SII-SWORD/CoKE huggingface dataset:
IcaR, C-terminal (IcaR_C)
Type: Domain

IcaR belongs to the tetracycline repressor (TetR) family of proteins, which are involved in a wide variety of gene regulations. It binds to a 42 bp region immediately upstream of the icaA gene. This entry represents the C-terminal domain which is involved in dimerization .
Inward rectifier potassium channel, C-terminal (IRK_C)
Type: Domain

This entry represents the C-terminal domain of inward rectifier potassium channel. This cytoplasmic domain has an Ig fold .
Rank, cysteine-rich repeat domain 2 (RANK_CRD_2)
Type: Domain

This domain is found in the receptor activator of the NF-KB (RANK) present in Mus musculus. RANK and its cognate ligand RANKL play a role in bone remodelling, immune function and mammary gland development in conjunction with various cytokines and hormones. The binding of RANKL to RANK causes trimerisation of the receptor, which activates the signalling pathway and results in osteoclastogenesis from progenitor cells and the activation of mature osteoclasts receptor activator of the NF-KB. This domain is the second of four cysteine rich pseudo-repeat domains (CRDs) and so is known as CRD2. RANK moves via a hinge region between CRD2 and CRD3 to make close contact with RANKL .
Anti-sigma factor NepR (NepR)
Type: Domain

The general stress response sigma factor in alphaproteobacteria, sigma EcfG is inactivated by the anti-sigma factor NepR, which is itself regulated by the response regulator PhyR. NepR forms two helices that extend over the surface of the PhyR subdomains. Homology modeling and comparative analysis of NepR, PhyR and sigmaEcfG mutants indicate that NepR contacts both proteins with the same determinants, showing sigma factor mimicry at the atomic level. This entry represents NepR domains found in alphaproteobacteria .
Swt1-like HEPN (HEPN_Swt1)
Type: Domain

This HEPN domain might have a role in binding and sensing unspliced pre-mRNAs that are specifically targeted by the Swt1 nuclease at the nuclear envelope .
Domain of unknown function DUF5610 (DUF5610)
Type: Domain

This is a domain of unknown function found in bacterial proteins.
Domain of unknown function DUF5616 (DUF5616)
Type: Domain

This domain is found in a number of prokaryotic proteins. It is mostly found fused with the N-terminal domain. This C-terminal domain is suggested to be a PIN like domain .
Importin repeat 4 (Importin_rep_4)
Type: Repeat

The importin subunit beta-3 has a superhelical structure composed of tandem repeats structurally similar to HEAT repeats . This entry includes a single repeat unit.
Styrene monooxygenase StyA, putative substrate binding domain (StyA_sbd)
Type: Domain

This domain is found in the 46kDa FAD-specific styrene epoxidase (SMOA, also known as StyA) protein, comprises a part of the styrene monooxygenase (SMO) two-component flavoprotein monooxygenase enzyme. Structural analysis indicates that SMOA monomer comprises two globular domains spanned by a long α-helix. This domain contains a putative substrate binding site .
Domain of unknown function DUF5607 (DUF5607)
Type: Domain

The structure of this domain in Pyrobaculum spherical virus has been determined (PDB:2X4J) .
Tetratrico peptide repeat, group 5 (TPR_5)
Type: Domain

BH0479 of Bacillus halodurans is a hypothetical protein which contains a tetratrico peptide repeat (TPR) structural motif. The TPR motif is often involved in mediating protein-protein interactions. This protein is likely to function as a dimer. The first 48 amino acids are not present in the clone construct. This entry represents the tetratricopeptide-like repeats classified as TPR_5 in Pfam.
Helix-turn-helix domain, group 17 (HTH_17)
Type: Domain

This domain is a DNA-binding helix-turn-helix domain. It has been classified as group 17 in Pfam. It can be found in excisionase, such as Xis from Salmonella phage P22 .
Dynein heavy chain AAA lid domain (AAA_lid_11)
Type: Domain

This family represents the AAA lid domain found near the C-terminal region of dynein heavy chain.
Argonaute, PAZ domain, Aquifex (Paz_1)
Type: Domain

This is a Paz domain found in Argonaute proteins from Aquifex aeolicus bacteria. The PAZ core fold in Aquifex aeolicus bacteria Ago (Aa-Ago) proteins is closely related to the human hAgo1 PAZ domain . Structural and functional studies of Aa-Ago indicate that conformational rearrangement of the PAZ domain may be critical for the catalytic cycle of Argonaute and the RNA-induced silencing complex .
ZN622/Rei1/Reh1, zinc finger C2H2-type (ZN622/Rei1/Reh1_Znf-C2H2)
Type: Domain

This domain contains two copies of a C2H2-like zinc finger. Proteins containing this domain include cytoplasmic 60S subunit biogenesis factor ZNF622 from animals , Reh1 and Rei1 from budding yeasts, and core trichothecene cluster protein 15 (TRI15) from Fusarium.

