SII-SWORD/CoKE huggingface dataset:
Myotubularin-related 12-like C-terminal domain (MTMR12-like_C)
Type: Domain

This domain is found at the C terminus of myotubularin-related (MTMR) proteins MTMR10, MTMR11 and MTMR12; and is typically between 115 and 138 amino acids in length. Myotubularin-related protein 12 (also known as the phosphatidylinositol-3 phosphate 3-phosphatase adapter subunit, 3-PAP) is a catalytically inactive member of the myotubularin gene family, which plays a role as an adapter for the phosphatidylinositol 3-phosphate-3-phosphatase myotubularin . MTMR10 and MTMR11 are also catalytically inactive.
Protein of unknown function DUF2659 (DUF2659)
Type: Family

This bacterial family of proteins has no known function.
Protein of unknown function DUF2660 (DUF2660)
Type: Family

This is a bacterial group of proteins with unknown function found in Rickettsiales.
Peroxisome proliferator-activated receptor gamma, N-terminal (PPARgamma_N)
Type: Domain

This domain is found in eukaryotes, and is typically between 42 and 65 amino acids in length. It is found N-terminal to

and

. There are two completely conserved residues (D and Y) that may be functionally important. Peroxisome proliferator-activated receptors (PPAR) are nuclear hormone receptors that control the expression of genes involved in lipid homeostasis in mammals.
Transcription initiation factor TFIID subunit 1, histone acetyltransferase domain (TAF1_HAT_dom)
Type: Domain

Transcription initiation factor TFIID is a multimeric protein complex that plays a central role in mediating promoter responses to various activators and repressors. The complex includes TATA binding protein (TBP) and various TBP-associated factors (TAFS). TFIID is a RNA polymerase II-specific TATA-binding protein-associated factor (TAF) that is essential for viability.

This group represents a transcription initiation factor TFIID subunit 1 (TAF1, also known as cell cycle gene 1 protein) . This is the largest subunit and the core scaffold of the complex, contains Ser/Thr kinase domains which can autophosphorylate or transphosphorylate other transcription factors including TP53, GTF2A1 and GTF2F1 , and has acetyltransferase activity towards histones H3 and H4 . It is essential for progression of the G1 phase of the cell cycle .

This entry represents the histone acetyltransferase domain (HAT, formerly known as DUF3591) that is found centrally in the protein TAF1 from eukaryotes. This region is highly conserved from yeast to human. X-ray determination of the crystal structure show it has a compact architecture that consists of a winged helix (WH) domain that folds on top of a triple barrel and a C-terminal α-helical region. The WH domain has intrinsic DNA-binding activity .
Nucleolar protein 19 (Nucleolar_19)
Type: Family

Nucleolar protein 19 (NOP19) plays an essential role in 40S ribosomal subunit biogenesis .
2-oxoisovalerate dehydrogenase, E1 alpha subunit, N-terminal domain (Oxoisoval_DH_suAlpha_N_dom)
Type: Domain

This domain is part of the N-terminal tail and β-sheet region of the bacterial 2-oxoisovalerate dehydrogenase E1 alpha subunit . It is found N-terminal to the dehydrogenase component

. There are two conserved sequence motifs: VPEP and RPG.
Autographa californica nuclear polyhedrosis virus (AcMNPV), 30.6kDa (AcMNPV_30.6kDa)
Type: Family

This group of viral proteins has no known function.
Enterobacter phage Enc34, ssDNA-binding protein (Enc34_ssDNA-bd)
Type: Family

This entry includes protein 50 from Bacteriophage APSE-1 and ssDNA-binding protein from Enterobacter phage Enc34 (

), which shows a globular shape with a mixed α/β architecture consisting mainly of β-strands that clearly resembles the oligosaccharide/oligonucleotide-binding (OB)-fold .
G protein-coupled receptor GPR1/2/3, C-terminal (GPR1/2/3_C)
Type: Domain

This domain is found in the yeast G protein-coupled receptor GPR1 and related fungal proteins including GPR2 and GPR3.

GPR1 associate with GPA2 and acts as G protein-coupled receptor that senses glucose and controls filamentous growth . GPR1 interacts with glucose and sucrose as agonists, while mannose acts as an antagonist . It forms part of a GPCR system with Gpa2 and Rgs2 for glucose sensing . This entry represents the conserved C-terminal domain.

