SII-SWORD/CoKE huggingface dataset:
BsaWI restriction endonuclease type 2 (RE_BsaWI)
Type: Domain

Type II restriction endonucleases recognize short 4-8 bp nucleotide sequences and cleave phosphodiester bonds within or close to their target site. BsaWI restriction endonuclease from the thermophilic bacterium Bacillus stearothermophilus W1718 belongs to a group of restriction endonucleases that share CCGG motif within their target sites, termed 'CCGG-family'. However, the R-(D/E)R motif residues, which are supposed to recognize CCGG from the major groove side, are poorly ordered and located far away from the DNA bases. BsaWI contacts with the CCGG tetranucleotide from the minor groove side. It is folded into two domains an N-terminal helical domain and a C-terminal catalytic domain. Furthermore, it carries a PDXKXE motif at the putative active site .
UvrA DNA-binding domain (UvrA_DNA-bd)
Type: Domain

This is the DNA-binding domain found in the UvrABC system protein A.

In Eubacteria and some Archaea, the first steps in nucleotide excision repair are carried out by the coordinated action of the UvrA, UvrB, and UvrC proteins. A damage recognition complex composed of 2 UvrA and 2 UvrB subunits scans DNA for abnormalities. Upon binding of the UvrA(2)B(2) complex to a putative damaged site, the DNA wraps around one UvrB monomer. DNA wrap is dependent on ATP binding by UvrB and probably causes local melting of the DNA helix, facilitating insertion of UvrB β-hairpin between the DNA strands. Then UvrB probes one DNA strand for the presence of a lesion. If a lesion is found the UvrA subunits dissociate and the UvrB-DNA preincision complex is formed. This complex is subsequently bound by UvrC and the second UvrB is released. If no lesion is found, the DNA wraps around the other UvrB subunit that will check the other stand for damage .
Nuclear pore complex protein Nup214, phenylalanine-glycine (FG) domain (Nup214_FG)
Type: Domain

CRM1 is the major nuclear export receptor. During translocation through the nuclear pore, transport complexes transiently interact with phenylalanine-glycine (FG) repeats of multiple nucleoporins. On the cytoplasmic side of the nuclear pore, CRM1 tightly interacts with the nucleoporin Nup214. Nup214 binds to N- and C-terminal regions of CRM1, thereby clamping CRM1 in a closed conformation and stabilizing the export complex. This entry represents an FG repeat region within the C terminus of Nup214 which is required for its interaction with CRM1 .
Macroglobulin domain MG3 (MG3)
Type: Domain

This entry corresponds to the MG3 domain found in thioester-containing proteins (TEPs) such as alpha-2-macroglobulin, complement components C3, C4 and C5, and complement-like proteins .
Disulfide isomerase DsbG, N-terminal (DsbG_N)
Type: Domain

This is the N-terminal domain found in DsbG, a protein disulfide isomerase present in the periplasm of Helicobacter pylori. The formation of correct disulfide bonds is critical in the folding process of many secretory and membrane proteins in bacteria. Non-native disulfides are corrected by the isomerase DsbC, and, to a lesser extent, by DsbG. The N-terminal domain is involved in dimerization. The dimer interface of Helicobacter pylori's DsbG is stabilized by hydrophobic interactions and hydrogen bonds involving alpha 1, beta-3 to beta-4 loop, beta-4 and beta-4 to alpha-2 loop. This pattern of dimerization is similar to that of E. coli's DsbG .
Mucin binding domain (MucBP_2)
Type: Domain

This domain is found in bacterial cell surface proteins that interact with mucins. The archetypal member of this family is the Mub-R5 B1 domain . This domain has a β-grasp fold .
DNA ligase, ATP-dependent, bacteriophage T7-type, C-terminal (DNA_ligase_ATP-dep_T7_C)
Type: Domain

This is the C-terminal domain found in ATP-Dependent DNA ligase from Bacteriophage T7. This domain has no ligase activity, however together with the N-terminal domain (domain 1) they bind to double-stranded DNA consistent with the idea that the DNA-binding site is between the domains in the intact protein. While the fold of domain 2 (this domain) is very similar to a number of other proteins that bind single-stranded DNA, this domain does not bind to single-stranded DNA but instead has a high affinity for double-stranded DNA .
FMR1, tudor domain (Tudor_FRM1)
Type: Domain

This entry represents the tandem Tudor domains (also known as Agenet) found in fragile X messenger ribonucleoprotein 1 (FMR1) and its paralogues, fragile X-related proteins 1/2 (FXR1/2) .

