SII-SWORD/CoKE huggingface dataset:
Cyclic GMP-AMP synthase DncV-like, nucleotidyltransferase domain (DncV-like_NTFase)
Type: Domain

This is the nucleotidyltransferase domain of DncV from Vibrio cholerae (also known as Cyclic GMP-AMP synthase) and related proteins . DncV catalyses the synthesis of 3'3'-cyclic GMP-AMP (3'3'-cGAMP) from GTP and ATP. It is part of the CBASS (cyclic oligonucleotide-based antiphage signalling system) which provides immunity against bacteriophage . This protein is required for efficient V.cholerae intestinal colonisation and and down-regulates the colonisation-influencing process of chemotaxis.
Cyclic GMP-AMP synthase, C-terminal domain (DncV_C)
Type: Domain

This domain is found Cyclic GMP-AMP synthase from Vibrio cholerae (DncV), a prokaryotic cGAS-like enzyme that synthesises cyclic GMP- AMP (c-GAMP) and stimulates intestinal colonisation. DncV adopts a structure and topology that are typical of the nucleotidyltransferase superfamily. It is organised into two domains: an N-terminal domain that contains the catalytic loop (

) and a C- terminal helix bundle that consists of eight helices and one pair of antiparallel β-sheets, represented in this entry .
DUF1980, C-terminal domain (DUF1980_C)
Type: Domain

Members of this family are found in a set of prokaryotic hypothetical proteins. Their exact function has not, as yet, been defined. This entry represents the C-terminal domain.
DNA polymerase III subunit tau-like, C-terminal domain (DnaX-like_C)
Type: Domain

This domain is found at the C-terminal end of sequences similar to the subunit tau of bacterial DNA polymerase III (DnaX), such as

from Thermus aquaticus. It binds to the C-terminal of the alpha subunit of the same complex through its C-terminal helix and the adjacent loop .
YhfX-like, C-terminal domain (YhfX-like_C)
Type: Domain

This domain is found at the C-terminal of a group of bacterial proteins, including the uncharacterised protein YhfX from Escherichia coli, which may be related to DNA recombination. The function of this domain is still unknown. It is often found associated to

.
Glucosidase YgjK, N-terminal domain (YgjK_N)
Type: Domain

This domain is found at the N-terminal end of Glucosidase YgjK from Escherichia coli and similar bacterial enzymes from the glycoside hydrolase family 63 (GH63). YgjK is organised into N- and A- domains and a linker that connects them. This entry includes the N-domain and the linker region. The N-domain is composed of 18 antiparallel β-strands divided into two β-sheets and is classified as a super-β-sandwich. The linker is composed of two α-helices and produces a significant curvature between the two domains .
tRNA-modifying protein YgfZ-like, beta-barrel domain (YgfZ_barrel)
Type: Domain

tRNA-modifying protein YgfZ is a folate-binding protein involved in regulating the level of ATP-dnaA and in the modification of some tRNAs . It consists of a folate-binding domain at the N terminus

and a six-stranded antiparallel β-barrel at the C-terminal. This entry represents the C-terminal domain that is structurally similar to the C-terminal domain of elongation factors Tu, eEF-1alpha and the initiation factor eIF2 gamma . Homologues of YgfZ are found exclusively in gammaproteobacteria.
Mastermind-like protein 2, transcriptional activation domain (MAML2_TAD)
Type: Domain

This entry represents the TAD domain from human MAML2 and similar sequences from vertebrates.

Mastermind-like proteins (MAML1-3) were first described as transcriptional co-activators for Notch signalling but more recently they have been also implicated as transcriptional co-activators in other signal transduction pathways including muscle differentiation and myopathies, tumour suppressor pathway (p53) and colon carcinoma survival (beta-catenin) . The N-terminal basic domain (

) of MAML1-3 is the most conserved region of this proteins, outside this region their sequences are quite divergent. However, they all have transactivation domains (TADs) at the C-terminal end , suggesting different functions among them as they cooperate differentially with various Notch receptors in the activation of target genes. Recently, MAML1 and MAML2 have been identified as transcriptional coactivators of the Hippo pathway . A structural feature of the MAML family is the presence of polyglutamine (polyQ) tracts, which, in some polyQ proteins, expansion of this tracts cause protein inestability and the formation of nuclear inclusions in neurons, leading to neurotoxicity .
DNA primase DnaG, catalytic core, helical bundle (DnaG_cat_HB)
Type: Domain

