SII-SWORD/CoKE huggingface dataset:
Nine-heme cytochrome c (9HemeCytC)
Type: Family

Nine-heme cytochrome c proteins are characterized by the presence of nine heme groups arranged into two tetraheme clusters, with an additional heme located asymmetrically between the two regions. These proteins may form part of a transmembrane redox complex, facilitating electron transfer to the cytoplasm for the reduction of sulfate. This family includes proteins such as the nine-heme cytochrome c from Desulfovibrio desulfuricans (strain ATCC 27774 / DSM 6949 / MB), which is encoded by the Ddes_2038 gene.
Indoleacetate decarboxylase activating enzyme (Ind_deCO2_activ)
Type: Family

This entry represents the indoleacetate decarboxylase activating enzyme. This enzyme catalyzes the activation of indoleacetate decarboxylase under anaerobic conditions by generating an organic free radical on a glycine residue through the homolytic cleavage of S-adenosyl-L-methionine (SAM). The enzyme belongs to the organic radical-activating enzymes family and is involved in the metabolic pathway of indoleacetate decarboxylation. The activation process is crucial for the enzyme's function in anaerobic environments, facilitating the decarboxylation reaction necessary for the metabolic pathway.
Chondroitinase-AC (ChondaseAC)
Type: Family

Chondroitinase-AC, also known as chondroitinase AC, is an enzyme that belongs to the polysaccharide lyase 8 family. This enzyme is involved in the degradation of chondroitin sulfate, a glycosaminoglycan found in the extracellular matrix of animal tissues. Chondroitinase-AC specifically cleaves the glycosidic bonds in chondroitin sulfate, producing disaccharides containing unsaturated uronic acids. The enzyme is encoded by the cslA gene in Pedobacter heparinus (strain ATCC 13125 / DSM 2366 / CIP 104194 / JCM 7457 / NBRC 12017 / NCIMB 9290 / NRRL B-14731 / HIM 762-3). This enzyme plays a crucial role in the breakdown and remodeling of glycosaminoglycans, which is important for various biological processes, including tissue repair and development.
Iron transporter MagA (FeTrans_MagA)
Type: Family

Iron transporter MagA is a protein found in Paramagnetospirillum magneticum (strain ATCC 700264 / AMB-1). It plays a crucial role in the synthesis of bacterial magnetic particles (BMPs) by transporting iron from the environment into the cytoplasm across the cell membrane, and subsequently from the cytoplasm into the BMP lipid vesicle across the BMP membrane. MagA belongs to the monovalent cation:proton antiporter 2 (CPA2) transporter family (TC 2.A.37).
Digeranylgeranylglycerophospholipid reductase family (DGGPL_reductase)
Type: Family

Digeranylgeranylglycerophospholipid reductase is an enzyme involved in the reduction of 2,3-digeranylgeranylglycerophospholipids (unsaturated archaeols) into 2,3-diphytanylglycerophospholipids (saturated archaeols) in the biosynthesis of archaeal membrane lipids. This enzyme catalyzes the formation of archaetidic acid (2,3-di-O-phytanyl-sn-glyceryl phosphate) from 2,3-di-O-geranylgeranylglyceryl phosphate (DGGGP) via the hydrogenation of each double bond of the isoprenoid chains. It belongs to the geranylgeranyl reductase family, specifically the DGGGPL reductase subfamily. The enzyme can use both NADH and NADPH as electron donors and also catalyzes the reduction of naturally occurring 2,3-di-O-geranylgeranylglyceryl phosphate derivatives such as 2,3-di-O-phytyl-sn-glyceryl phosphate (DPHGP), 3-O-(2,3-di-O-phytyl-sn-glycero-phospho)-sn-glycerol (DPHGPG), and 2,3-di-O-phytyl-sn-glycero-phosphoethanolamine (DPHGPE). It is not active toward 2,3-di-O-geranylgeranylglycerol.
Hexaprenyl-diphosphate synthase large subunit (HxpDPsynlarge)
Type: Family

