SII-SWORD/CoKE huggingface dataset:
26S proteasome regulatory complex, non-ATPase subcomplex, Rpn2/Psmd1 subunit (26S_Psome_Rpn2)
Type: Family

This group represents a 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn2/Psmd1 subunit.

Intracellular proteins, including short-lived proteins such as cyclin, Mos, Myc, p53, NF-kappaB, and IkappaB, are degraded by the ubiquitin-proteasome system. The 26S proteasome is a self-compartmentalising protease responsible for the regulated degradation of intracellular proteins in eukaryotes . This giant intracellular protease is formed by several subunits arranged into two 19S polar caps, where protein recognition and ATP-dependent unfolding occur, flanking a 20S central barrel-shaped structure with an inner proteolytic chamber. This overall structure is highly conserved among eukaryotes and is essential for cell viability. Proteins targeted to the 26S proteasome are conjugated with a polyubiquitin chain by an enzymatic cascade before delivery to the 26S proteasome for degradation into oligopeptides.

The 26S proteasome can be divided into two subcomplexes: the 19S regulatory particle (RP) and the 20S core particle (CP) . The 19S component is divided into a "base" subunit containing six ATPases (Rpt proteins) and two non-ATPases (Rpn1, Rpn2), and a "lid" subunit composed of eight stoichiometric proteins (Rpn3, Rpn5, Rpn6, Rpn7, Rpn8, Rpn9, Rpn11, Rpn12) . Additional non-essential and species specific proteins may also be present. The 19S unit performs several essential functions including binding the specific protein substrates, unfolding them, cleaving the attached ubiquitin chains, opening the 20S subunit, and driving the unfolded polypeptide into the proteolytic chamber for degradation. The 26s proteasome and 19S regulator are of medical interest due to their involvement in burn rehabilitation .
26S proteasome regulatory complex, non-ATPase subcomplex, Rpn1 subunit (26S_Psome_Rpn1)
Type: Family

Intracellular proteins, including short-lived proteins such as cyclin, Mos, Myc, p53, NF-kappaB, and IkappaB, are degraded by the ubiquitin-proteasome system. The 26S proteasome is a self-compartmentalising protease responsible for the regulated degradation of intracellular proteins in eukaryotes . This giant intracellular protease is formed by several subunits arranged into two 19S polar caps, where protein recognition and ATP-dependent unfolding occur, flanking a 20S central barrel-shaped structure with an inner proteolytic chamber. This overall structure is highly conserved among eukaryotes and is essential for cell viability. Proteins targeted to the 26S proteasome are conjugated with a polyubiquitin chain by an enzymatic cascade before delivery to the 26S proteasome for degradation into oligopeptides.

The 26S proteasome can be divided into two subcomplexes: the 19S regulatory particle (RP) and the 20S core particle (CP) . The 19S component is divided into a "base" subunit containing six ATPases (Rpt proteins) and two non-ATPases (Rpn1, Rpn2), and a "lid" subunit composed of eight stoichiometric proteins (Rpn3, Rpn5, Rpn6, Rpn7, Rpn8, Rpn9, Rpn11, Rpn12) . Additional non-essential and species specific proteins may also be present. The 19S unit performs several essential functions including binding the specific protein substrates, unfolding them, cleaving the attached ubiquitin chains, opening the 20S subunit, and driving the unfolded polypeptide into the proteolytic chamber for degradation. The 26s proteasome and 19S regulator are of medical interest due to their involvement in burn rehabilitation .

This group represents a 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn1 (regulatory-particle non-ATPase subunit 1). This subunit is essential for embryogenesis in Arabidopsis thaliana .
T-DNA border endonuclease virD2 (VirD2)
Type: Family

This entry represents the rhizobacteria endonuclease, virD2. Tumour formation by A.tumefaciens involves the transfer and integration of a defined segment (T-DNA) of Ti plasmid DNA into the plant nuclear genome. The virD operon encodes a site-specific endonuclease that cleaves at a unique site within both 24 bp direct repeats flanking the T-DNA .
Uncharacterised conserved protein UCP016134 (UCP016134)
Type: Family

There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function

A related protein (

) from Methanopyrus kandleri has this domain fused to the ProFAR isomerase (

) domain.
Alpha-(1, 3)-fucosyltransferase/alpha-(1, 4)-fucosyltransferase, Helicobacter (Alpha-1_3/4-FUT_helico)
Type: Family

