SII-SWORD/CoKE huggingface dataset:
Beta-N-acetylglucosaminidase, C-terminal domain (NagA_C)
Type: Domain

This domain is found at the C-terminal end of Beta-N- acetylglucosaminidase from Thermotoga maritima (NagA,

), which hydrolyses chitooligomers into monomer beta-N-acetylglucosamine. NagA forms a dimer structure in which the monomer structure is organised into an N- and a C-terminal domain (

and this entry, respectively). This domain shows an α-β-α-sandwich fold, which comprises six β-strands with two α-helices on either side of the β-sheet .
NagJ-like, helical domain (NagJ-like_helical)
Type: Domain

This domain is located at the C-terminal of proteins predominantly found in actinomicetes and firmicutes that are members of family 84 glycoside hydrolases. These enzymes directly hydrolyse O-GlcNAcylated peptides, including O-GlcNAcase NagJ from Clostridium perfringens. This domain folds into a five helical bundle with up-and-down topology. It may function in substrate binding or recognition .
PRKAA1/2, autoinhibitory domain (PRKAA1/2_AID)
Type: Domain

This domain is found in the catalytic subunit (alpha, PRKAA1 and PRKAA2) of the enzymatic complex AMP-activated protein kinase (AMPK). These proteins are organised into an N-terminal kinase domain (KD,

) and a regulatory C-terminal domain, which contains an autoinhibitory domain (AID) and a adenylate sensor domain (

).

This entry represents the AID which forms a compact domain that stabilizes the KD and binds to CBS-2 of the gamma-subunit .
AmiR, N-terminal (AmiR_N)
Type: Domain

This is the N-terminal domain of Aliphatic amidase regulator (AmiR), which acts as a transcriptional antitermination factor. It positively controls AmiE, the gene for aliphatic amidase .
Phosphoacetylglucosamine mutase AMG1, domain III (AMG1_III)
Type: Domain

Phosphoacetylglucosamine mutase (AMG1) catalyses the conversion of GlcNAc-6-P into GlcNAc-1-P during the synthesis of uridine diphosphate/UDP-GlcNAc. It consists of four domains, the first three have the same fold of four β-strands between two α-helices.

This entry represents domain III of eukaryotic AMG1, which contains the sugar-binding loop .
Phosphoacetylglucosamine mutase AMG1, domain II (AMG1_II)
Type: Domain

Phosphoacetylglucosamine mutase (AMG1) catalyses the conversion of GlcNAc-6-P into GlcNAc-1-P during the synthesis of uridine diphosphate/UDP-GlcNAc. It consists of four domains, the first three have the same fold of four β-strands between two α-helices.

This entry represents domain II of eukaryotic AMG1, which contains the metal-binding loop .
AIR2-like, CCHC-type 1 zinc finger 4 (AIR2-like_ZnK4)
Type: Conserved_site

This motif is found in AIR1 and AIR2 from Saccharomyces cerevisiae (also known as Arginine methyltransferase-interacting RING finger proteins 1 and 2) and similar proteins from yeasts. AIR2 is an RNA-binding subunit of the TRAMP complex which has a poly(A) RNA polymerase activity and is involved in a post-transcriptional quality control mechanism limiting inappropriate expression of genetic information. This protein contain five tandemly arranged zinc-knuckle (ZnK) motifs of the CCHC-type (CX2CX4HX4C), which been shown to bind nucleic acids and proteins in unrelated proteins. This entry represents the fourth CCHC-type 1 zinc finger (ZnK4) of AIR2, which is important for TRAMP functions and integrity .
Allograft inflammatory factor 1-like, EF-hand domain pair (AIF-1_EF_pair)
Type: Domain

This entry represents an EF hand pair domain found in Allograft inflammatory factor 1 (AIF-1), EF-hand domain-containing protein D2 (EFHD2, also known as swiprosin-1) and similar proteins. AIF-1 is an actin-binding protein that enhances membrane ruffling and RAC activation . EFHD2 may regulate B-cell receptor -(BCR) induced immature and primary B-cell apoptosis. It plays a role as negative regulator of the canonical NF-kappa-B-activating branch and controls spontaneous apoptosis through the regulation of BCL2L1 abundance .
Baseplate wedge protein gp6-like, N-terminal helical domain (Gp6-like_N)
Type: Domain