Hexaprenyl-diphosphate synthase large subunit catalyzes the condensation of three molecules of isopentenyl diphosphate with farnesyl diphosphate (FPP) to yield (all-E)-hexaprenyl diphosphate (HexPP; C30), the precursor of the prenyl side chain of menaquinone-6. The large subunit, Hexs-B, is responsible for the condensation reaction, and the final product chain length is cooperatively regulated by both the Hexs-A and Hexs-B subunits using the whole size of the hydrophobic cleft as a ruler. This protein belongs to the FPP/GGPP synthase family.
Bile acid--coenzyme A ligase (Bile_CoA_ligase)
Type: Family

This entry represents bile acid--coenzyme A ligase (BaiB), an enzyme found in Clostridium scindens (strain JCM 10418 / VPI 12708). BaiB belongs to the ATP-dependent AMP-binding enzyme family and plays a crucial role in the bile acid 7alpha-dehydroxylation pathway. This pathway is responsible for the formation of secondary bile acids via the 7alpha-dehydroxylation of primary bile acids, a process carried out by intestinal anaerobic bacteria. BaiB catalyzes the initial step in this pathway, which involves the ATP-dependent thioesterification of primary bile acids with coenzyme A. The enzyme is active with C-24 bile acids that have free carboxyl groups, such as cholate, deoxycholate, and chenodeoxycholate. The reaction produces AMP and pyrophosphate in addition to the bile acid-CoA thioester. BaiB activity is regulated by inhibition with diphosphate.
3(1)-hydroxy-L-isoleucine 4-dioxygenase (Il_dioxgen_HilB)
Type: Family

This entry represents the enzyme 3(1)-hydroxy-L-isoleucine 4-dioxygenase, also known as HilB, from Pantoea ananatis (strain AJ13355). HilB belongs to the iron/ascorbate-dependent oxidoreductase family and catalyzes the hydroxylation of L-4'-hydroxyisoleucine (4'-HIL) at the C-4 position to form L-4,4'-dihydroxyisoleucine (4,4'-DIHIL). Together with HilA, HilB catalyzes the two-step conversion of L-isoleucine into L-4,4'-dihydroxyisoleucine. In vitro, in the absence of HilA, HilB can also catalyze the oxidation of L-methionine and the C-4-hydroxylation of L-leucine and L-isoleucine.
Aldehyde dehydrogenase AldH (AldDh_AldH)
Type: Family

This entry represents aldehyde dehydrogenase (AldH) proteins, which belong to the aldehyde dehydrogenase family. These enzymes are capable of oxidizing various aldehydes such as formaldehyde, glyceraldehyde, butyraldehyde, glutaraldehyde, and benzaldehyde in vitro. They are likely involved in the oxidative D-xylose degradation pathway, catalyzing the oxidation step of 2-oxoglutarate semialdehyde to 2-oxoglutarate. These enzymes can utilize both NAD(+) and NADP(+), with a preference for NADP(+). They do not display succinate semialdehyde dehydrogenase activity. This entry includes proteins from Paenarthrobacter nicotinovorans.
MG319/MPN454 family protein (MPN454_MG319)
Type: Family

This entry represents the MG319/MPN454 family of proteins. The family includes uncharacterized proteins such as MG319 from Mycoplasma genitalium and its homolog MPN454 from Mycoplasma pneumoniae. The exact function of these proteins is currently unknown. Further research is needed to elucidate their roles within the cell.
DNA double-strand break repair ATPase Rad50 (Rad50_ATPase_DNA_repair)
Type: Family

The DNA double-strand break repair ATPase Rad50 is a crucial component of the Rad50/Mre11 complex, which plays a significant role in the early stages of DNA double-strand break (DSB) repair. This complex is thought to facilitate the opening of processed DNA ends, aiding in the recruitment of other proteins such as HerA and NurA. Rad50 is responsible for controlling the balance between DNA end bridging and DNA resection through ATP-dependent structural rearrangements of the Rad50/Mre11 complex. The protein contains a zinc-hook domain, where two conserved cysteine residues bind zinc, forming a V-shaped homodimer with another Rad50 molecule. This domain is essential for the structural integrity and function of the Rad50/Mre11 complex. Rad50 belongs to the SMC family, specifically the RAD50 subfamily, and is conserved across various species, including Sulfolobus acidocaldarius and Sulfurisphaera tokodaii.
Cyclohexane-1-carbonyl-CoA dehydrogenase (CyhCrbnylCoADH)
Type: Family