Cytoplasmic 60S subunit biogenesis factor ZNF622, Reh1 and Rei1 are involved in maturation of the large (60S) ribosomal subunit. Rei1 is required for re-importing the 60S subunit export factor Arx1 from the cytoplasm to the nucleus, and both Reh1 and Rei1 are required for cytoplasmic maturation of the 60S subunit, that the two proteins have redundant functions, but without both the 6OS subunit is labile to salt .
SusD-like 2 (SusD-like_2)
Type: Family

SusD is a secreted starch-binding protein with an N-terminal lipid tail that allows it to associate with the outer membrane . This entry represents a group of SusD homologues that has been classified as SusD-like 2 in Pfam.
DisA/LigA, helix-hairpin-helix motif (DisA/LigA_HHH)
Type: Domain

This HhH domain is a DNA-binding domain . It can be found in bacterial checkpoint control protein DisA, NAD-dependent DNA ligase LigA, UvrABC system protein C and in the ATP-dependent DNA helicase Hel308 (also known as HelQ) .

DNA integrity scanning protein (DisA) participates in a DNA-damage check-point that is active prior to asymmetric division when DNA is damaged. DisA forms globular foci that rapidly scan along the chromosomes during sporulation, searching for lesions. When a lesion is present, disA pauses at the lesion site. This triggers a cellular response that culminates in a temporary block in sporulation initiation .
Orc1-like, AAA ATPase domain (AAA_16)
Type: Domain

This domain contains a P-loop motif that is characteristic of the AAA superfamily. This domain has been classified as AAA_16 in Pfam and can be found in the Origin Recognition Complex (ORC) subunits and serine/threonine-protein kinase PknK.
Cupin-like domain 8 (Cupin_8)
Type: Domain

This cupin-like domain shares similarity to the JmjC domain.
Rh5 coiled-coil domain (Rh5_CC)
Type: Domain

This is a helical coiled-coil domain found in reticulocyte-binding protein homologue 5 (RH5), a Plasmodium falciparum protein essential for erythrocyte invasion .
Tetracyclin repressor SlmA-like, C-terminal domain (TetR_C_15)
Type: Domain

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.

This entry represents the C-terminal domain found in a number of different TetR transcription regulator proteins including SlmA proteins found in E. coli. Unlike other TetR proteins, SlmA functions not as a transcription regulator but rather as an NO (nucleoid occlusion) factor . 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 .
Zinc knuckle (Znf-CCHC_6)
Type: Domain

This Zinc knuckle is found in FAM90A and transcription initiation factor TFIID proteins.
Csm1 N-terminal domain (Csm1_N)
Type: Domain

In the budding yeast Saccharomyces cerevisiae, sister chromatid co-orientation in meiosis I depends on the four-protein monopolin complex (Mam1, Csm1, Lrs4, and Hrr25/casein kinase 1), which localizes to centromeres from meiotic prophase through metaphase I. Csm1 and Lrs4, form a complex that resides in the nucleolus during interphase and relocalizes to centromeres during meiotic prophase, accompanied by phosphorylation of Lrs4. This is the N-terminal domain of Csm1 which forms a coiled-coil .
Bap31/Bap29 cytoplasmic coiled-coil domain (Bap31/Bap29_C)
Type: Domain

Bap31 is a polytopic integral protein of the endoplasmic reticulum membrane and a substrate of caspase-8. Bap31 is cleaved within its cytosolic domain, generating pro-apoptotic p20 Bap31 . This entry represents the cytoplasmic domain which forms a heterodimeric coiled-coil with Bap29 . Bap29 and Bap31 are homologous to each other and this entry includes both proteins.
Tetracyclin repressor-like, C-terminal domain 23 (TetR_C_23)
Type: Domain

This is a C-terminal domain present in putative TetR family transcriptional regulators found in bacteria. This entry is a member of a Pfam clan for the TetR superfamily.
Tetracyclin repressor SCO1712-like, C-terminal domain (TetR_C_22)
Type: Domain

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 over multiple 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 .

