SII-SWORD/CoKE huggingface dataset:
YhfZ, helix-turn-helix domain (HTH_41)
Type: Domain

This helix-turn-helix domain is found in uncharacterized protein YhfZ from E. coli and in other bacterial proteins.
RuvB, AAA lid domain (AAA_lid_4)
Type: Domain

The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair. Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein . This entry contains the AAA lid domain that is found to the C terminus of the AAA domain.
Mannosidase Ig/CBM-like domain (Mannosidase_ig)
Type: Domain

This domain corresponds to domain 4 in the structure of Bacteroides thetaiotaomicron beta-mannosidase, BtMan2A . This domain has an Ig-like fold.
Tumor necrosis factor receptor member 16, transmembrane domain (TNFR16_TM)
Type: Domain

This is the helical trans-membrane domain found in tumor necrosis factor receptor superfamily member 16 (also known as p75 neurotrophin receptor , and nerve growth factor receptor-NGFR). p75 plays prominent biological functions such the induction of cell death, and it demonstrates several other activities, like survival, axonal growth, and cell migration. The trans-membrane (TM) domain of p75 stabilizes the receptor dimers through a disulfide bond, essential for the NGF signalling Structural and mutational analysis indicate that Cys257 plays the key role in this stabilisation process. Furthermore, although the p75-C257A mutant is still capable to form dimers and bind to NGF, it is unable to transduce the signals triggered by NGF binding in some cell signalling paradigms .
Phosphoserine phosphatase, N-terminal (SerB_N)
Type: Domain

This entry represents the N-terminal domain of phosphoserine phosphatases, which catalyzes the dephosphorylation of phosphoserine (P-Ser). It also catalyzes the hydrolysis of phosphothreonine (P-Thr) .
ToxB-like N-terminal, ascomycota (ToxB-like_N_ascomy)
Type: Domain

This entry includes the N-terminal domain of ToxB and other similar proteins found in ascomycota. This domain has been shown to be crucial for toxin activity. There are two amino acid differences between ToxB and toxb, an inactive homologue of ToxB. These two differences are a Val at position 3 in ToxB compared to a Thr in toxb, and an Ala at position 12 in ToxB compared to a Val in toxb. Both ToxB and Toxb are matched by this entry. AvrPiz-t, a secreted avirulence protein produced by the rice blast fungus, is a structural homologue to ToxB .
ATP-dependent RecD2 DNA helicase, SH3 domain (RecD2_SH13)
Type: Domain

This is an SH3 (SRC homology domain 3) domain found in ATP-dependent RecD2 DNA helicase and related sequences (

) that belong to the bacterial Superfamily 1B (SF1B). This superfamily of helicases translocate in a 5'-3' direction and are required for a range of cellular activities across all domains of life . Studies of RecD in E. coli revealed that the SH3 domain interacts with the ssDNA tail in a location different to that normally occupied by a peptide in canonical eukaryotic SH3 domains, thus retaining the potential to bind peptide at the same time as the ssDNA tail . RecD2 may favor replication restart by preventing RecA from binding to blocked replication forks, avoiding unnecessary recombination during replication restart. It acts as a negative modulator of the RecA-ssDNA filament, it may disassemble RecA threads, and can act as both a positive and negative regulator of strand exchange .
APAF-1 helical domain (APAF1_C)
Type: Domain

This domain represents the C-terminal α helical domain of the apoptotic protease-activating factor 1 (Apaf-1) .
Suv3, N-terminal (Suv3_N)
Type: Domain

This is the N-terminal domain of Suv3 from animals. Suv3 is an NTP-dependent RNA/DNA helicase that is necessary for the degradation of mature mtRNAs. Suv3 has been found to interact in vitro with polynucleotide phosphorylase .
BsuBI/PstI restriction endonuclease, HTH domain (BsuBI/PstI_N)
Type: Domain

This entry represents the N terminus of bacterial enzymes similar to type II restriction endonucleases BsuBI and PstI (

). The enzymes of the BsuBI restriction/modification (R/M) system recognise the target sequence 5'CTGCAG and are functionally identical with those of the PstI R/M system .
CxC2-like cysteine cluster, KDZ transposase-associated (CxC2_KDZ-assoc)
Type: Domain

This is a predicted Zinc chelating domain present N-terminal to the KDZ transposase domain .
Rv3651-like, N-terminal (Rv3651-like_N)
Type: Domain

This domain is found in Rv3651 from Mycobacterium tuberculosis (

) and similar proteins from Actinobacteria. Rv3651 adopts a three-domain configuration. This entry represents the N-terminal domain, a GAF domain that shows a central antiparallel β-sheet of six β-strands .
Polyvalent protein, metallopeptidase domain (MPTase-PolyVal)
Type: Domain

Polyvalent proteins are predicted to be transmitted by genomic parasites such as conjugative elements, plasmids, and phages during the initial phase of infection along with their DNA. They are typified by the presence of multiple domains with disparate activities .