Cyclohexane-1-carbonyl-CoA dehydrogenase is an enzyme that belongs to the acyl-CoA dehydrogenase family. This enzyme is involved in the anaerobic degradation of cyclohexane carboxylic acid (CHC). It catalyzes the 1,2-dehydrogenation of cyclohexane-1-carbonyl-CoA (CHCoA) to cyclohex-1-ene-1-carbonyl-CoA (CHeneCoA). In Geobacter metallireducens, it also converts cyclohex-3-ene-1-carboxyl-CoA to cyclohexadiene-1-carboxyl-CoA isomers at a reduced rate. In Syntrophus aciditrophicus, it mediates the conversion of cyclohexane-1-carbonyl-CoA into cyclohex-1-ene-1-carbonyl-CoA during the biosynthesis of cyclohexane-1-carboxylate, a by-product produced during the fermentation of benzoate and crotonate to acetate.
46 kDa surface antigen (SurfProtP46)
Type: Family

The 46 kDa surface antigen (P46) is a protein found in Mesomycoplasma hyopneumoniae, specifically in strains J (ATCC 25934 / NCTC 10110) and 232. This protein is implicated in the surface structure of the bacterium, potentially playing a role in host-pathogen interactions. The P46 protein is 416 amino acids in length and is a significant component of the bacterial surface, which may be involved in immune evasion or adhesion to host tissues. Further functional characterization is required to fully understand the role of P46 in the pathogenesis of Mesomycoplasma hyopneumoniae.
Bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase FolD (FolD_Thplmales)
Type: Family

This entry represents the bifunctional protein FolD, which belongs to the tetrahydrofolate dehydrogenase/cyclohydrolase family. The FolD enzyme catalyzes two sequential reactions in the folate metabolism pathway: the oxidation of 5,10-methylenetetrahydrofolate to 5,10-methenyltetrahydrofolate, followed by the hydrolysis of 5,10-methenyltetrahydrofolate to 10-formyltetrahydrofolate. This protein is essential for the proper functioning of the folate cycle, which is crucial for the synthesis of nucleotides and amino acids. The FolD enzyme is found in various organisms, including Thermoplasma volcanium, Picrophilus torridus, and Thermoplasma acidophilum. The enzyme's activity is vital for cellular processes that require one-carbon units, such as DNA synthesis and repair.
Dimethylsulfonioproprionate lyase DddY (DimsulpropLyDddY)
Type: Family

Dimethylsulfonioproprionate lyase DddY is an enzyme found in Alcaligenes faecalis that cleaves dimethylsulfonioproprionate (DMSP), releasing dimethyl sulfide (DMS). DMS is the principal form by which sulfur is transported from oceans to the atmosphere. This enzyme plays a crucial role in the global sulfur cycle by facilitating the conversion of DMSP to DMS, which has significant implications for atmospheric chemistry and climate regulation .
Esterase EstD (Esterase_EstD)
Type: Family

Esterase EstD from Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8) is a member of the AB hydrolase superfamily, specifically the Esterase 10 family. This enzyme exhibits significant esterase activity with a preference for short acyl chain esters (C4-C8) in vitro. Its physiological function is not known. The enzyme is strongly inhibited by phenylmethylsulfonyl fluoride (PMSF), a serine protease inhibitor, and by mercury chloride (HgCl2). Diethyl pyrocarbonate, a histidine modifier, also inhibits the reaction, albeit less pronounced than PMSF. EDTA and dithiothreitol have no effect on enzyme activity. The enzyme does not display proteolytic activity using casein as substrate, nor peptidase activity when assayed with L-leucine p-nitroanilide and L-proline p-nitroanilide.
Glycerate 2-kinase (Gly_kinase)
Type: Family

Glycerate 2-kinase (EC 2.7.1.165) catalyzes the ATP-dependent phosphorylation of D-glycerate to 2-phosphoglycerate. This enzyme belongs to the glycerate kinase type-1 family and is involved in the glycerate pathway. It can also partially utilize GTP, CTP, or UTP as phosphate donors. The enzyme is found in various organisms, including Picrophilus torridus, where it plays a role in metabolic processes. The glycerate kinase type-1 family is characterized by its ability to phosphorylate glycerate, a key intermediate in several metabolic pathways.
Cytochrome c-554 Puf2C (Cyt554Puf2C)
Type: Family