This domain is found in Baseplate wedge protein gp6 from Enterobacteria phage T4 (

) and similar sequences from tailed bacteriophages and bacterial prophages. Gp6 is a protein involved in tail assembly. This entry represents its N-terminal helical domain .
Baseplate structural protein gp6, C-terminal domain I (Gp6_C-I)
Type: Domain

This entry represents a domain that has been described as C-terminal domain I in Baseplate wedge protein gp6 from Enterobacteria phage T4 (

). It adopts a two-layer β-sandwich fold. Members of this group are found in tailed bacteriophages and bacterial prophages.

Baseplate structural protein gp6 is located next to the tail tube and is an intermediate (or inner) baseplate protein involved in tail assembly. Two molecules of gp6 form a complex with gp25 and gp7 which is involved sheath contraction .
Baseplate structural protein gp6, C-terminal domain II (gp6_C-II)
Type: Domain

This entry represents the second part of domain II, which is found in the C-terminal of gp6 from bacteriophage T4 (

). This domain adopts a β-barrel fold.

Baseplate structural protein gp6 is located next to the tail tube and is an intermediate (or inner) baseplate protein involved in tail assembly. Two molecules of gp6 form a complex with gp25 and gp7 which is involved sheath contraction .
Baseplate wedge protein gp6, domain II, first (Gp6_II_1st)
Type: Domain

This entry represents the first part of Domain II from Baseplate wedge protein gp6 from Enterobacteria phage T4 and similar sequences predominantly from tailed bacteriophages .

Baseplate structural protein gp6 is located next to the tail tube and is an intermediate (or inner) baseplate protein involved in tail assembly. Two molecules of gp6 form a complex with gp25 and gp7 which is involved sheath contraction .
AI2M/AI1M-like, HNH endonuclease domain (AI2M-like_HNH)
Type: Domain

This is the HNH endonuclease domain found in a set of group II intron proteins, including AIM1/2 from yeast and its orthologue from S. pombe. This domain is also found in related bacterial sequences .
T2SS protein K, first SAM-like domain (T2SSK_SAM-like_1st)
Type: Domain

This entry represents a SAM-like domain found in proteins involved in the Type II protein secretion system (T2SS), including Type II secretion system protein K from Escherichia coli. The T2SK family includes proteins such as ExeK, PulK, OutX and XcpX. They consist of three domains, two of which are arranged in tandem and share structural similarity to SAM-like domains. This entry represents the first SAM-like domain that is involved in interaction with the minor pseudopilin XcpW or its homologues (

) .
Pyrogallol hydroxytransferase large subunit-like, N-terminal domain (AhtL-like_N)
Type: Domain

This domain is found at the N-terminal of Pyrogallol hydroxytransferase large subunit from Pelobacter acidigallici (AthL), which is involved in the isomerisation of pyrogallol to phloroglucin. This protein contains four domains, all of them similar to the domains of the DMSO reductase family .
Beta-agarase/YXIM esterase-like, galactose-binding domain-like (AGA-YXIM_GBD)
Type: Domain

This entry represents the galactose-binding domain found in the middle of beta-agarase A from Zobellia galactanivorans and at the N-terminal of the uncharacterised esterase YXIM from Bacillus subtilis and similar sequences.
SPI-1 type 3 secretion system secretin, N0 domain (T3S_SPI-1_N0)
Type: Domain

SPI-1 type 3 secretion system secretin forms a ring-shaped multimeric structure which is used to inject bacterial effector proteins into eukaryotic host cells . It consists of several N-terminal short domains and a C-terminal secretin domain (

). This entry represents the N-terminal N0 domain.
ATP-dependent helicase/deoxyribonuclease subunit B, N-terminal (ADDB_N)
Type: Domain