Helicobacter pylori is a prevalent bacterial, gastroduodenal pathogen of humans that can express Lewis (Le) and related antigens in the O-chains of its surface lipopolysaccharide. The alpha1,3-fucosyltransferase VI (FUT VI) protein is a key enzyme for synthesis of sialyl Lewis X and Lewis X in epithelial cells . Despite striking functional similarity, there is low sequence homology between the bacterial and mammalian alpha(1,3/4)-and alpha(1,2)-fucosyltransferases. Le antigen expression and fucosylation have multiple biological effects on pathogenesis and disease outcome of H. pylori . The sialyl-Lewis X (SLe(x)) determinant is important in leukocyte extravasation, metastasis and bacterial adhesion . Changes in enzyme activity and the expression levels of alpha(1,6)fucosyltransferase [alpha(1,6)FT] occur in certain types of malignant transformations. Alpha(1,6)FT activity is higher in tumour tissue than in healthy tissue. Increased alpha(1,6)FT expression is also found in tumour tissues as compared to healthy and transitional tissues, inflammatory lesions and adenomas .

This group represents an alpha-(1,3)-fucosyltransferase/alpha-(1,4)-fucosyltransferase, found in Helicobacter species.
Probable ribonuclease VapC, Thermococci (VapV_Thermo)
Type: Family

This entry represents a family of nucleic acid-binding proteins with PIN domain from Thermococci . It appears to be related to the VapC family of proteins.
Uncharacterised conserved protein UCP016175, prenyltransferase beta-subunit-related (UCP016175_prenyltrans-rel)
Type: Family

There is currently no experimental data for members of this group. However, they are distantly related to the beta subunits of protein prenyltransferases--protein farnesyltransferase (FTase) and protein geranylgeranyl transferase type II (GGTase-II). Protein prenyltransferases catalyse the posttranslational modification of cysteines by isoprenoid hydrocarbon chains . The binding sites for both peptide and isoprenoid substrates reside primarily on the beta subunit of these enzymes .
Glial cell line-derived neurotrophic factor (GDNF)
Type: Family

This group represents glial cell line-derived neurotrophic factor (GDNF). This is a neurotrophic factor that enhances survival and morphological differentiation of dopaminergic neurons and increases their high-affinity dopamine uptake . Defects in GDNF are a cause of congenital central hypoventilation syndrome (also known as Ondine's curse) and are also linked with Hirschsprung disease .
Eukaryotic translation initiation factor 3 subunit E (eIF3e)
Type: Family

Eukaryotic translation initiation factor 3 subunit E (eIF3e) is a component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is involved in protein synthesis and, together with other initiation factors, stimulates binding of mRNA and methionyl-tRNAi to the 40S ribosome . In humans, eIF3e is required for nonsense-mediated mRNA decay .
Leucine carboxyl methyltransferase 1 (LCMT1)
Type: Family

This group represents the Ppm1 (also known as LCMT1) subgroup of leucine carboxymethyltransferases.

Ppm1 regulates the activity of serine/threonine phosphatase 2A (PP2A) through methylation of the C-terminal leucine residue of the catalytic subunit of PP2A . This affects the heteromultimeric composition of PP2A which in turn affects protein recognition and substrate specificity. Like many other methyltransferases Ppm1 uses S-adenosylmethionine (SAM) as the methyl donor. Ppm1 contains the common SAM-dependent methyltransferase core fold, with various insertions and additions creating a specific PP2A binding site .
Ubiquitinyl hydrolase (Ubiquitinyl_hydrolase)
Type: Family

This entry includes a group of ubiquitinyl hydrolases, also known as ubiquitin carboxyl-terminal hydrolases, including USP13 and USP5 from animals, and Ubp14 from plants and fungi.
tRNA (guanine(9)-N(1))-methyltransferase TRM10/TRM10A (TRM10/TRM10A)
Type: Family

Yeast tRNA (guanine(9)-N1)-methyltransferase TRM10 catalyses the formation of N(1)-methylguanine at position 9 (m1G9) in cytoplasmic tRNAs . This group also includes metazoa homologue A (TRM10A). In humans there are three TRM10 orthologues; a nonsense mutation in TRMT10A has been associated with microcephaly .
U6 snRNA-associated Sm-like protein LSm2 (U6_snRNA_Lsm2)
Type: Family

This group represents an U6 snRNA-associated Sm-like protein LSm2. It is a component of LSm protein complexes, which are involved in RNA processing and may function in a chaperone-like manner. LSm2 binds specifically to the 3'-terminal U-tract of U6 snRNA .
Prefoldin subunit 3 (PFD3)
Type: Family