Fragile X messenger ribonucleoprotein 1 (FMRP/FMR1), and its paralogues, FXR1 and FXR2 (RNA-binding protein FXR1 and 2, respectively), comprise a family of RNA-binding proteins . They are highly similar to one another and also retain highly conserved domain architecture comprising two tandem Tudor Agenet-like domains at the N-terminal, three ribonucleoprotein K homology (KH) domains and a cluster of arginine and glycine residues that constitute the RGG box .

FMR1 protein is a multifunctional polyribosome-associated protein that plays a central role in neuronal development and synaptic plasticity. It regulates alternative mRNA splicing, mRNA stability, mRNA dendritic transport and postsynaptic local protein synthesis of a subset of mRNAs . FMR1 is thought to bind target mRNA in the nucleus to form a ribonucleoprotein complex which is transported to dendrites and spines . It is also required for ovary development and function . FMR1 has also been shown to interact with components of the miRNA pathway . A large expansion of the CGG trinucleotide repeat in the 5'-untranslated region of the FMR1 gene causes Fragile X syndrome (FXS), an inherited developmental disorder that causes a broad range of intellectual and physical challenges .

FXR1 and FXR2 interact with FMR1 and seem to have a related role; therefore they are likely to play important roles in the function of FMR1 and in the pathogenesis of the FXS syndrome . FXR1 is highly expressed in vertebrates muscle cells and is required for proper development of this tissue .
PglD, N-terminal (PglD_N)
Type: Domain

This α/β domain is found at the N terminus of proteins such as PglD . This domain binds a UDP-sugar substrate .
MCM, AAA-lid domain (MCM_lid)
Type: Domain

This entry represents the AAA-lid domain found in MCM proteins.

MCM proteins are DNA-dependent ATPases required for the initiation of eukaryotic DNA replication . In eukaryotes there is a family of six proteins, MCM2 to MCM7. They were first identified in yeast where most of them have a direct role in the initiation of chromosomal DNA replication by interacting directly with autonomously replicating sequences (ARS). They were thus called minichromosome maintenance proteins, MCM proteins .
STT3 subunit PglB, C-terminal domain (STT3_PglB_C)
Type: Domain

Asparagine-linked glycosylation is a post-translational modification of proteins containing the conserved sequence motif Asn-X-Ser/Thr. The attachment of oligosaccharides is implicated in diverse processes such as protein folding and quality control, organism development or host-pathogen interactions. The reaction is catalysed by oligosaccharyltransferase (OST), a membrane protein complex located in the endoplasmic reticulum. The central, catalytic enzyme of OST is the STT3 subunit, which has homologues in bacteria and archaea. Structural analysis of a bacterial OST, undecaprenyl-diphosphooligosaccharide protein glycotransferase (PglB,

), revealed two domains: a transmembrane domain and a periplasmic domain. This entry represents the C-terminal periplasmic β-barrel domain .
Sld7, N-terminal (Sld7_N)
Type: Domain

The initiation of eukaryotic chromosomal DNA replication requires the formation of an active replicative helicase at the replication origins of chromosomes. Yeast Sld3 and its metazoan counterpart treslin are the hub proteins mediating protein associations critical for formation of the helicase. The Sld7 protein interacts with Sld3, and the complex formed is thought to regulate the function of Sld3. Although Sld7 is a non-essential DNA replication protein that is found in only a limited range of yeasts, its depletion slowed the growth of cells and caused a delay in the S phase. Structure analysis indicates that the N-terminal domain of Sld7 binds to the N-terminal region of Sld3 .
Parkin, RING/Ubox like zinc-binding domain (Parkin_Znf-RING)
Type: Domain