GPR2 and GPR3 from the Nematode-trapping fungus Arthrobotrys oligospora are G protein-coupled receptors that sense nematode ascaroside pheromones and signals via adenylate cyclase to positively regulate trap formation for nematode capture .
Endoribonuclease antitoxin GhoS (GhoS)
Type: Family

GhoS is part of the GhoT-GhoS type V toxin-antitoxin (TA) system. GhoT is inhibited by antitoxin GhoS, which specifically cleaves its mRNA .
Long-chain fatty acyl-CoA thioesterase FcoT-like (FcoT_ThioEstase)
Type: Family

Proteins in this family have a HotDog fold. This family was formerly known as DUF2662. FcoT from M. tuberculosis (also known as (2E)-enoyl-[ACP] glycyltransferase) is involved in the biosynthesis of a unique class of isonitrile lipopeptides (INLPs) that seem to play a role in metal acquisition in M.marinum . Its structure suggested a thioesterase function. Assays showed that this protein was a thioesterase with a preference for long chain fatty acyl groups . The maximal Kcat was observed for palmitoyl-CoA, although longer and shorter molecules were also cleaved. In solution this protein forms a homo-hexameric complex.
Lysis protein, bacteriophage MS2 (Phage_MS2_lysis)
Type: Family

This entry represents putative lysis proteins from Bacteriophage MS2 and Bacteriophage BZ13.

The bacteriophage MS2 lysin protein

was identified as an overlapping cistron in the bacteriophage MS2 RNA . This proteins induces the formation of specific membrane adhesion sites between the inner and outer membranes, apparently leading to host cell lysis. Lysis may be performed via activation of host murein hydrolases .
Frog virus 3, Orf82R (Frog_virus-3_Orf82R)
Type: Family

This entry is represented by Frog virus 3, Orf82R; it is a family of uncharacterised Ranaviral proteins, a number of which are annotated as immediate early protein ICP-18.
Protein of unknown function DUF3160 (DUF3160)
Type: Family

This group of proteins has no known function.
Protein of unknown function DUF2813 (DUF2813)
Type: Family

This entry contains YbjD from Escherichia coli (strain K12), which is a conserved protein with a nucleotide triphosphate binding domain.
Domain of unknown function DUF3152 (DUF3152)
Type: Domain

This entry represents Actinobacteria proteins of unknown function. Some are annotated as membrane proteins, however this cannot be confirmed.
Protein of unknown function DUF2955 (DUF2955)
Type: Family

Some members in this group of proteins with unknown function are annotated as membrane proteins. However, this cannot be confirmed.
Protein of unknown function DUF2920 (DUF2920)
Type: Family

This bacterial family of proteins has no known function.
Domain of unknown function DUF2914 (DUF2914)
Type: Domain

This entry represents a domain of unknown function found in bacteria. It is often found at the C-terminal of an integral membrane region (PF19346).
Baseplate wedge protein gp53, bacteriophage T4 (Phage_T4_Gp53_baseplate_wedge)
Type: Family

The baseplate of Enterobacteria phage T4 controls host cell recognition, attachment, tail sheath contraction and viral DNA ejection. The structure of the baseplate suggests a mechanism of baseplate structural transition during the initial stages of T4 infection. The baseplate is assembled from six identical wedges that surround the central hub. Gp53, along with other T4 gene products, combine sequentially to assemble a wedge .
Transcription regulator SplA (Tscrpt_reg_SplA)
Type: Family

The SplA protein functions in trans as a negative regulator of the level of splB-lacZ expression in the developing forespore .
Protein suppressor of silencing, bacteriophage T7 (Phage_T7_5.5)
Type: Family

This family of phage proteins include Bacteriophage T7 gene 5.5 (also known as Protein suppressor of silencing) which plays a role in the inhibition of gene silencing by the host nucleoid-associated protein H-NS/hns. It disrupts higher-order H-NS-DNA complexes .
Long-chain fatty aldehyde decarbonylase (Ald_deCOase)
Type: Family

This cyanobacterial family of fatty aldehyde decarbonylases acts on mainly C16 and C18 substrates to form hydrocarbons and carbon monoxide . Note that the corresponding EC number (

) dating from 1989 refers to a nonorthologous Pisum sativum enzyme that acts on C18 and longer chains and attaches the overly narrow narrow name octadecanal decarbonylase.
CASAMP, second calponin-homology domain (CH_CAMSAP_2)
Type: Domain

This entry represents the second Calponin-homology (CH) domain found in CAMSAP and related proteins from animals.