Prefoldin subunit 3 (PFD3, also known as VBP-1) is part of the heteromeric co-chaperone complex, which delivers unfolded proteins to cytosolic chaperonin and acts as a cofactor. PFD3 binds specifically to cytosolic chaperonin (c-CPN) and transfers target proteins to it. It binds to nascent polypeptide chain and promotes folding . In fruit flies PFD3 (also known as mgr) interacts with von Hippel Lindau protein (Vhl) and betaTub56D/tubulin beta-1 chain. It is required for tubulin stability and spindle and centrosome formation in cooperation with Vhl .
Transcription initiation factor TFIIE, beta subunit (TFIIE-bsu)
Type: Family

Initiation of eukaryotic mRNA transcription requires melting of promoter DNA with the help of the general transcription factors TFIIE and TFIIH. In higher eukaryotes, the general transcription factor TFIIE consists of two subunits: the large alpha subunit (

) and the small beta (

). TFIIE beta has been found to bind to the region where the promoter starts to open to be single-stranded upon transcription initiation by RNA polymerase II. The approximately 120-residue central core domain of TFIIE beta plays a role in double-stranded DNA binding of TFIIE .

The TFIIE β-central core DNA-binding domain consists of three helices with a β-hairpin at the C terminus, resembling the winged helix proteins. It shows a novel double-stranded DNA-binding activity where the DNA-binding surface locates on the opposite side to the previously reported winged helix motif by forming a positively charged furrow .

This group represents a transcription initiation factor TFIIE, beta subunit.
Phosphoacetylglucosamine mutase (PAGM)
Type: Family

This group represents a phosphoacetylglucosamine mutase (PAGM; also known as phosphoglucomutase 3 or N-acetylglucosamine-phosphate mutase ). It is an essential enzyme found in eukaryotes that reversibly catalyzes the conversion of GlcNAc-6-phosphate into GlcNAc-1-phosphate as part of the UDP-N-acetylglucosamine (UDP-GlcNAc) biosynthetic pathway. UDP-GlcNAc is an essential metabolite that serves as the biosynthetic precursor of many glycoproteins and mucopolysaccharides. PAGM is a member of the alpha-D-phosphohexomutase superfamily , which catalyzes the intramolecular phosphoryl transfer of sugar substrates . The alpha-D-phosphohexomutases have four domains with a centrally located active site formed by four loops, one from each domain . All four domains are included in this alignment model.
DNA primase LEF1 (DNA_primase_LEF1)
Type: Family

Baculovirus late expression factor 1 (LEF-1) has been shown to have primase activity .
Transcription factor II-I (TF_II-I)
Type: Family

This group represents a general transcription factor II-I. TFII-I associates with multiple proteins to modulate both basal and signal-induced transcription . TFII-I transcription factors play an essential role during early vertebrate embryogenesis .
Kinase associated protein phosphatase (Kinase_assoc_Pase)
Type: Family

This entry represents a group of kinase associated protein phosphatases from plants, including KAPP (also known as protein phosphatase 2C 70) from Arabidopsis. KAPP dephosphorylates the Ser/Thr receptor-like kinase RLK5 . It is a component of a signaling pathway which mediates adaptation to NaCl stress .
Prefoldin, subunit 4 (PFDN4)
Type: Family

This group represents a prefoldin, subunit 4 (PFDN4, also known as Gim3 in budding yeasts). PFDN4 is part of the prefoldin heterohexamer copmlex (consists of two PFD-alpha type and four PFD-beta type subunits) that binds specifically to cytosolic chaperonin (c-CPN) and transfers targeted proteins to it. It binds to nascent polypeptide chain and promotes folding in an environment in which there are many competing pathways for nonnative proteins .
Acyl-CoA thioesterase, long chain (Acyl-CoA_thioEstase_long-chain)
Type: Family

Acyl-CoA thioesterases are a group of enzymes that catalyse the hydrolysis of acyl-CoAs to the free fatty acid and coenzyme A (CoASH). They consequently have the potential to regulate intracellular levels of acyl-CoAs, free fatty acids and CoASH. They may also be involved in the metabolic regulation of peroxisome proliferation.

Thioesters play a central role in cells as they participate in metabolism, membrane synthesis, signal transduction, and gene regulation. Thioesterases catalyse the hydrolysis of thioesters to the thiol and carboxylic acid components. Many thioesterases have a hot dog fold, including YciA from Escherichia coli and its close sequence homologue HI0827 from Haemophilus influenzae (HiYciA) .

In Helicobacter pylori, YbgC also belongs to the hot-dog family of proteins, with a epsilongamma tetrameric arrangement . YbgC proteins are bacterial acyl-CoA thioesterases associated with the Tol-Pal system. This system is important for cell envelope integrity and is part of the cell division machinery.