This is a RING zinc finger domain found in parkin proteins. Parkin consists of a ubiquitin-like (Ubl) domain and a 60-amino acid linker followed by this domain RING0 and three additional zinc finger domains characteristic of the RBR family. RING0 binds two coordinated zinc atoms at each extremity of the domain with a hairpin. Deletion of RING0 massively derepressed parkin activity supporting the role of RING0 in autoinhibition, point mutations in RING0 (Phe146 to Ala) or RING2 (Phe463 to Ala) both increased parkin activity. The REP (repressor element of parkin) and RING0 domains play a preeminent role in repressing parkin ligase activity through their interactions with RING1 and RING2, respectively .
Alpha-mannosidase 2, C-terminal sub-domain (AManII_C)
Type: Domain

This is a subdomain found in the C-terminal region of golgi alpha-mannosidase II present in Drosophila melanogaster. These proteins are important in glycoprotein processing and are thought to cleave mannosidic bonds through a double displacement mechanism involving a reaction intermediate. This subdomain is found only in Diptera proteins, following the glycosyl hydrolase family 38 C-terminal domain (

) .
COI1, F-box (COI1_F-box)
Type: Domain

Jasmonates are a family of plant hormones that regulate plant growth, development and responses to stress. COI1 is an F-box protein that functions as the substrate-recruiting module of the Skp1-Cul1-F-box protein (SCF) ubiquitin E3 ligase complex. The role of COI1-mediated JAZ degradation in jasmonate (JA) signaling is analogous to auxin signaling through the receptor F-box protein transport inhibitor response 1 (TIR1) , which promotes hormone-dependent turnover of the AUX/IAA transcriptional repressors. The crystal structure of COI1 reveals a TIR1-like overall architecture, with an N-terminal tri-helical F-box motif bound to ASK1 and a C-terminal horseshoe-shaped solenoid domain formed by 18 tandem leucine-rich repeats. This entry represents the N-terminal F-box domain which is also found in other auxin signaling f-box proteins such as AFB1, AFB2 and AFB3 .
TcA receptor binding domain (TcA_RBD)
Type: Domain

Tc toxin complexes are virulence factors of many bacteria such as the insect pathogen Photorhabdus luminescens. Tc toxins are composed of TcA, TcB and TcC subunits. TcA forms a large bell-shaped pentameric structure and enters the membrane like a syringe, forming a translocation channel through which the cytotoxic domain is probably transported into the cytoplasm. TcA has four receptor-binding domains. This domain is one of 4 receptor binding domains found in TcA. All four domains have an immunoglobulin (Ig)-like β-sandwich fold of two sheets with antiparallel β-strands. The domains are structurally reminiscent of the receptor-binding domains of the diphtheria and anthrax toxins .
AAA ATPase, AAA+ lid domain (AAA_lid_3)
Type: Domain

This entry represents the α-helical AAA+ lid domain that is found to the C terminus of AAA domains.
Protein of unknown function DUF5576 (DUF5576)
Type: Family

This is a family of unknown function found in Hominidae.
Laterosporulin defensin-like peptide (Laterosporulin)
Type: Family

This entry corresponds to a bacteriocin from the bacterium Brevibacillus laterosporus called laterosporulin. This peptide has a defensin-like structure .
Desmoplakin, spectrin-like domain (Desmoplakin_Spectrin-like)
Type: Domain

Desmoplakin (DP) is an integral part of desmosomes, where it links desmosomal cadherins to the intermediate filaments. The N-terminal region of DP contains a plakin domain common to members of the plakin family. Plakin domains contain multiple copies of spectrin repeats (SRs). Spectrin repeats (SRs) consist of three α-helices (A, B, and C) that form an antiparallel triple-helical bundle. This entry describes SR6 which has a divergent structure relative to the other SRs. SR6 shows significant deviations in helices A and B where they are significantly shorter than in other repeats. Structural comparison revealed that SR6 is more similar to other three-helix-bundle proteins, including target of Myb1 and the syntaxin Habc domain, than to other SR proteins. Due to these differences with other spectrin repeats, this region is termed spectrin-like repeat .