This entry represents the C-terminal domain present the TetR Transcriptional Repressor present in sco1712 proteins from Streptomyces coelicolor which act as a regulator of antibiotic production .
Pleckstrin homology domain 5 (PH_5)
Type: Domain

This Pleckstrin homology domain is found in fungal Rho1 guanine nucleotide exchange factors. It is a member of a pfam clan whose members share a PH-like fold.
DNA2/NAM7 helicase, helicase domain (DNA2/NAM7_AAA_11)
Type: Domain

This domain contains the ATP-binding region of DNA2. DNA2 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Proteins containing this domain also include Nam7 and other helicases. Dna2 is a DNA replication factor with single-stranded DNA-dependent ATPase, ATP-dependent nuclease, (5'-flap endonuclease) and helicase activities . Nam7 (also known as Upf1) is an ATP-dependent RNA helicase involved in the nonsense-mediated mRNA decay (NMD) pathway . This domain is known as AAA_11 in Pfam.
Tetracyclin repressor-like, C-terminal domain 16 (TetR_C_16)
Type: Domain

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.

This entry represents the C-terminal domain found in a number of different TetR transcription regulator proteins found mainly in Actinobacteria . 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 .
DNA2/NAM7 helicase-like, C-terminal (DNA2/NAM7-like_C)
Type: Domain

This domain contains a P-loop motif that is characteristic of the AAA superfamily. Proteins containing this domain are DEAD-like helicases belonging to superfamily (SF)1, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF2 helicases, SF1 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA .

Proteins containing this domain include helicases, such as Dna2 and Nam7. Dna2 is a DNA replication factor with single-stranded DNA-dependent ATPase, ATP-dependent nuclease, (5'-flap endonuclease) and helicase activities . Nam7 (also known as Upf1) is an ATP-dependent RNA helicase involved in the nonsense-mediated mRNA decay (NMD) pathway .
Pleckstrin homology domain 8 (PH_8)
Type: Domain

This entry represents a pleckstrin domain found in some oxysterol-binding protein-related proteins. It belongs to a pfam clan whose members share a PH-like fold.
Pleckstrin homology domain 9 (PH_9)
Type: Domain

This pleckstrin homology domain belongs to a pfam clan whose members share a PH-like fold.
AAA domain, group 14 (AAA_14)
Type: Domain

This domain contains a P-loop motif that is characteristic of the AAA superfamily. It is known as AAA_14 in Pfam.
PHD/FYVE-zinc-finger like domain (Znf-PHD-like)
Type: Domain

This domain appears to be a combination of several consecutive zinc-binding regions.
Endonuclease GajA/Old nuclease/RecF-like, AAA domain (AAA_GajA/Old/RecF-like)
Type: Domain

This domain contains a P-loop motif that is characteristic of the AAA superfamily. Proteins containing this domain include the homologues of RecF, which may be involved in DNA metabolism , structural maintenance of chromosomes proteins (SMCs), including nuclease SbcCD subunit C and OLD nucleases . This domain is also found at the N-terminal of endonuclease GajA, a component of antiviral defense system Gabija type I taht confers resistance to phages phi105, phi29, rho14, SpBeta and SBSphiC. It is an endonuclease that nicks dsDNA within the sequence 5'-TNNNCGGGNNA-3' in the absence of nucleotides (NTP, dNTP and NDPs). This domain no detected ATPase activity in GajA .
Zinc-finger CCCH domain (Znf-CCCH_3)
Type: Domain

This zinc-finger containing domain is found in eukaryotes.

Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates . Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few . Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target.
IprA, winged helix-turn-helix domain (HTH_46)
Type: Domain

This winged helix-turn-helix DNA-binding domain is found in IprA, a protein involved in oxidative stress resistance in Proteobacteria .
Orotate phosphoribosyltransferase-like (PRTase_2)
Type: Domain

This phosphoribosyl transferase (PRTase) domain is related to OPRTases , and are predicted to use orotate as substrate. These genes are found in the biosynthetic operon associated with the Ter stress-response operon and are predicted to be involved in the biosynthesis of a ribo-nucleoside involved in stress response .
Gamma-aminobutyric acid type B receptor subunit 2, coiled-coil domain (GBR2_CC)
Type: Domain

This is the intracellular coiled-coil domain found in Gamma-aminobutyric acid type B receptor subunit 2 (GBR2). The coiled-coil complex between the GABAB receptor subunits GBR1 and GBR2 is responsible for facilitating the surface transport of the intact receptor. Disruption of the hydrophobic coiled-coil interface with single mutations in either subunit impairs surface expression of GBR1, confirming that the coiled-coil interaction is required to inactivate the adjacent ER retention signal of GBR1 .
Cadherin-like domain (Cadherin_5)
Type: Domain

This cadherin-like domain is found in a variety of uncharacterised proteins.
Atg6/beclin, coiled-coil domain (Atg6/beclin_CC)
Type: Domain

In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells . Apg6, also known as Atg6 or Vps30p, has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway .

Beclin 1, the mammalian homologue of yeast Atg6/Vps30, is a tumour suppressor that coordinately regulates the autophagy and membrane trafficking involved in several physiological and pathological processes .
HHH domain 9 (HHH_9)
Type: Domain

This domain is part of a pfam clan of helix-hairpin-helix DNA-binding domains.
Glycosyl-transferase family 4_5 (Glyco_trans_4_5)
Type: Family

This family belongs to the Pfam clan GT-B that contains diverse glycosyltransferases that possess a Rossmann-like fold.
Oxidoreductase, N-terminal domain (ADH_N_2)
Type: Domain

This is the N-terminal domain of prostaglandin reductase and other oxidoreductases.
Glutathione S-transferase, C-terminal domain (GST_C_5)
Type: Domain

Leishmania major and Trypanosoma cruzi glutathione-S-transferase (GST) has undergone gene duplication, diversification, and gene fusion leading to an four domain enzyme which contains two repeats of a GST N-terminal domain followed by a GST C-terminal domain .
Bacteroidetes PKD-like domain (PKD_3)
Type: Domain

This PKD-like domain is found in various Bacteroidetes species.
Zinc-finger C2H2-type 11 (Znf-C2H2_11)
Type: Domain

This entry represents a zinc-finger of C2H2 type found in higher eukaryotes. It includes classical and closely related C2H2 or β-β-α zinc finger DNA-binding domains.
Methyltransferase domain 25 (Methyltransf_25)
Type: Domain

This is a methyltransferase domain, member of a Pfam clan that includes Rossmann-fold domains.
Lon protease, AAA domain (AAA_32)
Type: Domain

This entry includes a wide variety of AAA domains including some that have lost essential nucleotide binding residues in the P-loop. It is found in Lon proteases from bacteria and archaea.
Outer membrane protein beta-barrel domain 3 (OMP_b-brl_3)
Type: Domain

This domain is found in proteins annotated as TonB dependent receptors, but it is also likely to be found in other membrane β-barrel proteins with other functions. It is part of a Pfam clan that includes other outer membrane protein β-barrel domains.
Methionine import ATP-binding protein MetN, ATP-binding domain (MetN_ABC)
Type: Domain

MetN (also known as YusC) is an ABC-type transporter encoded by metN of the metNPQ operon in Bacillus subtilis that is involved in methionine transport. Other members of this system include the MetP permease and the MetQ substrate binding protein . ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins .
Magnesium-chelatase BchD/ChlD, VWA domain (BchD/ChlD_VWA)
Type: Domain

Magnesium chelatase catalyses the insertion of Mg into protoporphyrin IX (Proto). In chlorophyll biosynthesis, insertion of Mg2+ into protoporphyrin IX is catalysed by magnesium chelatase in an ATP-dependent reaction. The Mg-chelatase subunits are designated ChlI, ChlD and ChlH in plants and BchI, BchD and BchH in bacteriochlorophyll synthesis. BchD contains a AAA domain at its N terminus and a VWA domain at its C terminus. The VWA domain has been speculated to be involved in mediating protein-protein interactions. This entry represents the VWA domain found in bacterial BchD and plant ChlD .
Transcription termination factor Rho, ATP binding domain (Rho_factor_ATP-bd)
Type: Domain

Transcription termination factor rho is a bacterial ATP-dependent RNA/DNA helicase. It is a homohexamer . Each monomer consists of an N-terminal domain of the OB fold, which is responsible for binding to cysteine rich nucleotides. This entry represents the C-terminal ATP binding domain .
CFLE, GH18 catalytic domain (CFLE_GH18)
Type: Domain

Cortical fragment-lytic enzyme (CFLE) is a peptidoglycan hydrolase involved in bacterial endospore germination. CFLE is expressed as an inactive preprotein (called SleB) in the forespore compartment of sporulating cells. SleB translocates across the forespore inner membrane and is deposited as a mature enzyme in the cortex layer of the spore. As part of a sensory mechanism capable of initiating germination, CFLE degrades a spore-specific peptidoglycan constituent called muramic-acid delta-lactam that comprises the outer cortex. CFLE has a C-terminal glycosyl hydrolase family 18 (GH18) catalytic domain as well as two N-terminal LysM peptidoglycan-binding domains. In addition to SleB, proteins containing this domain also includes YaaH, YdhD, and YvbX from Bacillus subtilis .