ATP-dependent helicase/deoxyribonuclease subunit B (ADDB) forms a heterodimer with ADDA which acts as both an ATP-dependent DNA helicase and an ATP-dependent single-stranded exonuclease, acting in both directions. This entry represents the N-terminal domain of ADDB, which contains the Walker A motif involved in ATP binding .
AF_1763-like, C-terminal domain (AF_1763-like_C)
Type: Domain

This domain is found at the C-terminal of a group of prokaryotic proteins, including the putative lipase AF_1763 from Archaeoglobus fulgidus. This protein contains a C-terminal lipid binding domain, which is formed by two layers of seven β-strands . This entry represents the second half of this domain.
CDP-alcohol phosphatidyltransferase AF_2299-like, N-terminal domain (AF_2299-like_N)
Type: Domain

This domain is found at the N-terminal of CDP-alcohol phosphatidyltransferase from Archaeoglobus fulgidus (AF_2299) and similar archaeal proteins. AF_2299 is a member of a family of membrane-embedded enzymes known as CDP-alcohol phosphotransferases (CDP-APs) involved in the formation of polar phospholipids. This integral membrane phosphotransferase is organised into two distinct domains. This entry represents the N-terminal cytoplasmic domain, which has structural similarity to the cytidyltransferases .
ADAM10, cysteine-rich domain (ADAM10_Cys-rich)
Type: Domain

Disintegrin and metalloproteinase domain-containing protein 10 (ADAM10) is a transmembrane endopeptidase responsible for the proteolytic release of several cell-surface proteins, including the membrane-bound precursor of TNF-alpha, ligands and receptors of the Notch, Eph, and erbB families, thereby activating signaling pathways critical for tumour initiation and maintenance. This entry represents the cysteine-rich domain which mediates non-catalytic interactions with the substrate that are key for effective cleavage . This domain, together with disintegrin domain (

), plays an important modulatory role.
Regulator of microtubule dynamics protein 1-3, alpha helical repeats (RMD1-3_a_helical_rpt)
Type: Repeat

This entry represents α-helical repeats that form the C-terminal region of Regulator of microtubule dynamics proteins 1-3 (RMD1-3) and similar proteins from animals and bacteria. These are microtubule-binding proteins. RMD3 is involved in cellular calcium homeostasis regulation, and it may participate in differentiation and apoptosis of keratinocytes . RMD1 from C. elegans functions in chromosome segregation .
Regulator of MON1-CCZ1 complex, N-terminal (RMC1_N)
Type: Domain

This entry represents the N-terminal β-propeller of Regulator of MON1-CCZ1 complex (RMC1) and similar eukaryotic proteins. RMC1 is a component of the the CCZ1-MON1 complex, which functions as a guanine exchange factor (GEF) for RAB7 during endocytic and autophagic flux to the lysosome . This region may function analogously to the WIPI proteins to bind phosphoinositides at the membrane .
RalA-binding protein 1-like, Ral binding domain (RalBP1-like_Ral-bd)
Type: Domain

This entry represents a domain found in human RalA-binding protein 1 (RalBP1, also known as RLIP76), a multifunctional protein that interacts with multiple small G protein families and endocytosis proteins. The Ral binding domain is a coiled-coil. The orientation of its α-helices and the loop between them slightly changes upon binding to RalB. This interaction appears to be related to the cellular localisation of the complex .
T4 RNA ligase 1, C-terminal domain (T4_Rnl1_C)
Type: Domain

This domain is found at the C-terminal end of T4 RNA ligase 1 (Rnl1) from Bacteriophage T4 (

) and similar proteins from tailed bacteriophages. Rnl1 is involved in countering a host defense mechanism by repairing tRNA. The C-terminal domain shows an all α-helical fold and has a charge distribution and architecture for helix-nucleic acid groove interaction compatible with tRNA binding (

). It confers specificity for the repair of tRNAs with breaks in the anticodon loop .
RIOX1/NO66-like, C-terminal winged helix domain (RIOX1/NO66-like_C_WH)
Type: Domain