This domain can also be found in Plectin and Dystonin.
Domain of unknown function DUF5608 (DUF5608)
Type: Domain

The structure of

, an uncharacterised protein from Pyrobaculum spherical virus, has been determined (

) . This entry represents the C-terminal domain.
NADH-rubredoxin oxidoreductase, C-terminal (Rubredoxin_C)
Type: Domain

This is the C-terminal domain of NADH rubredoxin oxidoreductase present in Clostridium acetobutylicum. The majority of obligatory anaerobes detoxify micro-aerobic environments by consuming O2 via H2O-forming NADH oxidase. This enzyme offers an alternate reaction pathway for scavenging of O2 and reactive oxygen species, wherein the reducing equivalent is obtained from NADH .
Virulence factor Evf (Evf)
Type: Domain

This entry represents a domain found in Erwinia virulence factor (Evf). The structure of this domain has been solved in the Drosophila Pathogen, Erwinia carotovora (Pectobacterium carotovorum). Evf is able to bind to model membranes containing negatively charged phospholipids and to promote their aggregation. Palmitoic acid covalently binds to the completely conserved Cys209. The structure of Evf is unlike any virulence factors known to date .
Reverse transcriptase/retrotransposon-derived protein, RNase H-like domain (RT_RNaseH_2)
Type: Domain

DNA polymerase and ribonuclease H (RNase H) activities allow reverse transcriptases to convert the single-stranded retroviral RNA genome into double-stranded DNA, which is integrated into the host chromosome during infection . This domain can also be found in animal retrotransposon-like proteins .

This entry represents the RNase H-like domain found in a group of reverse transcriptases .
PIN like domain, group 8 (PIN_8)
Type: Domain

This is a domain of unknown function, suggested to be a member of PIN like domains clan . Proteins containing this domain have been classified as clan 8 in Pfam.
Pelovaterin (Pelovaterin)
Type: Domain

The pelovaterin peptide is a major intracrystalline peptide found in turtle eggshell. The global fold of pelovaterin is similar to that of human beta-defensins. Pelovaterin exhibits strong antimicrobial activity against two pathogenic Gram-negative bacteria, Pseudomonas aeruginosa and Proteus vulgaris .
Telomerase reverse transcriptase, thumb DNA-binding domain (TERT_thumb)
Type: Domain

The catalytic subunit of telomerase is structurally similar to retroviral reverse transcriptases, viral RNA polymerases and, to a lesser extent, the bacteriophage B-family DNA polymerases. Like its structural homologues, the core catalytic subunit of telomerase, TERT, contains the fingers, palm and thumb domains required for nucleic acid and nucleotide associations as well as catalysis. The four major TERT domains: the RNA binding domain (TRBD); the fingers domain, implicated in nucleotide binding and processivity; the palm domain, which contains the active site of the enzyme; and the thumb domain, implicated in DNA binding and processivity are organized into a ring configuration similar to that observed for the substrate-free enzyme. This is the thumb domain found in Tribolium castaneum telomerase catalytic subunit, TERT. Contacts between TERT and the DNA substrate are mostly mediated via backbone interactions with the thumb loop and helix. The thumb helix sits in the minor groove of the RNA-DNA heteroduplex, making extensive contacts with the phosphodiester backbone and the ribose groups of the RNA-DNA hybrid .
Glyoxalase-like domain, group 6 (Glyoxalase_6)
Type: Domain

This entry comprises a diverse set of domains related to the Glyoxalase domain. The exact specificity of these proteins is uncertain .
Tetracyclin repressor-like, C-terminal, group 31 (TetR_C_31)
Type: Domain