This group represents a group of acyl-CoA thioesterases that predominantly hydrolyse long-chain acyl-CoA molecules.
Myelin-oligodendrocyte glycoprotein (Myelin-oligodendrocyte_glycop)
Type: Family

This group represents a myelin-oligodendrocyte glycoprotein.
SAS complex subunit SAS5/transcription initiation factor TFIID subunit 14 (Sas5/TAF14)
Type: Family

This entry represents the Sas5 (Something About Silencing 5) subunit from the SAS complex, as well as subunit 14 (TAF14) from transcription initiation factor IID.

The native yeast SAS complex is a trimeric acetyltransferase complex composed of Sas2, Sas4, and Sas5. Sas2 is a member of the MYST protein family of histone acetyltransferases (HATs) . Sas5 is required for maximal histone acetyltransferase (HAT) activity of the complex, suggesting that it may be required to stabilise the complex or help in substrate recognition. SAS is capable of acetylating both free histones and nucleosomes, and is required for both histone H4 lysine-16 acetylation and histone H3 lysine-14 acetylation. This specific lysine preference corresponds to the role of SAS complex in antagonizing the spreading of Sir proteins at silent loci in Saccharomyces cerevisiae (Baker's yeast). The SAS complex is involved in transcriptional silencing at telomeres and at HML locus, as well as being involved in rDNA silencing.
TGF beta-induced protein/periostin (TGFBI/POSTN)
Type: Family

This entry includes TGF beta-induced protein (TGFBI, also known as betaig-H3 and keratoepithelin) and Periostin. They are are paralogues that contain a single emilin (EMI) and four fasciclin-1 (FAS1) modules and are secreted from cells .
Capsular polysaccharide synthesis, CpsB/CapC (Caps_polysacc_synth_CpsB/CapC)
Type: Family

Capsular polysaccharide biosynthesis proteins are critical for the production of a mature capsule in vitro. Members of Streptococcus pneumoniae have variable capsules, with about 90 known capsular serotypes that all have their own polysaccharide structure. cps14B to cps14H products are similar to other proteins involved in bacterial polysaccharide biosynthesis in both Gram-negative and -positive bacteria . CpsA to cpsD are common to most serotypes. CpsD is an autophosphorylating protein-tyrosine kinase. CpsC is required for CpsD tyrosine-phosphorylation, and CpsB is required for dephosphorylation of CpsD. CpsB is a novel manganese-dependent phosphotyrosine-protein phosphatase that belongs to the PHP (polymerase and histidinol phosphatase) family of phosphoesterases . Phosphorylation of proteins on hydroxyl amino acids (serine, threonine, tyrosine) occurs at different stages of pathenogenesis, including cell-cell interaction and adherence, translocation of bacterial effectors into host cells, and changes in host cellular structure and function induced by infection . CpsB, CpsC, CpsD, and ATP form a stable complex that enhances capsule synthesis and acts to regulate it .
NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial (NDUFS6)
Type: Family

NDUFS6 is an accessory subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I), that is believed not to be involved in catalysis . It harbours a Zn-binding site and is essential for biogenesis of mitochondrial complex I .
Interferon alpha/beta receptor 1 (Interferon_alpha/beta_rcpt-1)
Type: Family

The interferon-alpha/beta receptor 1 family of proteins associates with IFNAR2 to form the type I interferon receptor. Binding of interferons alpha and beta to type I IFNs triggers tyrosine phosphorylation of a number of proteins including JAKs, TYK2, STAT proteins and IFNR alpha- and beta-subunits themselves.
DNA damage-inducible transcript 3 (DNA_damage_induc_transcript_3)
Type: Family

This group represents the DNA damage-inducible transcript 3 protein, a C/EBP-homologous protein also known as C/EBP-zeta.
Acyl-protein synthetase, LuxE, bacterial (LuxE_bac)
Type: Family

LuxE is an acyl-protein synthetase found in bioluminescent bacteria. LuxE catalyses the formation of an acyl-protein thiolester from a fatty acid and a protein. This is the second step in the bioluminescent fatty acid reduction system, which converts tetradecanoic acid to the aldehyde substrate of the luciferase-catalysed bioluminescence reaction . A conserved cysteine found at position 364 in Photobacterium phosphoreum LuxE (

) is thought to be acylated during the transfer of the acyl group from the synthetase subunit to the reductase. The C-terminal of the synthetase is though to act as a flexible arm to transfer acyl groups between the sites of activation and reduction . A LuxE domain is also found in the Vibrio cholerae RBFN protein (

), which is involved in the biosynthesis of the O-antigen component 3-deoxy-L-glycero-tetronic acid.