This domain is found in Ribosomal oxygenase 1 from humans (RIOX1), Bifunctional lysine-specific demethylase and histidyl-hydroxylase NO66 from Drosophila melanogaster and similar proteins from animals. RIOX1 catalyse histidine-hydroxylation in ribosomal protein rpL28. The protein shows a JmjC domain followed by an helical dimerisation domain and a C-terminal winged-helix (WH)-domain (this entry) .
RIF2, ASCE domain (RIF2_ASCE)
Type: Domain

RIF2 is involved in transcriptional silencing and telomere length regulation . It belongs to the ATPase family associated with diverse cellular activities. This entry represents the ASCE (NTPase) domain described in .
RIF2, AAA+ lid domain (RIF2_lid)
Type: Domain

RIF2 is involved in transcriptional silencing and telomere length regulation . It belongs to the ATPase family associated with diverse cellular activities. This entry represents the α-helical AAA lid domain described in .
Non-reducing end beta-L-arabinofuranosidase-like, GH127 middle domain (Beta-AFase-like_GH127_middle)
Type: Domain

This entry represents the first of two β-sandwich domains found in Non-reducing end beta-L-arabinofuranosidase from Bifidobacterium longum (

also known as Beta-AFase) . This domain shows a similarity to C-terminal domains of GH44, GH27, and GH39 enzymes .

Beta-AFase, an unusual beta-L-arabinofuranosidase enzyme (

), releases l-arabinose from the l-arabinofuranose (Araf)-beta1,2-Araf disaccharide and also transglycosylates 1-alkanols with retention of the anomeric configuration. Terminal beta-l-arabinofuranosyl residues have been found in arabinogalactan proteins from a number of different plant species. Beta-l-Arabinofuranosyl linkages with 1-4 arabinofuranosides are also found in the sugar chains of extensin and solanaceous lectins, hydroxyproline (Hyp)2-rich glycoproteins that are widely observed in plant cell wall fractions. The critical residue for catalytic activity is Glu-338, in a ET/SCAS sequence context .
Recombination and repair protein UVSX-like, C-terminal domain (T4_UVSX-like_C)
Type: Domain

This domain is mainly found in proteins from tailed bacteriophages, including Recombination and repair protein from Bacteriophage T4 (UVSX) (

). This protein is organised into a larger N-terminal 'core' domain and a smaller C-terminal domain, represented in this entry, with mainly α-helical structure (

) .
REST corepressor, helical domain (REST_helical)
Type: Domain

This helical region is found in the REST corepressors 1-3 .

RCOR1 is an essential component of the BHC complex, a corepressor complex that represses transcription of neuron-specific genes in non-neuronal cells. The BHC complex is recruited at RE1/NRSE sites by REST and acts by deacetylating and demethylating specific sites on histones, thereby acting as a chromatin modifier. In the BHC complex, it serves as a molecular beacon for the recruitment of molecular machinery, including MeCP2 and SUV39H1, that imposes silencing across a chromosomal interval. It plays a central role in demethylation of Lys-4 of histone H3 by promoting demethylase activity of KDM1A on core histones and nucleosomal substrates and it also protects KDM1A from the proteasome .
Non-reducing end beta-L-arabinofuranosidase-like, GH127 C-terminal domain (Beta-AFase-like_GH127_C)
Type: Domain

This entry represents the second β-sandwich domain found in enzymes belonging to the glycosyl hydrolase 127 family, including Non-reducing end beta-L-arabinofuranosidase from Bifidobacterium longum (

also known as Beta-AFase) . The β-sandwich domain is somewhat similar to the N-terminal domain of ErbB4 kinase and is involved in formation of a dimer, which is created by a crystallographic 2-fold axis .