A predicted endoRNase of the Barnase-EndoU-ColicinE5/D-RelE like nuclease fold found in polyvalent proteins of phages and conjugative elements. The predicted active site contains a conserved histidine and threonine residues .
Molybdopterin oxidoreductase, N-terminal (Molybdopterin_N)
Type: Domain

This is the N-terminal domain of molybdopterin-containing oxidoreductase, such as dimethyl sulfoxide/trimethylamine N-oxide reductase, also known as DMSO reductase .
CdvA-like coiled-coil domain (CdvA_CC)
Type: Domain

This is a coiled coil region domain related to cell division CdvA-like proteins .
Bacterial Alpha-2-macroglobulin, MG6 domain (Bact_A2M_MG6)
Type: Domain

This macroglobulin domain is found in bacterial alpha 2 macroglobulin proteins. It adopts an Ig-like β sandwich fold .
LidA long coiled-coil domain (LidA_long_CC)
Type: Domain

LidA, another Rab1-interacting bacterial effector protein , is translocated by Legionella into the host cytosol at the beginning of infection, and it localized to the Legionella-containing vacuole (LCV) at the cytosolic surface . It has been shown that tight interaction with Rab1 allows LidA to facilitate the Legionella targeting factor (DrrA/SidM)-catalyzed release of Rab1 from GDP dissociation inhibitors (GDI) . The base of the protein is formed by two antiparallel coiled-coil structures forming a long coiled-coil domain. This region of LidA interacts with switch and interswitch regions of Rab1 the nucleotide binding pocket of Rab8a , hence blocking access to the GDP/GTP-binding site to a great extent .
TubC, N-terminal docking domain (TubC_N)
Type: Domain

This is the N-terminal docking domain (also termed the amino acid adenylation domain) found in TubC proteins from the tubulysin polyketide synthase and nonribosomal polypeptide synthetase (PKS-NRPS) system, which binds to C-terminal docking domain of TubB . This domain can also be found at the N terminus of bacitracin synthase 2 (BacB) from Bacillus licheniformis and Pyochelin synthetase PchF from Pseudomonas aeruginosa.
SfsA, N-terminal OB domain (SfsA_N)
Type: Domain

This entry represents the N-terminal OB fold found in sugar fermentation stimulation protein (SfsA), which is probably a regulatory factor involved in maltose metabolism. SfsA has been shown to bind DNA .
Dynein heavy chain, AAA 5 extension domain (Dynein_AAA5_ext)
Type: Domain

This entry corresponds to the extension domain of AAA domain 5 in the dynein heavy chain . This domain is composed of 8 α-helices .
HTH-type transcriptional repressor Sco4008, C-terminal (Sco4008_C)
Type: Domain

This entry represents the C-terminal domain found in Sco4008, which is suggested to be a transcriptional repressor of Sco4007 responsible for the multidrug resistance system in S. coelicolor A3 .

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 .
ParB/Spo0J, HTH domain (HTH_ParB/Spo0J)
Type: Domain

This entry represents the HTH domain found in ParB and its homologue, Spo0J .

ParB plays a vital role in chromosome partitioning and nucleoid occlusion. These proteins are essential for ensuring proper chromosome segregation during cell division by binding to the DNA origin of replication and localising to both poles of the predivisional cell following DNA replication. ParB proteins share significant sequence and structural similarity with Sulfiredoxin (Srx), a sulfinic acid reductase identified in eukaryotes. Sequence comparison and phylogenetic analysis of the Srx and ParB protein families suggest that Srx evolved via truncation of ParB, resulting in the removal of the entire C-terminal half of the protein including the HTH domain . ParB comprises three highly conserved domains: an N-terminal nucleotide-binding domain (NBD)

, a central helix-turn-helix parS-binding domain

, non-structured linker region, and a C-terminal dimerisation domain

that tightly links the two subunits of the ParB dimer .
Subtilisin-like protease, fibronectin type-III domain (Subtilisin-like_FN3)
Type: Domain

This FN3 (fibronectin type-III) like domain is found at the C terminus of subtilisin-like proteases, such as the cucumisin protein .
Gamma tubulin complex component protein, N-terminal (GCP_N)
Type: Domain

This is the N-terminal domain found in components of the gamma-tubulin complex proteins (GCPs). Proteins containing this domain include spindle pole body (SBP) components such as Spc97 and Spc98 which function as the microtubule-organizing centre in yeast . Proteins containing this domain also include human GCP4 (Gamma-tubulin complex component 4), which has been structurally elucidated .

