomal instability . Nkap promotes the proliferation, migration and invasion of Ewing sarcoma cells, through the AKT signalling pathway .

NKAP is divided into approximately three domains, N-terminal RS repeats, a highly basic middle domain and the C-terminal DUF 926 .
CCDC66 domain (CCDC66_dom)
Type: Domain

This domain can be found in coiled-coil domain-containing protein 66 (CCDC). It is approximately 160 amino acids in length. CCDC66 protein is detected mainly in the inner segments of photoreceptors in many vertebrates including mice and humans. It has been found in dogs, that a mutation in the CCDC66 gene causes generalized progressive retinal atrophy (gPRA). This shows that the protein encoded for by this gene is vital for healthy vision and guards against photoreceptor cell degeneration. The structure of CCDC66 proteins includes a heptad repeat pattern which contains at least one coiled-coil domain. There are at least two or more α-helices which form a cable-like structure .
TRAF3-interacting protein 1, N-terminal (TRAF3IP1_N)
Type: Domain

This entry represents the N-terminal domain of TRAF3-interacting protein 1.

TRAF3-interacting protein 1 (TRAF3IP1, also known as IFT54) recruits TRAF3 (tumour necrosis factor receptor-associated factor 3) and DISC1 (Disrupted-In-Schizophrenia 1) to the microtubules and is conserved from worms to humans . The N-terminal region is the microtubule binding domain and is well-conserved; the C-terminal 100 residues, also well-conserved, constitute the coiled-coil region which binds to TRAF3. The central region of the protein is rich in lysine and glutamic acid and carries KKE motifs which may also be necessary for tubulin-binding, but this region is the least well-conserved . In humans, it plays an inhibitory role on IL13 signaling by binding to IL13RA1. It is involved in suppression of IL13-induced STAT6 phosphorylation, transcriptional activity and DNA-binding .
Vexin (Vexin)
Type: Family

This family includes Xenopus laevis Vexin and its human homologue, C8orf46. Vexin is transiently expressed in differentiating progenitors in the developing central nervous system (CNS) and is required for neurogenesis in the neural plate and retina .
Synaptic functional regulator FMRP, KH0 domain (FMRP_KH0)
Type: Domain

This entry corresponds to the KH0 domain from the FMRP protein . This is a divergent KH domain that was discovered through solving the structure of an N-terminal fragment of the FMRP protein . KH0 does not have the canonical G-X-X-G motif between helices A and B . It has been suggested that this domain may be involved in RNA binding .
NusG, additional domain (NusG_add)
Type: Domain

This domain is found in Thermotoga maritima NusG, which interacts with RNA polymerase and other proteins to form multi-component complexes that modulate transcription. This domain is referred to as Domain II and is an additional domain inserted into the N-terminal domain .
Ubiquitin-like protein MDY2, C-terminal domain (MDY2_C)
Type: Domain

This entry represents the C-terminal domain of Ubiquitin-like protein MDY2 from S. cerevisiae (also known as Get5) and related proteins found in Saccharomycetes. It is an homodimerisation domain, responsible for the formation of a heterotetrameric Get4/Get5 complex . This domain folds into helical hairpin that dimerises to form a four helical bundle (

).

Tail-anchored trans-membrane proteins are targeted to membranes post-translationally. The proteins Get4 and Get5 form an obligate complex that catalyses the transfer of tail-anchored proteins destined to the endoplasmic reticulum from Sgt2 to the cytosolic targeting factor Get3 .
Surface glycan-binding protein B, xyloglucan binding domain (SGBP_B_XBD)
Type: Domain

This is the C-terminal domain found in the surface glycan-binding protein-B (SGBP-B) from Bacteroides ovatus. SGBP-B is a cell-surface-localized, xyloglucan-specific binding protein. The C-terminal domain mediates xyloglucan binding. The domain displays similarity to the C-terminal β-sandwich domain of many GH13 enzymes .
RNase II/RNase R, cold shock domain (CSD2)
Type: Domain

Crystallographic structure analysis of E. coli wild-type RNase II revealed that the amino-terminal region starts with an α-helix followed by two consecutive five-stranded anti-parallel β-barrels, identified as cold-shock domains (CSD1 and CSD2). This entry relates to CSD2 which lacks the typical sequence motifs RNPI and RNPII but contributes to RNA binding .
Lysine-specific demethylase 4-like, Tudor domain (KDM4-like_Tudor)
Type: Domain