Beta-AFase, an unusual beta-L-arabinofuranosidase enzyme (

), releases l-arabinose from the l-arabinofuranose (Araf)-beta1,2-Araf disaccharide and also transglycosylates 1-alkanols with retention of the anomeric configuration. Terminal beta-l-arabinofuranosyl residues have been found in arabinogalactan proteins from a number of different plant species. Beta-l-Arabinofuranosyl linkages with 1-4 arabinofuranosides are also found in the sugar chains of extensin and solanaceous lectins, hydroxyproline (Hyp)2-rich glycoproteins that are widely observed in plant cell wall fractions. The critical residue for catalytic activity is Glu-338, in a ET/SCAS sequence context .
Novel STAND NTPase 3 (nSTAND3)
Type: Domain

This entry represents a novel domain of the STAND-superfamily of AAA+ ATPases found in bacterial conflict systems and in metazoan TRADD-N associated counter-invader proteins .
Novel STAND NTPase 2 (nSTAND2)
Type: Domain

This is an inactive STAND-NTPase domain found in a mobile two-gene bacterial conflict systems. nSTAND2 is fused to various effector molecules. The neighbouring gene is an active STAND domain. These STAND NTPases define a novel family close to CR-ATPases, the mitochondrial apoptotic ribosomal protein S29/Dap3 and the mitochondria-associated STAND NTPase RNA12 .
Novel STAND NTPase 1 (nSTAND1)
Type: Domain

This is a novel domain of the STAND-superfamily of AAA ATPases found in bacterial conflict systems .
Alpha fucosidase A-like, C-terminal domain (AFCA-like_C)
Type: Domain

This domain is found in Alpha-fucosidase (AFCA) from Bifidobacterium bifidum and in other members of the glycoside hydrolase family 95 from fungi, plants and bacteria. AFCA hydrolyses the glycosidic linkage of Fuc1-2Gal via an inverting mechanism. This entry represents the C-terminal β-sandwich domain that is next to the the catalytic region of this protein. The domain forms a two-layered jelly-roll fold. Its specific function remains unknown .
Nitrile hydratase beta subunit-like, N-terminal domain (CN_hydtase_beta-like_N)
Type: Domain

Nitrile hydratases (NHases) (

) are unusual metalloenzymes that catalyse the hydration of nitriles to their corresponding amides. They are used as biocatalysts in acrylamide production, one of the few commercial scale bioprocesses, as well as in environmental remediation for the removal of nitriles from waste streams.

Nitrile hydratases are composed of two subunits, alpha and beta, and they contain one iron atom per alpha-beta unit . Beta subunit consists of an N-terminal helical domain, represented in this entry, and an SH3-like domain (

) . Thiocyanate hydrolase (SCNase) is a member of the NHase family and comprises alpha, beta and gamma subunits, which share amino acid sequence similarities with NHase beta subunit C-terminal, beta subunit N-terminal and NHase alpha subunit, respectively .
NDC10, N-terminal domain (NDC10_N)
Type: Domain

Kinetochores link centromeric DNA to spindle microtubules and ensure faithful chromosome segregation during mitosis. In point-centromere yeasts, the CBF3 complex Skp1-Ctf13-(Cep3)(2)-(Ndc10)recognizes a conserved centromeric DNA element through contacts made by Cep3 and NDC10. This entry represents the N-terminal domain of NDC10 .
NAD-glutamate dehydrogenase, helical motif 3 (NAD_Glu_DH_HM3)
Type: Conserved_site

This entry represents the third helical motif (HM3) found in a group of NAD-specific glutamate dehydrogenases.

Glutamate dehydrogenases (GDHs) are a broadly distributed group of enzymes that catalyse the reversible oxidative deamination of glutamate to ketoglutarate and ammonia . The structure of GDH from Mycobacterium smegmatis revealed that it has a long N- and C-terminal segments flanking the catalytic core, comprising several domains. The flexible N-terminal domain comprises ACT-like and PAS-type domains which could act as metabolic sensors for allosteric regulation . It also contains three α-helical motifs (HM1-3).
Infectious salmon anemia virus nucleoprotein, N-terminal domain (NCAP_ISAV_N)
Type: Domain

This entry represents the N-terminal domain of the salmon anemia virus nucleoprotein which has an α/β fold consisting of three antiparallel β-strands and two α-helices in an extended shape and interacts with the rest of the structure . This domain may regulate the dynamics of the NP RNA binding.
NAD-glutamate dehydrogenase, helical motif 2 (NAD_Glu_DH_HM2)
Type: Conserved_site

This entry represents the second helical motif (HM2) found in a group of NAD-specific glutamate dehydrogenases.