This domain is found in DNA primase from Staphylococcus aureus (DnaG) and similar proteins from Staphylococcus. DnaG is an RNA polymerase that catalyses the synthesis of short RNA molecules used as primers for DNA polymerase during DNA replication. This entry represents the helical bundle (HB) found at the C-terminal of the catalytic core of DnaG .
YetF-like, N-terminal transmembrane domain (YetF_N)
Type: Domain

This entry represents the N-terminal region of the YetF protein from Bacillus subtilis (

) and related bacterial proteins that include the uncharacterised proteins YdfS and YkjA. This domain is composed of three transmembrane helices.
Mastermind-like 1/3, transactivation domain 2 (MAML1_3_TAD2)
Type: Domain

This entry represents the transactivation domain 2 (TAD2) found at the C-terminal of Mastermind-like protein 1/3 (MAML1/3). TAD2 from MAML1 enhances the phosphorylation of CBP/p300 and ICN, required for Notch induced transcription . This is a glutamine rich domain that govern the MAML1 transcriptional activity . This domain directly recruits the cyclin C:CDK8 (cyclin-dependent kinase 8) complex that inhibits Notch signalling by promoting phosphorylation-dependent ubiquitination of nuclear ICN and its sequential proteasomal degradation .

Mastermind-like proteins (MAML1-3) were first described as transcriptional co-activators for Notch signalling but more recently they have been also implicated as transcriptional co-activators in other signal transduction pathways including muscle differentiation and myopathies, tumour suppressor pathway (p53) and colon carcinoma survival (beta-catenin) . The N-terminal basic domain (

) of MAML1-3 is the most conserved region of this proteins, outside this region their sequences are quite divergent. However, they all have transactivation domains (TADs) at the C-terminal end , suggesting different functions among them as they cooperate differentially with various Notch receptors in the activation of target genes. Recently, MAML1 and MAML2 have been identified as transcriptional coactivators of the Hippo pathway . A structural feature of the MAML family is the presence of polyglutamine (polyQ) tracts, which, in some polyQ proteins, expansion of this tracts cause protein inestability and the formation of nuclear inclusions in neurons, leading to neurotoxicity .
Mastermind-like 1/3, transactivation domain 1 (MAML1_3_TAD1)
Type: Domain

This is the Transactivation domain 1 (TAD1) found in the central region of Mastermind-like proteins 1 and 3 (MAML1-3) which contains a nuclear localisation sequence (NLS) and recruits CBP/p300 to promote nucleosome acetylation at Notch enhancers . This domain is essential for the formation of the ICN-CSL-MAML1 ternary complex, which binds the promoters of specific target genes and determines their transcriptional activation. It is required to sustain Notch-dependent transcription .

Mastermind-like proteins (MAML1-3) were first described as transcriptional co-activators for Notch signalling but more recently they have been also implicated as transcriptional co-activators in other signal transduction pathways including muscle differentiation and myopathies, tumour suppressor pathway (p53) and colon carcinoma survival (beta-catenin) . The N-terminal basic domain (

) of MAML1-3 is the most conserved region of this proteins, outside this region their sequences are quite divergent. However, they all have transactivation domains (TADs) at the C-terminal end , suggesting different functions among them as they cooperate differentially with various Notch receptors in the activation of target genes. Recently, MAML1 and MAML2 have been identified as transcriptional coactivators of the Hippo pathway . A structural feature of the MAML family is the presence of polyglutamine (polyQ) tracts, which, in some polyQ proteins, expansion of this tracts cause protein inestability and the formation of nuclear inclusions in neurons, leading to neurotoxicity .
Ribosomal RNA small subunit methyltransferase F, pre-PUA domain (YebU_pre-PUA_dom)
Type: Domain

This domain is found in Ribosomal RNA small subunit methyltransferase F from Escherichia coli (YebU) and similar proteins mainly from gammaproteobacteria. YebU requires S-adenosyl-l-methionine (SAM) to specifically methylate the cytosine at position 1407 of assembled 30 S rRNA subunits. This protein is organised into two distinct structural domains: the N-terminal MTase domain (catalytic domain), which can be divided in

and

, and the C-terminal, also consisting of two subdomains. This entry represents the first of these subdomains, which is found N-terminal to the PUA-like domain

. The pre-PUA domain has six β-strands that form a central sheet in an antiparallel fashion, and three α-helices packing against the edges of the sheet .
MalQ, N-terminal beta-sandwich domain (MalQ_N)
Type: Domain

This entry represents the N-terminal domain of domain of 4-alpha-glucanotransferase from Mycobacterium tuberculosis (MalQ) and similar sequences mainly found in proteobacteria and actinomycetes. This domain, also called N2, resembles a β-sandwich consisting of a five-stranded mixed β-sheet and a short two-stranded antiparallel β-sheet. The N2 structure is reminiscent of carbohydrate-binding modules (CBMs) . However, a comparison with structurally known CBMs did not reveal significant similarities.