Functional studies have shown that the N-terminal domain defines the functional identity of GCPs, suggesting that all GCPs are incorporated into the helix of gamma-tubulin small complexes (gTURCs) via lateral interactions between their N-terminal domains. Thereby, they define the direct neighbours and position the GCPs within the helical wall of gTuRC . Sequence alignment of human GCPs based on the GCP4 structure helped delineate conserved regions in the N- and C-terminal domains . In addition to the conserved sequences, the N-terminal domains carry specific insertions of various sizes depending on the GCP, i.e. internal insertions or N-terminal extensions. These insertions may equally contribute to the function of individual GCPs as they have been implied in specific interactions with regulatory or structural proteins. For instance, GCP6 carries a large internal insertion phosphorylated by Plk4 and containing a domain of interaction with keratins, whereas the N-terminal extension of GCP3 interacts with the recruitment protein MOZART1 .
UvrB, interaction domain (UvrB_inter)
Type: Domain

This domain is found in the UvrB protein where it interacts with the UvrA protein . This domain can also be found at the N terminus of the transcription-repair-coupling factor Mfd.
BL00235/CARNS1, N-terminal (BL00235/CARNS1_N)
Type: Domain

This is the N-terminal domain found in BL00235 present in Bacillus licheniformis. BL00235 is a ATP-grasp superfamily protein that catalyzes the formation of an alpha-peptide bond between two L-amino acids in an ATP-dependent manner. BL00235 has a highly restricted substrate specificity: the N-terminal substrate is confined to L-methionine an L-leucine, while the C-terminal substrates include small residues such as L-alanine, L-serine, L-threonine and L-cysteine .

This domain can also be found in human CARNS1 (also known as ATPGD1) protein, which catalyzes the synthesis of carnosine and homocarnosine .
CtsR, C-terminal dimerization domain (CtsR_C)
Type: Domain

This entry corresponds to the C-terminal dimerization domain of CtsR. CtsR of L. monocytogenes negatively regulates the clpC, clpP and clpE genes belonging to the CtsR regulon .
HTH-type transcriptional repressor NicS, C-terminal (NicS_C)
Type: Domain

This domain can be found at the C terminus of NicS, a HTH-type transcriptional repressor for the nicAB operon, encoding the upper aerobic nicotinate degradation pathway . The C-terminal domain can be found in a number of different TetR transcription regulator proteins. It is multi-helical and is interlocked in the homodimer with the helix-turn-helix (HTH) DNA-binding domain.
His-Me finger endonuclease, beta4-alpha2 domain (His_Me_b4a2)
Type: Domain

This domain is found in Hpy991 present in Helicobacter pylori. Hpy991 is a β-β-α-Me restriction endonuclease that recognises the CGWCG target sequence and cleaves both DNA strands with a stagger that leads to 5'-recessed ends in the cleavage products. This domain is the first of two beta4-alpha2 repeats found after the N-terminal domain. The two repeats have low overall sequence similarity but readily identified by a structural comparison. Both repeats contain two CXXC motifs that map to the first β-hairpin and the first α-helix. The four cysteine residues coordinate a structurally bound Zn2+ ion tetrahedrally. The major groove is in contact with the first repeat, with the β-hairpin 2 inserting deeply into the groove .
TRAF3-interacting protein 1, C-terminal domain (TRAF3IP1_C)
Type: Domain

TRAF3IP1, also known as MIP-T3, which interacts with both microtubules and TRAF3 (tumour necrosis factor receptor-associated factor 3), 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 .
Domain of unknown function DUF5577 (DUF5577)
Type: Domain

This domain is found in uncharacterised proteins from Metazoa.
Tetracyclin repressor-like, C-terminal domain 27 (TetR_C_27)
Type: Domain