This is the C-terminal domain found in putative transcriptional regulator, TetR family proteins. Proteins containing this domain have been classified as group 31 in Pfam.
Predicted pPIWI-associating nuclease, group 2 (Put_pPIWI_pnuc_2)
Type: Domain

This entry represent the predicted nuclease effector domain associating with prokaryotic PIWI-centred conflict systems . Proteins containing this domain have been classified as group 2 in Pfam.
LepB GAP domain, N-terminal subdomain (LepB_GAP_N)
Type: Domain

This is a subdomain of a Rab GTPase-activating protein (GAP) effector from??Legionella pneumophilia. This GAP modulates Rab enzymes that act as molecular switches in regulating vesicular transport in eukaryotic cells. This N-terminal subdomain belongs to the the GAP domain of the protein. The catalytic arginine finger (Arg444) is located within this sub-domain and it is the only arginine residue required for GAP activity .
PsrA, tetracyclin repressor-like, C-terminal domain (PsrA_TetR_C)
Type: Domain

This entry represents the C-terminal domain present in the Pseudomonas aeruginosa PsrA which regulates the fadBA5 beta-oxidation operon. Functional analysis of PsrA indicated its importance in regulating b-oxidative enzymes . It has also been suggested that PsrA, a member of the TetR family of repressors, could affect global gene expression including activation of rpoS .

TetR family regulators are involved in the transcriptional control of multidrug efflux pumps, pathways for the biosynthesis of antibiotics, response to osmotic stress and toxic chemicals, control of catabolic pathways, differentiation processes, and pathogenicity . The TetR proteins identified in overm ultiple genera of bacteria and archaea share a common helix-turn-helix (HTH) structure in their DNA-binding domain. However, TetR proteins can work in different ways: they can bind a target operator directly to exert their effect (e.g. TetR binds Tet(A) gene to repress it in the absence of tetracycline), or they can be involved in complex regulatory cascades in which the TetR protein can either be modulated by another regulator or TetR can trigger the cellular response . TetR regulates the expression of the membrane-associated tetracycline resistance protein, TetA, which exports the tetracycline antibiotic out of the cell before it can attach to the ribosomes and inhibit protein synthesis . TetR blocks transcription from the genes encoding both TetA and TetR in the absence of antibiotic. The C-terminal domain is multi-helical and is interlocked in the homodimer with the helix-turn-helix (HTH) DNA-binding domain .
Pesticidal crystal protein Cry, domain V (Cry_V)
Type: Domain

This entry represents a domain is found in the protoxin portion of insecticidal proteins (parasporins, or Cry proteins) such as Cry1Ac from Bacillus thuringiensis (Bt). These proteins contain a proteolytically labile protoxin segment (in the C-terminal region) and a three-domain toxic core at the N terminus (domains I-III). This entry describes domain V, one of the four protoxin domains (domains IV-VII). Domains V and VII are β-rolls (similar to domain II or III) that closely resemble carbohydrate-binding modules found in sugar hydrolases. However, it is unclear which particular carbohydrates (if any) may serve as their ligands because residues on the putative sugar-binding interfaces are conserved neither in sequence nor in local structure. Structural analysis of Bt Cry1Ac indicates that there are putative disulfide crosslinks at the dimer interface mediated by cysteines within region 783-823 of this domain. Together with other cysteines, these create a three-dimensional network of cross-links across the crystal which may play a role in stabilizing mature Bt Cry1Ac .
Integrase zinc-binding domain (Integrase_H2C2)
Type: Domain

This zinc-binding domain is found in a wide variety of integrase proteins.
Dynein heavy chain 3, AAA+ lid domain (DNAH3_AAA_lid_1)
Type: Domain

This domain represents the AAA lid domain from dynein heavy chain 3 and related proteins .
O-phosphoserine--tRNA(Cys) ligase, C-terminal domain (SepRS_C)
Type: Domain

This domain is mainly found in Archaea. The domain makes up part of the anticodon binding domain at the C-terminal of O-phosphoserine--tRNA(Cys) ligase .
OCRE domain (OCRE)
Type: Domain