The calmodulin-regulated spectrin-associated (CAMSAP) proteins are defined by a CKK domain that binds microtubules . It includes CAMSAPs from vertebrates and Patronin from invertebrates . CAMSAP1 is the representative member. It contains a conserved region, CC1, that binds to both spectrin and Ca2+/calmodulin in vitro and links spectrin-binding to neurite outgrowth . Patronin binds to and protects the MT minus-end against depolymerization . CAMSAP2 is a key microtubule-organising protein that specifically binds the minus end of non-centrosomal microtubules and regulates their dynamics and organisation. CAMSAP proteins carry an N-terminal region that includes two CH domains represented by

and

, a central region including a predicted coiled-coil, and a C-terminal CKK domain

, which is involved in binding CAMSAP proteins to microtubules .
Herpesvirus UL96 family (Herpesvirus_UL96)
Type: Family

The proteins in this entry belong to the Herpesviridae UL96 family. They include protein UL96 and protein U68. Currently no function is known.
Na(+)-translocating NADH-quinone reductase subunit A, C-terminal domain (NqrA_C_domain)
Type: Domain

This domain is found in bacterial Na(+)-translocating NADH-quinone reductase subunit A (NQRA) proteins. The Na(+)-translocating NADH: ubiquinone oxidoreductase (Na(+)-NQR) generates an electrochemical Na(+) potential driven by aerobic respiration . The function of this domain has not been characterised.
Glycosyl hydrolase, family 4, C-terminal (Glyco_hydro_4_C)
Type: Domain

Glycoside hydrolase family 4 (

) is a protein family that comprises enzymes with several known activities; 6-phospho-beta-glucosidase (

); 6-phospho-alpha-glucosidase (

); alpha-galactosidase (

). These enzymes require both NAD(H) and divalent metal (such asMn2+, Fe2+, Co2+, or Ni2+) for its activity .

This domain is found primarily in bacterial family 4 glycosyl hydrolases. It is found in the C terminus.
Rad60/SUMO-like domain (Rad60/SUMO-like_dom)
Type: Domain

This entry includes small ubiquitin-related modifier (SUMO) proteins. SUMOs are small proteins that are covalently attached to lysines as post-translational modifications and are used to control multiple cellular process including signal transduction, nuclear transport and DNA replication and repair . Unlike ubiquitin, they are not involved in protein degradation.
Defensin-like protein 20-28 (Defensin-like_20-28)
Type: Family

This is a family of plant antifungal proteins, including defensin-like protein 20-28. It has insecticidal and antifungal activity against certain plant pathogens .
Domain of unknown function DUF2666 (DUF2666)
Type: Domain

This entry represents a domain found in archaeal proteins, including PF2050 from Pyrococcus furiosus (

). PF2050, with an overall globular structure, contain this domain twice, each showing an antiparallel β-sheet and an α-helical bundle, and shows a positively charged basic cleft on one side. This protein interacts with circular and linear dsDNA .
Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf72 (AcMNPV_Orf72)
Type: Family

This entry is represented by Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf72; it is a family of uncharacterised viral proteins.

This Alphabaculovirus family of proteins has no known function.
Domain of unknown function DUF3492 (DUF3492)
Type: Domain

This domain is functionally uncharacterised and is found in bacteria, archaea and eukaryotes. It is typically between 259 to 282 amino acids in length. This region is found N-terminal

. There are two conserved sequence motifs: GGVS and EHGIY.
Glycosyl transferase family 4 domain (Glyco_trans_4)
Type: Domain

This presumed domain is functionally uncharacterised and found in bacteria. This region is about 170 amino acids in length and is found N-terminal to

. There is a single completely conserved residue G that may be functionally important.
Type I restriction enzyme R protein, C-terminal (TypeI_RM_Rsu_C)
Type: Domain

EcoR124 is made up of three subunits, HsdR, HsdS and HsdM. The R subunit has ATPase and restriction endonuclease activity. The enzyme has been characterised and shown to belong to a new family of the type I class of restriction and modification enzymes. After locating an unmethylated recognition site, the enzyme complex may serve as a molecular motor that translocates DNA in an ATP-dependent manner until a collision occurs that triggers cleavage. The enzyme undergoes major structural changes to bring the motor domains into contact with DNA, allowing DNA translocation. This prevents DNA access to the catalytic domains of both the R and M subunits, preventing both restriction and methylation . These enzymes are involved in bacterial defence by making double strand breaks in specific double stranded DNA sequences, e.g. that of invading bacteriophages. This entry represents the domain found in the C terminus of Type I restriction and modification enzymes .
Protein of unknown function DUF2740 (DUF2740)
Type: Family