This is the tudor domain found in lysine-specific demethylase 4A-C (KDM4A, also known as JMJD2A-C, respectively). KDM4A/B are histone demethylases that specifically demethylate 'Lys-9' and 'Lys-36' residues of histone H3, while KDM4B specifically demethylates 'Lys-9'. Structure and function analysis indicate that this domain can recognize equally well two unrelated histone peptides, H3K4me3 and H4K20me3, by means of two very different binding mechanisms . KDM4 belongs to the conserved iron (II)-dependent jumonji-domain demethylase subfamily that is essential during development. Vertebrate KDM4A-C proteins contain a conserved double tudor domain (DTD) .

This entry also includes PHD finger protein 19 (PHF19), Metal-response element-binding transcription factor 2 (MTF2) and PHD finger protein 1 (PHF1) which are polycomb group (PcG) proteins that specifically binds histone H3 trimethylated at 'Lys-36' and recruits the PRC2 complex . PHD finger protein 20-like protein 1 negative regulator of proteasomal degradation of a set of methylated proteins is also included in this entry.
BDBT FKBP like, N-terminal (FKBP_N_2)
Type: Domain

This is the N-terminal domain of the beta chain found in Drosophila melanogaster protein BDBT (a FK506-Binding Protein) which stimulates the DBT circadian function. The domain contains the DBT-binding site. The domain is structurally homologous to the peptidyl prolyl isomerase (PPIase) regions of FK506-binding proteins despite low sequence homology. BDBT is structurally related to the immunophilin FKBP51 and it shares a common domain organization consisting of PPIase-like and TPR domains with noncanonical immunophilins such as FKBP38 or FKBPL .
Protein masquerade, clip-domain (CLIP_SPH_mas)
Type: Domain

The clip domain is a structural/regulatory unit in many arthropod serine proteases . The clip domain superfamily also includes serine protease homologs (SPHs) . This entry describes clip domains in the SPHs (CLIP subfamily A), which belong to group-3. SPHs usually carry between 1 to 5 clip domains . One of the most prominent family members is masquerade (mas). Deletion in drosophila models lead to defects in somatic muscle attachment and in the formation of the nervous system during embryogenesis .
DnaT, DNA-binding domain (DnaT_DNA_bind)
Type: Domain

This domain is found in E.coli primosomal protein 1 (Pp1). PP1 domain (residues 84-153) in

can bind to different types of ssDNA, which is fundamental for its physiological substrate bindings. Functional analysis indicate that both N and C termini are essential to having the cooperative effect in binding ssDNA. The ssDNA bound complex displays a spiral filament assembly that is adopted by many proteins that are involved in DNA replication, such as DnaA, RecA and PriB. This domain is similar to

except that it contains an extra loop at the N terminus (84-99). Structural analysis indicate that this extra loop might be essential for the stabilisation of the three-helix bundle .
Trimeric autotransporter adhesin, Trp ring domain (Trp_ring)
Type: Domain

Autotransporters are synthesized as precursor proteins with three functional domains, namely, an N-terminal signal peptide, an internal passenger domain, and a C-terminal pore-forming translocator domain. The C-terminal translocator domain is embedded in the outer membrane and facilitates delivery of the internal passenger domain to the bacterial surface. In conventional autotransporters, the C-terminal translocator domain contains approximately 300 amino acids and is monomeric. In contrast, in trimeric autotransporters, the translocator domain contains 60 to 70 amino acids and forms trimers in the outer membrane . This entry represents a Trp-ring domain which is found in the translocator region of H. influenzae Hia autotransporter, an adhesive protein that promotes adherence to respiratory epithelial cells . Trp-ring domains appear to be crucial repeated modular units in Hia, both in the general architecture of the passenger domain and in the structure of the binding domains .
PatG domain (PatG_dom)
Type: Domain

This domain can be found in PatG proteins, which are involved in processing the precursor peptide to yield the cyclic peptide patellamide. PatG can be found in Prochloron sp. .
LepB GAP domain, C-terminal subdomain (LepB_GAP_C)
Type: Domain