Glutamate dehydrogenases (GDHs) are a broadly distributed group of enzymes that catalyse the reversible oxidative deamination of glutamate to ketoglutarate and ammonia . The structure of GDH from Mycobacterium smegmatis revealed that it has a long N- and C-terminal segments flanking the catalytic core, comprising several domains. The flexible N-terminal domain comprises ACT-like and PAS-type domains which could act as metabolic sensors for allosteric regulation . It also contains three α-helical motifs (HM1-3).
NAD-glutamate dehydrogenase, helical motif 1 (NAD_Glu_DH_HM1)
Type: Conserved_site

This entry represents the first helical motif (HM1) found in a group of NAD-specific glutamate dehydrogenases.

Glutamate dehydrogenases (GDHs) are a broadly distributed group of enzymes that catalyse the reversible oxidative deamination of glutamate to ketoglutarate and ammonia . The structure of GDH from Mycobacterium smegmatis revealed that it has a long N- and C-terminal segments flanking the catalytic core, comprising several domains. The flexible N-terminal domain comprises ACT-like and PAS-type domains which could act as metabolic sensors for allosteric regulation . It also contains three α-helical motifs (HM1-3).
Infectious salmon anemia virus nucleoprotein, helical bundle (NCAP_ISAV_hel)
Type: Domain

This entry represents the helical bundle of Infectious salmon anemia virus (ISAV) nucleoprotein, that forms the head domain described in . The head and body domains from this protein affect the equilibrium-state RNA binding.
NarE-like (NarE-like)
Type: Family

This is a group of short bacterial sequences that includes NarE from Neisseria meningitidis. NarE is a protein with predicted ADP-ribosyltransferase activity. It shows an α/β structure.
NAD-glutamate dehydrogenase, ACT2 domain (NAD_Glu_DH_ACT2)
Type: Domain

This entry represents the ACT2 domain of a bacterial family of NAD-specific glutamate dehydrogenases. The ACT domains of these proteins differ from the archetypal ACT fold in that strand strand β1 is located in the position usually occupied by strand β4 creating an ACT-like topology with a β1-4 antiparallel sheet .

Glutamate dehydrogenases (GDHs) are a broadly distributed group of enzymes that catalyse the reversible oxidative deamination of glutamate to ketoglutarate and ammonia . The structure of GDH from Mycobacterium smegmatis revealed that it has a long N- and C-terminal segments flanking the catalytic core, comprising several domains. The flexible N-terminal domain comprises ACT-like and PAS-type domains which could act as metabolic sensors for allosteric regulation .
Trehalose-6-phosphate phosphatase, C-terminal domain (T6PP_C)
Type: Domain

This entry represents the catalytic C-terminal domain of trehalose-6-phosphate phosphatase (TPP) from nematodes such as Caenorhabditis elegans and Brugia malayi.

TPP catalyses the hydrolysis of trehalose 6-phosphate to trehalose and phosphate, preventing the accumulation of toxic levels of trehalose 6-phosphate. This domain adopts a C2B-type HAD phosphatase fold (

) . In C. elegans, TPP is essential for survival due to the toxic effect(s) of the accumulation of trehalose 6-phosphate .

This domain is also found in a number of bacterial TPPs.
NAD-glutamate dehydrogenase, ACT3 domain (NAD_Glu_DH_ACT3)
Type: Domain

This entry represents the ACT3 domain of a bacterial family of NAD-specific glutamate dehydrogenases. The ACT domains of these proteins differ from the archetypal ACT fold in that strand strand β1 is located in the position usually occupied by strand β4 creating an ACT-like topology with a β1-4 antiparallel sheet .

Glutamate dehydrogenases (GDHs) are a broadly distributed group of enzymes that catalyse the reversible oxidative deamination of glutamate to ketoglutarate and ammonia . The structure of GDH from Mycobacterium smegmatis revealed that it has a long N- and C-terminal segments flanking the catalytic core, comprising several domains. The flexible N-terminal domain comprises ACT-like and PAS-type domains which could act as metabolic sensors for allosteric regulation .