This family of proteins with unknown function has a highly conserved sequence. They are found in Enterobacteria and Enterobacteria phages.
Domain of unknown function DUF3502 (DUF3502)
Type: Domain

This domain is about 140 amino acids in length and is functionally uncharacterised. It can be found at the C terminus of the SP_0092 protein from Streptococcus pneumoniae serotype 4. SP_0092 is a carbohydrate ABC transporter substrate-binding protein .
S-adenosylmethionine synthetase, N-terminal (S-AdoMet_synt_N)
Type: Domain

The three domains of S-adenosylmethionine synthetase have the same α+β fold. This entry represents the N-terminal domain of S-adenosylmethionine synthetase and is found in association with

and

.

S-adenosylmethionine synthetase (MAT,

) is the enzyme that catalyzes the formation of S-adenosylmethionine (AdoMet) from methionine and ATP . AdoMet is an important methyl donor for transmethylation and is also the propylamino donor in polyamine biosynthesis.

In bacteria there is a single isoform of AdoMet synthetase (gene metK), there are two in budding yeast (genes SAM1 and SAM2) and in mammals while in plants there is generally a multigene family.

The sequence of AdoMet synthetase is highly conserved throughout isozymes and species. The active sites of both the Escherichia coli and rat liver MAT reside between two subunits, with contributions from side chains of residues from both subunits, resulting in a dimer as the minimal catalytic entity. The side chains that contribute to the ligand binding sites are conserved between the two proteins. In the structures of complexes with the E. coli enzyme, the phosphate groups have the same positions in the (PPi plus Pi) complex and the (ADP plus Pi) complex and are located at the bottom of a deep cavity with the adenosyl group nearer the entrance .
S-adenosylmethionine synthetase, central domain (S-AdoMet_synt_central)
Type: Domain

The three domains of S-adenosylmethionine synthetase have the same α+β fold. This entry represents the central domain and is found in association with

and

.

S-adenosylmethionine synthetase (MAT,

) is the enzyme that catalyzes the formation of S-adenosylmethionine (AdoMet) from methionine and ATP . AdoMet is an important methyl donor for transmethylation and is also the propylamino donor in polyamine biosynthesis.

In bacteria there is a single isoform of AdoMet synthetase (gene metK), there are two in budding yeast (genes SAM1 and SAM2) and in mammals while in plants there is generally a multigene family.

The sequence of AdoMet synthetase is highly conserved throughout isozymes and species. The active sites of both the Escherichia coli and rat liver MAT reside between two subunits, with contributions from side chains of residues from both subunits, resulting in a dimer as the minimal catalytic entity. The side chains that contribute to the ligand binding sites are conserved between the two proteins. In the structures of complexes with the E. coli enzyme, the phosphate groups have the same positions in the (PPi plus Pi) complex and the (ADP plus Pi) complex and are located at the bottom of a deep cavity with the adenosyl group nearer the entrance .
S-adenosylmethionine synthetase, C-terminal (S-AdoMet_synt_C)
Type: Domain

The three domains of S-adenosylmethionine synthetase have the same α+β fold. This entry represents the C-terminal domain of S=adenosylmethionine synthetase and is found in association with

and

.

S-adenosylmethionine synthetase (MAT,

) is the enzyme that catalyzes the formation of S-adenosylmethionine (AdoMet) from methionine and ATP . AdoMet is an important methyl donor for transmethylation and is also the propylamino donor in polyamine biosynthesis.

In bacteria there is a single isoform of AdoMet synthetase (gene metK), there are two in budding yeast (genes SAM1 and SAM2) and in mammals while in plants there is generally a multigene family.

The sequence of AdoMet synthetase is highly conserved throughout isozymes and species. The active sites of both the Escherichia coli and rat liver MAT reside between two subunits, with contributions from side chains of residues from both subunits, resulting in a dimer as the minimal catalytic entity. The side chains that contribute to the ligand binding sites are conserved between the two proteins. In the structures of complexes with the E. coli enzyme, the phosphate groups have the same positions in the (PPi plus Pi) complex and the (ADP plus Pi) complex and are located at the bottom of a deep cavity with the adenosyl group nearer the entrance .
S-adenosylmethionine synthetase, conserved site (ADOMET_SYNTHASE_CS)
Type: Conserved_site

Two conserved site signatures are present in S-adenosylmethionine synthetase. The more N-terminal site represents a hexapeptide which is thought to be involved in ATP binding whilst the C-terminal conserved site is an almost perfectly conserved glycine-rich nonapeptide.