This subdomain is found in the Rab1 GTPase-activating protein (GAP) domain of GAP LepB present in Legionella pneumophilia. LepB inactivates Rab1, a key regulator of the secretory vesicular trafficking machinery, by acting as a GTPase-activating protein. LepB is also an antagonist of DrrA, which promotes Rab1. LepB acts by an atypical RabGAP mechanism that is reminiscent of classical GAPs. This is the C-terminal subdomain of the GAP domain and consists of an unusual fold .
Exportin-1, repeat 3 (XPO1_repeat_3)
Type: Repeat

Chromosome region maintenance 1 / Exportin 1 mediates the nuclear transport of proteins bearing a leucin-rich nuclear export signal (NES). It contains helical repeats that are structurally similar to HEAT repeats, but share little sequence similarity with them . N-, C-terminal and central repeats show slightly different structural arrangements, with N- and C- terminal repeats interacting with each other.
Peptidase family M23, N-terminal (Peptidase_M23_N)
Type: Domain

This is the N-terminal domain of in some M23 peptidases (

), mostly found in proteobacteria.
Flax-rust effector AvrM-A (AvrM-A)
Type: Domain

This domain is found in AvrM-A present in Melampsora lini. AvrM-A is a natural variant of AvrM which is a secreted effector protein that can internalize into plant cells in the absence of the pathogen and bind to phosphoinositides. AvrM results in effector-triggered immunity. This domain makes up part of the C-terminal region, which is highly conserved in AvrM. The domain is required for M-dependent effector-triggered immunity .
Domain of unknown function DUF5626 (DUF5626)
Type: Domain

This is a domain of unknown function mostly found in firmicutes.
Galactofuranosyltransferase GlfT2, N-terminal (GlfT2_N)
Type: Domain

This is the N-terminal β-barrel domain found in the polymerizing galactofuranosyltransferase GlfT2 (Rv3808c). This enzyme synthesizes the bulk of the galactan portion of the mycolyl-arabinogalactan complex, which is the largest component of the mycobacterial cell wall such as in Mycobacterium tuberculosis. The N-terminal domain contains two short helices preceding a 10-stranded β-sandwich with jelly roll topology .
Protein of unknown function DUF5518 (DUF5518)
Type: Family

This is a family of unknown function found in Archaea. Family members have multiple predicted trans-membrane regions.
DNA topoisomerase VI, subunit B, C-terminal (Top6b_C)
Type: Domain

This is the C-terminal domain found in archaeal type 2 DNA topoisomerase 6 subunit B (

). This region is a small helix-two turns-helix (H2TH) domain inserted between the GHKL and transducer domains which adopts an immunoglobulin-like fold. Mutation analysis of this C-terminal domain showed that the overall activity of the mutant mesophilic methanogen M. mazei Top6B (MmT6) is modestly reduced but its relative activity on different substrates is not affected. Due to the similarity of the B subunit's CTD to known protein- and carbohydrate-binding modules, it has been suggested that it could regulate topo VI spatially, perhaps by localizing the enzyme to a specific subcellular region or functional partner .
CCDC81-like prokaryotic HU domain 1 (HU-CCDC81_bac_1)
Type: Domain

First of two HU domains found in bacterial proteins typically fused to a C-terminal transmembrane helix and an extracellular peptidoglycan-binding domain. The HU domains in many of these proteins are predicted to function in tethering the nucleoid to the cell envelope .
Prokaryotic pPIWI_RE, MID domain (MID_pPIWI_RE)
Type: Domain

This is the MID domain of the pPIWI_RE PIWI/Argonaute module. pPIWI_RE is found in a conserved three-gene island that also contains a DinG-type helicase and an REase nuclease. This three gene island is predicted to form a conflict system which targets R-loop formation of invasive plasmids during plasmid replication .
Glucosyltransferase 24, catalytic domain (Glyco_transf_24)
Type: Domain

This is the catalytic domain found in UDP-glucose:glycoprotein glucosyltransferase (UGGT). This domain belongs to glucosyltransferase 24 family (GT24) A-type domain. The GT domain displays the expected glycosyltransferase type A (GT-A) fold .
PriA DNA helicase, Cys-rich region (CRR) domain (PriA_CRR)
Type: Domain

This is a cys-rich region (CRR) domain found in PriA DNA helicases. The CRR region which is embedded within the C-terminal helicase lobe

has been identified to bind two Zn2+ ions. This 50-residue insertion forms a structure on the surface of the helicase core in which two Zn2+ ions are coordinated by invariant Cys residues. Biochemical experiments have shown that sequence changes to Zn2+-binding Cys residues in the PriA CRR can eliminate helicase, but not ATPase, activity and can block assembly of PriB onto DNA-bound PriA, implicating the CRR in multiple functions in PriA .