Amylomaltase MalQ is essential for the metabolism of maltose and maltodextrins in Escherichia coli. It catalyses transglycosylation/disproportionation reactions in which glycosyl or dextrinyl units are transferred among linear maltodextrins of various lengths .
DNA2, rift barrel domain (DNA2_Rift)
Type: Domain

This entry represents ar barrel domain found in the DNA replication ATP-dependent helicase/nuclease DNA2 protein . This domain lies between the nuclease and helicase domains . The DNA2 nuclease-helicase maintains genomic integrity by processing DNA double-strand breaks, Okazaki fragments and stalled replication forks. DNA2 requires ssDNA ends, and is dependent on the ssDNA-binding protein Rpa, which controls cleavage polarity.
Dermonecrotic toxin, C3 domain (ToxA_C3)
Type: Domain

Dermonecrotic toxin (ToxA), also known as Pasteurella multocida toxin (PMT),inhibits osteoblastic differentiation in mammals and birds. Its N-terminal region binds to target cells, while its C-terminal region, with a Trojan horse-like shape, carries the intracellularly active moiety. The latter consists of three distinct domains: C1 (

), C2 and C3. This entry represents the C-terminal catalytic domain C3, which has a Cys-His-Asp triad known to perform acyl-hydrolysis such as peptidase activity or an acyl-transfer reaction. This domain adopts a typical α/β protein fold with seven β-strands and eight helices. It is organised into two subdomains that form the the biologically active cleft space .
Dermonecrotic toxin-like, C2 domain (ToxA-like_C2)
Type: Domain

Dermonecrotic toxin (ToxA), also known as Pasteurella multocida toxin (PMT), inhibits osteoblastic differentiation in mammals and birds. Its N-terminal region binds to target cells, while its C-terminal region, with a Trojan horse-like shape, carries the intracellularly active moiety. The latter consists of three distinct domains: C1 (

), C2 and C3 (

). This entry represents the larger of these domains, the central region C2, which has 18 helices and nine β-strands and is organised into two subdomains with typical α-β structures characteristic of nucleotide-binding proteins . This domain is also found in the multifunctional-autoprocessing repeats-in-toxin (MARTX) toxin from Vibrio vulnificus, responsible for the disruption of host innate immune defences during infection .
YDR124W, N-terminal domain (YDR124W_N)
Type: Domain

This entry includes mitochondrial proteins of unknown function found in yeast. Null mutant showed severe fragmentation of mitochondria and its expression is strongly induced by alpha factor. Members of this entry may have a role in maintenance of mitochondrial morphology . This entry represents the N-terminal domain which may have an α/β fold.
YchJ-like, zinc-binding domain (YchJ-like_N)
Type: Domain

This domain is found at the N-terminal of the functionally uncharacterised YchJ family protein from Psychrobacter arcticus (

) and related proteins from Psychrobacter species. The structure of YchJ (

) shows that this domain folds into an α-helical structure. This domain contains the same type of C4 zinc finger as in SEC-C motif (

) located at the C terminus of YchJ, suggesting internal duplication in the YchJ family.
MalF, N-terminal region, transmembrane helices (MalF_N_TM)
Type: Domain

MalF (Maltose/maltodextrin transport system permease protein MalF) is a component of the maltose uptake system found in proteobacteria, an ATP-binding cassette (ABC) transporter. This protein is composed of eight transmembrane (TM) helices and folds in a way its concave surface faces the similar assembly of MalG to enclose the maltose. This entry represents the first TM helices of this structure, which are located N-terminal to the large periplasmic loop (P2,

) .
Maestro-like, HEAT-repeats domain (Maestro-like_HEAT)
Type: Domain

This entry represents a domain consisting of HEAT repeats from maestro heat-like repeat-containing proteins. Maestro (Male-specific Transcription in the developing Reproductive Organs (MRO)) is expressed in human granulosa cumulus cells and in testicular germ cells . SPIF (also known as MRO2B) may play a role in the process of sperm capacitation .
DNA polymerase III delta subunit-like, C-terminal domain (DNA_pol3_delta-like_C)
Type: Domain

This entry represents the C-terminal domain of the delta subunit from the clamp-loader complex of Bacillus subtilis and similar poorly characterised proteins from other bacteria, which is structurally similar to that of the DNApol3 delta subunit from E.coli (represented in

) . This domain interacts with other subunits in the complex (tau and delta') and the nature of these interactions appear to be hydrophilic in contrast with the one observed in Gram-negative bacteria .
MACPF protein, D3 domain (MACPF_D3)
Type: Domain