S-adenosylmethionine synthetase (MAT,

) is the enzyme that catalyzes the formation of S-adenosylmethionine (AdoMet) from methionine and ATP . AdoMet is an important methyl donor for transmethylation and is also the propylamino donor in polyamine biosynthesis.

In bacteria there is a single isoform of AdoMet synthetase (gene metK), there are two in budding yeast (genes SAM1 and SAM2) and in mammals while in plants there is generally a multigene family.

The sequence of AdoMet synthetase is highly conserved throughout isozymes and species. The active sites of both the Escherichia coli and rat liver MAT reside between two subunits, with contributions from side chains of residues from both subunits, resulting in a dimer as the minimal catalytic entity. The side chains that contribute to the ligand binding sites are conserved between the two proteins. In the structures of complexes with the E. coli enzyme, the phosphate groups have the same positions in the (PPi plus Pi) complex and the (ADP plus Pi) complex and are located at the bottom of a deep cavity with the adenosyl group nearer the entrance .
DNA polymerase III, beta sliding clamp, N-terminal (DNA_polIII_beta_N)
Type: Domain

DNA polymerase III is a complex, multichain holoenzyme responsible for most of the replicative synthesis in bacteria . It functions by adding nucleotide triphosphate (dNTP) residues to the 5'-end of a growing DNA chain, using a complementary DNA as template. The elongation factor beta-clamp, also called beta subunit, is part of the DNA polymerase III holoenzyme. However, beta-clamp is not attached to polymerase III permanently like the other subunits. It is loaded on the DNA, by clamp loader, a subunit of DNA Pol III .

The beta clamp forms a ring shaped dimer that encircles dsDNA (sliding clamp) in bacteria. The bacterial beta clamp is a homodimer; each monomer consists of three globular domains to yield a six-domain ring . It is structurally similar to the trimeric ring formed by proliferating cell nuclear antigen (PCNA) (found in eukaryotes and archaea) and the processivity factor (found in bacteriophages T4 and RB69) . This structural correspondence further substantiates the mechanistic connection between eukaryotic and prokaryotic DNA replication that has been suggested on biochemical grounds.

This entry describes the N-terminal domain of the beta sliding clamp.
DNA polymerase III, beta sliding clamp, C-terminal (DNA_polIII_beta_C)
Type: Domain

DNA polymerase III is a complex, multichain holoenzyme responsible for most of the replicative synthesis in bacteria . It functions by adding nucleotide triphosphate (dNTP) residues to the 5'-end of a growing DNA chain, using a complementary DNA as template. The elongation factor beta-clamp, also called beta subunit, is part of the DNA polymerase III holoenzyme. However, beta-clamp is not attached to polymerase III permanently like the other subunits. It is loaded on the DNA, by clamp loader, a subunit of DNA Pol III .

The beta clamp forms a ring shaped dimer that encircles dsDNA (sliding clamp) in bacteria. The bacterial beta clamp is a homodimer; each monomer consists of three globular domains to yield a six-domain ring . It is structurally similar to the trimeric ring formed by proliferating cell nuclear antigen (PCNA) (found in eukaryotes and archaea) and the processivity factor (found in bacteriophages T4 and RB69) . This structural correspondence further substantiates the mechanistic connection between eukaryotic and prokaryotic DNA replication that has been suggested on biochemical grounds.

This entry describes the C-terminal domain of the beta sliding clamp.
S-adenosylmethionine synthetase superfamily (S-AdoMet_synthetase_sfam)
Type: Homologous_superfamily

S-adenosylmethionine synthetase (MAT,

) is the enzyme that catalyzes the formation of S-adenosylmethionine (AdoMet) from methionine and ATP . AdoMet is an important methyl donor for transmethylation and is also the propylamino donor in polyamine biosynthesis.

In bacteria there is a single isoform of AdoMet synthetase (gene metK), there are two in budding yeast (genes SAM1 and SAM2) and in mammals while in plants there is generally a multigene family.

The sequence of AdoMet synthetase is highly conserved throughout isozymes and species. The active sites of both the Escherichia coli and rat liver MAT reside between two subunits, with contributions from side chains of residues from both subunits, resulting in a dimer as the minimal catalytic entity. The side chains that contribute to the ligand binding sites are conserved between the two proteins. In the structures of complexes with the E. coli enzyme, the phosphate groups have the same positions in the (PPi plus Pi) complex and the (ADP plus Pi) complex and are located at the bottom of a deep cavity with the adenosyl group nearer the entrance .