This group represents an acyl-protein synthetase, LuxE type found in bacteria.
Polyketide biosynthesis protein CurC, predicted (Polyketide_Synth_CurC_prd)
Type: Family

This group represents a predicted polyketide biosynthesis protein CurC and related proteins that are members of cupin superfamily.
Histamine N-methyltransferase-like (HHMT-like)
Type: Family

This group represents histamine N-methyltransferase, which inactivates histamine by N-methylation. It plays an important role in degrading histamine and in regulating the airway response to histamine . This entry also includes chicken carnosine N-methyltransferase, which may be a paralogue of histamine N-methyltransferase .

Methyltransferases (EC [ec:2.1.1.-]) constitute an important class of enzymes present in every life form. They transfer a methyl group most frequently from S-adenosyl L-methionine (SAM or AdoMet) to a nucleophilic acceptor such as oxygen leading to S-adenosyl-L-homocysteine (AdoHcy) and a methylated molecule . All these enzymes have in common a conserved region of about 130 amino acid residues that allow them to bind SAM . The substrates that are methylated by these enzymes cover virtually every kind of biomolecules ranging from small molecules, to lipids, proteins and nucleic acids . Methyltransferase are therefore involved in many essential cellular processes including biosynthesis, signal transduction, protein repair, chromatin regulation and gene silencing . More than 230 families of methyltransferases have been described so far, of which more than 220 use SAM as the methyl donor.
Sphingomyelinase D/Phospholipase D (SMase_D/PLipase_D)
Type: Family

This family of enzymes includes sphingomyelinase D from Aspergillus flavus and phospholipase D from actinobacteria and fungi, which displays sphingomyelinase and hemolytic activity. In corynebacterium pseudotuberculosis and other pathogens, the enzyme acts as a virulence factor affecting bacterial dissemination and survival within the host .
Uncharacterised conserved protein UCP016666 (UCP016666)
Type: Family

There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. Members of this entry are mainly found in proteobacteria.
Phospholipid/glycerol acyltransferase, predicted (P_lipid/glycerol_AcTrfase_prd)
Type: Family

This group represents a predicted phospholipid/glycerol acyltransferase from bacteria.
Uncharacterised conserved protein UCP016817, ATP-dependent carboligase (UCP016817_carboligase)
Type: Family

This group represents a predicted ATP-dependent carboligase related to biotin carboxylase.
Mono-ADP-ribosyltransferase C3/Edin (Mono-ADP_RibTrfase_C3/Edin)
Type: Family

This group represents a group of mono-ADP-ribosyltransferases, including Edin (epidermal cell differentiation inhibitor) from Staphylococcus aureus and C3 from phage. Edin inhibits terminal differentiation of cultured mouse keratinocytes . C3 is an ADP-ribosyltransferase .
Transcription factor, GATA, plant (TF_GATA_pln)
Type: Family

This group represents GATA transcription factors found in plants. They may be involved in the regulation of some light-responsive genes .
NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 8 (NDUFA8)
Type: Family

This group represents a NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 8 .
Succinylglutamate desuccinylase (SuccinylGlu_desuccinylase)
Type: Family

This entry describes succinylglutamate desuccinylase (ASTE, also known as N-succinyl-L-glutamate amidohydrolase, N2-succinylglutamate desuccinylase, and SGDS; EC 3.5.1.96) that catalyses the fifth and last step in arginine catabolism by the arginine succinyltransferase pathway. It hydrolyzes N-succinyl-L-glutamate to succinate and L-glutamate .
Flagella accessory protein D, predicted, archaeal (FlaD_prd_arc)
Type: Family

This group represents a predicted flagella accessory protein D, archaeal type.
Glycosyl transferase, family 28, RedA, predicted (Glyco_trans_28_RedA_prd)
Type: Family

The biosynthesis of disaccharides, oligosaccharides and polysaccharides involves the action of hundreds of different glycosyltransferases. These enzymes catalyse the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. A classification of glycosyltransferases using nucleotide diphospho-sugar, nucleotide monophospho-sugar and sugar phosphates ([ec:2.4.1.-]) and related proteins into distinct sequence based families has been described . This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. The same three-dimensional fold is expected to occur within each of the families. Because 3-D structures are better conserved than sequences, several of the families defined on the basis of sequence similarities may have similar 3-D structures and therefore form 'clans'.

Glycosyltransferase family 28

comprises enzymes with a number of known activities; 1,2-diacylglycerol 3-beta-galactosyltransferase (

); 1,2-diacylglycerol 3-beta-glucosyltransferase (

); beta-N-acetylglucosamine transferase (

).
Structural analysis suggests the C-terminal domain contains the UDP-GlcNAc binding site.

This group represents a predicted family 28 glycosyltransferase, RedA.