This domain is found in proteins of the membrane-attack complex/perforin (MACPF) family from Bacteroidetes. These transmembrane pore- forming proteins are organised into three structured domains: an MACPF domain (

) and two C-terminal domains, D2 and D3. This entry represents the D3 domain, which adopts an α/β fold and functions as a wedge between D2 and MACPF .
MACPF protein, D2 domain (MACPF_D2)
Type: Domain

This domain is found in proteins of the membrane-attack complex/perforin (MACPF) family from Bacteroidetes. These transmembrane pore- forming proteins are organised into three structured domains: an MACPF domain (

) and two C-terminal domains, D2 and D3. This entry represents the D2 domain, which adopts an α/β fold .
YchJ-like, middle NTF2-like domain (YchJ-like_M)
Type: Domain

This entry represents the NTF2-like domain found in the functionally uncharacterised YchJ protein from Psychrobacter arcticus (

) and related proteins. This domain is usually found flanked by either (

) and (

) at the N and C-terminal or flanked on both sides by (

). The structure of YchJ (

) shows that this domain adopts a structure typical for NFT2 that consists of a curved three-stranded β-sheet and an array of α-helices packed on one side of it. The function of this domain is unknown.
Mevalonate-3-kinase, C-terminal domain (M3K_C)
Type: Domain

This entry represents the C-terminal domain of M3K and similar archaeal proteins.

Mevalonate-3-kinase (M3K) is a mevalonate diphosphate decarboxylase (MDD) homologue from Thermoplasma acidophilum, which catalyses phosphorylation of (R)-mevalonate without concomitant decarboxylation .
Mevalonate-3-kinase (M3K)
Type: Family

This entry represents Mevalonate 3-kinase from Thermoplasma acidophilum (M3K) and similar archaeal proteins.

Mevalonate-3-kinase (M3K) is a mevalonate diphosphate decarboxylase (MDD) homologue from Thermoplasma acidophilum, which catalyses phosphorylation of (R)-mevalonate without concomitant decarboxylation .
DNA polymerase III subunit alpha, C-terminal domain (DNA_pol_IIIA_C)
Type: Domain

This domain is found at the C-terminal end of DNA polymerase III subunit alpha and similar proteins from Proteobacteria and Actinobacteria. This protein, which is the replicative DNA polymerase, consists of six domains that form an irregular pyramid around a central cavity. The C-terminal domain lies on top of this structure .
Integron cassette protein (M1E1E6-like)
Type: Domain

This entry represents a group of bacterial uncharacterised sequences from mobile gene cassettes, including Integron cassette protein from Vibrio cholerae (

). This protein forms a dimer in which each protomer adopts a two-layered α/β fold with an anti-parallel β-sheet of five strands which curves around a pair of antiparallel α-helices . Its specific function is unknown.
Integron cassette protein superfamily (M1E1E6-like_sf)
Type: Homologous_superfamily

This entry represents a group of bacterial uncharacterised sequences from mobile gene cassettes, including Integron cassette protein from Vibrio cholerae (

). This protein forms a dimer in which each protomer adopts a two-layered α/β fold with an anti-parallel β-sheet of five strands which curves around a pair of antiparallel α-helices . Its specific function is unknown.
MG281-like, antibody-binding region (MG281-like_Ab-bd)
Type: Domain

This domain is found in proteins from Mycoplasmatota, including Uncharacterized protein MG281 from Mycoplasma genitalium, also known as protein M. This virulence protein consists of two domains. The larger one, represented in this entry, binds the IgG light chain to block the binding of antibody to antigen. It includes a leucine-rich repeat (LRR)-like subdomain, which faces away from the antibody molecule .
LytM, N-terminal domain (LytM_N)
Type: Domain

This domain is found at the N-terminal end of the peptidase from the M23 family LytM found in Ruminococcus gnavus (

) and similar proteins predominantly found in firmicutes. This protein is predicted to have glycyl-glycine endopeptidase activity. This domain adopts an α-helical structure.
YceM-like, C-terminal domain (YceM-like_C)
Type: Domain

This domain is found at the C-terminal of putative oxidoreductase YceM from Escherichia coli and similar bacterial sequences. It adopts an α/β structure consisting of a central five-stranded parallel β-sheet packed on both sides with helices (

). It is often associated with (

).
LSM12, LSM domain (LSM12_LSM)
Type: Domain

This is the LSM domain from the eukaryotic protein LSM12, which binds Nicotinic acid adenine dinucleotide phosphate (NAADP) and mediates association with the endolysosomaltwo-pore channel . LSM12 confers NAADP sensitivity to the TPCs by acting as TPC accessory protein necessary for NAADP-evoked Ca2 release . This proteins consist of an N-terminal LSM domain and an anticodon-binding domain (AD,