The OCtamer REpeat (OCRE) has been annotated as a 42-residue sequence motif with 12 tyrosine residues in the spliceosome trans-regulatory elements RBM5 and RBM10 (RBM [RNA-binding motif]), which are known to regulate alternative splicing of Fas and Bcl-x pre-mRNA transcripts . The structure of the domain consists of an anti-parallel arrangement of six β strands.
Inorganic pyrophosphatase domain (Inorganic_Pase)
Type: Domain

This entry represents the type I inorganic pyrophosphatase domain that is found in polyvalent proteins .
RNA ligase Pab1020, C-terminal domain (Lig_Pab1020_C)
Type: Domain

This is the C-terminal region of RNA ligase Pab1020 present in Pyrococcus abyssi. Pab1020 catalyzes the nucleotidylation of oligo-ribonucleotides in an ATP-dependent reaction. This region contains both a dimerization domain and a C-terminal domain .
L,D-transpeptidase C-terminal domain (Ldt_C)
Type: Domain

This is the C-terminal domain found in L,D-transpeptidases (Ldt) homologues from E.coli. Three of these enzymes (YbiS, ErfK, YcfS) have been shown to cross-link Braun's lipoprotein to the peptidoglycan (PG), while the other two (YnhG, YcbB) form direct meso-diaminopimelate (DAP-DAP, or 3-3) cross-links within the PG. Family members include erfK (ldtA), ybiS (ldtB), ycfS (ldtC), and ynhG (ldtE) .
Methionine--tRNA ligase, N-terminal (MARS_N)
Type: Domain

This is the N-terminal (GST-N) domain containing a thioredoxin fold. This domain can be found in methionyl-tRNA synthetase (MetRS), a multi-tRNA synthetase complex (MSC) component .
Phage protein Gp138 N-terminal domain (Gp138_N)
Type: Domain

This domain is found at the N terminus of gene product 138 (gp138) in bacteriophage phi92. Gp138 is thought to be involved in the process of opening the host cell membrane during infection. The domain has an OB-fold with an intramolecular disulfide bond between C114 and C120 .
Effector immunity protein Tgi2PP (Tgi2PP)
Type: Domain

Tgi2PP from Pseudomonas protegens is part of the Tge2PP- Tgi2PP Effector-immunity pair secreted by the type VI secretion system (T6SS). Tgi2PP interacts predominantly by hydrogen bonding and hydrophobic interactions with Tge2PP via the insertion of the β-sheet core of Tgi2PP into the substrate-binding groove of Tge2PP. Tgi2PP contains a similar topology to the periplasmic E. coli colicin M immunity protein .
Fluorescence recovery protein (FRP)
Type: Family

This entry represents the fluorescence recovery protein (FRP), the structure of which has been solved for the cyanobacteria Synechocystis (PDBe:4JDQ).

Cyanobacteria contain antenna complexes called phycobilisomes, which are quenched by orange carotenoid protein (OCP) under high light conditions. FRP causes the dissociation of OCP from the phycobilisomes by interacting with the C-terminal domain of OCP, accelerating the conversion of the active red OCP (OCPr) to the inactive orange form (OCPo). A patch of residues (W50, D54, H53, and R60) contributed by both chains of the FRP dimer cause the acceleration of the OCPr to OCPo conversion. Mutation of the absolutely conserved amino acid (R60) affects the activity of FRP .
Quercetin 2,3-dioxygenase, C-terminal cupin domain (Quercetinase_C)
Type: Domain

This entry represents the C-terminal domain of quercetin 2,3-dioxygenase (also known as quercetinase), such as the YhhW protein from E. coli. This is one of the two cupin domains that make up the protein . Proteins containing this domain also include the Pirin-like protein, YhaK, from E. coli .
YvdT, C-terminal (YvdT_C)
Type: Domain

This entry represents the C-terminal domain present in putative HTH-type transcriptional regulator YvdT.