This is a C-terminal domain present in putative TetR transcriptional regulators. It is part of a clan that features transcriptional regulators for multidrug efflux pumps, which belong to the TetR superfamily. They are induced by the presence of a variety of factors, such as antibiotics or organic solvents. The C-terminal region featured in these families is thought to contain the inducer-binding site; the divergent sequences in this region allow for the binding of a variety of different inducers .
TetR transcriptional regulator CgmR-like, C-terminal domain (TetR_CgmR_C)
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 . 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 in CgmR (C. glutamicum multidrug-responsive transcriptional repressor), previously called CGL2612 protein. CgmR (CGL2612) from Corynebacterium glutamicum is a multidrug-resistance-related transcription factor belonging to the TetR family. It regulates expression of the immediately upstream gene cgmA (cgl2611) by binding to the operator cgmO in the cgmA promoter. The cgmA gene encodes a permease belonging to the major facilitator superfamily, a protein family composed of bacterial multidrug exporters, and the pair of CgmR and CgmA confers multidrug resistance on C. glutamicum .
Cysteine-rich interdomain region 1 gamma (CIDR1_gamma)
Type: Domain

Rosetting is the capacity of infected RBCs to bind uninfected RBCs, which is consistently associated with severe malaria in African children. The rosette-forming PfEMP1 adhesins, namely IT4/R29, Palo Alto 89F5 VarO, 3D7/PF13_0003 and IT4/var60, belong to a specific sub-group called groupA/UpsA var genes and all four present a specific Duffy Binding-Like and and Cysteine-Rich Interdomain Region (DBL1alpha1-CIDR1gamma) double domain Head region found at the extracellular region of PfEMP1. This entry represents the CIDR1gamma domain which increases the binding affinity to VarO (Palo Alto VarO parasites) .
COP9 signalosome complex subunit 7, helix I (CSN7_helixI)
Type: Domain

This entry describes the C-terminal helix I domain found in COP9 signalosome complex (CSN) subunit 7. The composition of the human CSN has been described, in which the helix I domain from CSN7 is reported to contact CSN6 helices I and II .
LSDAT, prokaryote (LSDAT_prok)
Type: Domain

The SLOG superfamily contains a specific form of the Rossmannoid fold, and is involved in a range of nucleotide-related functions. This domain, LSDAT (LOG-Smf/DprA in TRPM), is part of the SLOG superfamily. It is fused to or operonically associating with SLATT domain in diverse prokaryotes. It is predicted to function as ligand sensor in conjunction with the SLATT transmembrane domain .
Tetracyclin repressor-like, C-terminal domain 34 (TetR_C_34)
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 . 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 in putative TetR family transcriptional regulators found in bacteria. It is a member of a Pfam clam for the the TetR superfamily.
TetR transcriptional regulator Rv1219c-like, C-terminal domain (TetR_C_25)
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 . 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 in Rv1219c of Mycobacterium tuberculosis. Structural studies indicate that the helix alpha 10 of the C-terminal end of Rv1219c forms a long arm feature, a feature which is unique in Rv1219c compared to some other members of the TetR family. Furthermore, it has been shown that substrate binding occurs in the C-terminal regulatory domain of Rv1219c .
QsdR, TetR regulatory C-terminal domain (TetR_C_36)
Type: Domain

This is a C-terminal TetR regulatory domain found in QsdR proteins (quorum-sensing degradation regulation) .
NAD(+) hydrolase ThsA, Sir2/TIR-associating SLOG domain (ThsA_STALD)
Type: Domain

This is the SLOG-like domain of ThsA proteins, which is part of the SLOG superfamily . This domain is found at the C-terminal of ThsA proteins binds NAD+ derivatives, such as ADPR molecules produced by ThsB, which drives an oligomeric state change in ThsA and activates the NADase activity .

Thoeris is a bacterial antiphage defense system, which consists of two genes, thsA and thsB, via NAD degradation . ThsA has robust NAD cleavage activity and and a two-domain architecture containing a N-terminal NAD-binding domain (denoted as sirtuin-like or Macro) and C-terminal SLOG-like domain. In some instances, such as in B. amyloliquefaciens, ThsA has an N-terminal transmembrane domain . ThsB (also referred to as TIR1 and TIR2) is structurally similar to TIR domain proteins but without enzymatic activity.
HEPN/Toprim N-terminal domain 1 (HEPN/Toprim-NTD1)
Type: Domain

This is an alpha and beta domain. It is fused to two distinct HEPN domains: MAE_28990 and ERFG_01251, to a TOPRIM domain nuclease, and a REase fold DNase domain of Mrr family .
PDZ domain 6 (PDZ_6)
Type: Domain

This entry represents the PDZ domain from a wide variety of proteins. It is part of the Pfam clan PDZ-like (CL0466). PDZ domains are peptide binding sites.