) at the C terminus.
Ybfg-like, C-terminal domain (Ybfg_C)
Type: Domain

This is the presumed C-terminal domain found the uncharacterised protein YbfG from Bacillus subtilis. This domain may adopt an α/β structure. YbfG has a peptidoglycan-binding domain at the N terminus (

) and a central catalytic glycosyl hydrolase family 25 (GH25) domain (

). YbfG has a significant degree of similarity to BacA from E. faecalis, which together with BacL1, show cell wall lytic activity .
LRIM1/APL1C-like, dimerization domain (LRIM1_APL1C-like_dimer)
Type: Domain

This entry represents the C-terminal coiled-coil dimerisation region of the anopheles proteins LRIM1, APL1C and similar sequences mainly found in Anopheles gambiae and Anopheles coluzzii. In LRIM1, this region heterodimerises with a region of the APL1C protein . LRIM1 and APL1C are members of a family of proteins secreted by mosquitoes that contain an N-terminal LRR domain followed by a cysteine-rich region and a variable C terminus .
GH141-like, insertion domain (GH141_ins)
Type: Domain

This domain is found in bacterial proteins that belong to Glycoside hydrolase family 141 (GH141). This domain consists of two subdomains: a β-sandwich and a partly open β-barrel that are inserted into the catalytic domain comprising a right-handed parallel β-helix domain (

).
Lpg1496-like, N-terminal domain (Lpg1496-like_N)
Type: Domain

This domain is found at the N terminus of the uncharacterised Lpg1496 (also known as Lem10) protein from Legionella pneumophila (

,

). It is also known as KLAMP domain. This domain adopts an α/β structure with two α-helices flanked on one side by a five-stranded β-sheet and a four-stranded on the other. Lpg1496 contains two copies of this domain, known as KLAMP1 and KLAMP2 .
LOC400499-like (LOC400499-like)
Type: Family

This entry represents the human protein of unknown function LOC400499 (

) and similar sequences from vertebrates. It has a remarkable high confidence structure prediction showing an extended single β-sheet composed of a single long meander. No obvious sequence repeat is present in the sequence. Some members of this family contain lipovitellin homologous regions additionally to the N terminus of this family. Lipovitellin contains similar open β-structures which are used to bind to lipids suggesting that this family is also involved in lipid binding and storage.
Conserved oligomeric Golgi complex subunit 5, helical domain (COG5_helical)
Type: Domain

This entry represents an α-helical bundle domain found in COG5. This domain is found at the C-terminal of yeast sequences (such as

or

) and centrally located in animals (

), plants (

) and similar fungal proteins. Cog5 is a component of the conserved oligomeric Golgi (COG) complex which is involved in intra-Golgi protein trafficking and consists of eight subunits arranged in two lobes bridged by Cog1 . Cog5 is a member of the complexes associated with tethering containing helical rods (CATCHR) fold family, which is homologous to subunits of other multisubunit tethering complexes (MTCs) such as Dsl1, exocyst and Golgi-associated retrograde protein (GARP) complexes . COG5 is located in the smaller B lobe together with subunits 6-8, and interacts with subunits 1 and 7.
Phosphoprotein, C-terminal domain, cytorhabdovirus (PP_C_cytorhabdovirus)
Type: Domain

This entry represents the C-terminal domain of lettuce necrotic yellows virus phosphoprotein (PP) (

) and similar sequences from cytorhabdovirus. This protein adopts a lollipop-shaped structure comprising five helices .
DnaK suppressor protein-like, N-terminal domain (DksA-like_N)
Type: Domain

This domain is found at the N-terminal of DnaK suppressor protein from Agrobacterium fabrum (DksA) and similar proteins predominantly found in proteobacteria. This domain shows an all-α structure and is often found N-terminal to

.
1,3-alpha-isomaltosidase-like, N-terminal domain (AIMA-like_N)
Type: Domain

This entry represents a domain found at the N-terminal of 1,3-alpha-isomaltosidase from Kribbella flavida (AIMA, also known as Kfla1895) and similar sequences from actinomycetes. AIMA is involved in the intracellular degradation of the cyclic tetrasaccharide cyclobis-1-6-alpha-nigerosyl formed extracellularly from starch. It catalyses the hydrolysis of the alpha-1,3-glucosidic linkage of cyclobis-1-6-alpha-nigerosyl to yield isomaltose via a possible linear tetrasaccharide . This domain folds into an Ig-like β-sandwich.