Primosomal protein N', also known as ATP-dependent helicase PriA, is a component of the primosome, which is involved in replication, repair, and recombination. PriA serves as a sensor/stabiliser for an arrested replication fork, which is lethal in bacteria if left unrepaired and eventually promotes restart of DNA replication through the assembly of a primosome. It also serves as a checkpoint protein that prevents the replicase from advancing in a strand displacement reaction on forks that do not contain a functional replicative helicase . This protein shows a modular arrangement in which its central helicase core is surrounded by several DNA-binding elements, including a 3'DNA-binding domain

at the N-terminal. This domain is usually followed by a circularly permuted winged helix (WH) domain

. At the C-terminal, there is a Cys-rich region (CRR) domain

, which is embedded within the C-terminal helicase lobe

, followed by the C-terminal domain (CTD)

.
TFA2, Winged helix domain 2 (TFA2_Winged_2)
Type: Domain

This is the second winged helix domain can be found in TFA2 proteins present in Saccharomyces cerevisiae. In form 2, the domain interacts directly with Rad3, a DNA helicase .
Endo-alpha-N-acetylgalactosaminidase, domain 6 (GH101_dom-6)
Type: Domain

Proteins containing a galactose-binding domain-like fold can be found in several different protein families, in both eukaryotes and prokaryotes. The common function of these domains is to bind to specific ligands, such as cell-surface-attached carbohydrate substrates for galactose oxidase and sialidase , phospholipids on the outer side of the mammalian cell membrane for coagulation factor Va , membrane-anchored ephrin for the Eph family of receptor tyrosine kinases , and a complex of broken single-stranded DNA and DNA polymerase beta for XRCC1 . The structure of the galactose-binding domain-like members consists of a β-sandwich, in which the strands making up the sheets exhibit a jelly-roll fold .

This entry represents a galactose-binding domain, referred to as domain 6, found in endo-alpha-N-acetylgalactosaminidases from bacteria .
tRNA uridine(34) hydroxylase, N-terminal (TRHO_N)
Type: Domain

This domain is found at the N terminus of tRNA uridine(34) hydroxylase TrhO from bacteria. TrhO (also known as YceA in E. coli) catalyzes oxygen-dependent 5-hydroxyuridine (ho5U) modification at position 34 in tRNAs, the first step in 5-carboxymethoxyuridine (cmo5U) biosynthesis . This domain can also be found in rhodanese-like domain-containing proteins from eukaryotes.
TFIIF, beta subunit, N-terminal (TFIIF_beta_N)
Type: Domain

Accurate transcription in vivo requires at least six general transcription initiation factors, in addition to RNA polymerase II. Transcription initiation factor IIF (TFIIF) is a tetramer of two beta subunits associate with two alpha subunits which interacts directly with RNA polymerase II. The beta subunit of TFIIF is required for recruitment of RNA polymerase II onto the promoter .
Family of unknown function DUF5537 (DUF5537)
Type: Family

This is a family of unknown function found mostly in chordata.
RACo linker region (RACo_linker)
Type: Domain

Proteins containing this domain include reductive activator of CoFeSP (RACo,

) proteins. Structure analysis of RACo indicate that it contains 4 regions: N-terminal region (residues 3-94) binding the [2Fe-2S] cluster, a linker region (residues 95-125), the middle region (residues 126-206), and the large C-terminal domain (residues 207-630). This entry pertains to the linker region. The linker region is only present in RACE (reductive activases for corrinoid enzymes) protein sequences with the N-terminal [2Fe-2S] cluster and is absent in the RamA-like RACE proteins, suggesting that the linker domain and the N-terminal domain form one functional unit .
Protein of unknown function DUF5540 (DUF5540)
Type: Family

This is a family of unknown function found in primates.