Cytochrome c-554, encoded by the puf2C gene in Chloroflexus aurantiacus, serves as the immediate electron donor to the oxidized bacteriochlorophyll dimer (BChl2) during the initial step of light-induced charge separation. This protein can also oxidize low-potential substrates, playing a crucial role in the electron transport chain of photosynthetic organisms. Cytochrome c-554 is a 414 amino acid protein that is essential for efficient photosynthesis in Chloroflexus aurantiacus.
Nucleoside kinase (NucKin)
Type: Family

This entry represents nucleoside kinases, which belong to the carbohydrate kinase PfkB family. These enzymes catalyze the phosphorylation of various nucleosides to their corresponding nucleoside 5'-mono-phosphates in the presence of phosphate donors and divalent cations. The nucleoside kinase from Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165) displays broad substrate specificity, with the highest activity observed for guanosine, followed by inosine, cytidine, and adenosine. It shows negligible activity with thymidine, uridine, and 2-deoxyadenosine. ATP is the most efficient phosphate donor, although GTP and ITP can also be used. This enzyme does not exhibit sugar kinase activity, as it cannot phosphorylate ribose, fructose-1-phosphate, or fructose-6-phosphate.
Hexaprenyl-diphosphate synthase, small subunit (HexA)
Type: Family

This entry represents the small subunit of Hexaprenyl-diphosphate synthase (HexA) found in bacterial proteins. It is composed of mostly antiparallel α-helices joined by connecting loops .

Hexaprenyl-diphosphate synthase from Micrococcus luteus is made of a small subunit (HexA) and a large subunit (HexB). HexA catalyses the condensation of three molecules of isopentenyl diphosphate with farnesyl diphosphate (FPP) to yield (all-E)-hexaprenyl diphosphate (HexPP; C30), which is the precursor of the prenyl side chain of menaquinone-6. HexB catalyses the condensation reaction, and the final product chain length is cooperatively regulated by both the HexA and HexB subunits using the whole size of the hydrophobic cleft as a ruler .
Uncharacterised protein MPN160 family (MPN160_family)
Type: Family

This entry represents a family of uncharacterised proteins, including the uncharacterised protein MG147 homolog from Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1) and the uncharacterised protein MG147 from Mycoplasma genitalium (strain ATCC 33530 / DSM 19775 / NCTC 10195 / G37). The function of these proteins is currently unknown.
L-2-amino-4-chloropent-4-enoate dechlorinase/desaturase (PAGG_Syn_BesB)
Type: Family

This entry represents the enzyme L-2-amino-4-chloropent-4-enoate dechlorinase/desaturase, also known as BesB, from Streptantibioticus cattleyicolor (strain ATCC 35852 / DSM 46488 / JCM 4925 / NBRC 14057 / NRRL 8057). This enzyme is involved in the biosynthesis of terminal alkyne-containing amino acids such as L-propargylglycine (Pra) and L-beta-ethynylserine, which are produced as antibiotics by S. cattleya. BesB catalyzes the gamma-elimination of chloride from 4-chloro-allyl-L-glycine (L-2-amino-4-chloropent-4-enoate), followed by an isomerization to form the terminal-alkyne product L-propargylglycine. This enzyme belongs to the trans-sulfuration enzymes family.
GLD-3, KH2 domain (GLD-3_KH2)
Type: Domain

This is KH2 domain of defective in germline development protein 3 (GLD-3) from C. elegans, a protein required maternally for germline survival and embryogenesis. This is the first KH domain of the globular structure unit also formed by KH3, KH4 and KH5 .
GLD-3, KH3 domain (KH-I_CeGLD3_3rd)
Type: Domain

GLD-3 from C.elegans, also called defective in germ line development protein 3, is a Bicaudal-C (Bic-C) homologue that is involved in the translational control of germline-specific mRNAs during embryogenesis. It interacts with the cytoplasmic poly(A)-polymerase GLD-2. The two proteins cooperate to recognize target mRNAs and convert them into a polyadenylated, translationally active state. CeGLD-3 contains four K-homology (KH) RNA-binding domains, which are divergent KH domains that lacks the RNA-binding GXXG motif. This entry corresponds to the third KH domain.
CFAP410, C-terminal domain (CFAP410_C)
Type: Domain

This entry represents the C-terminal domain of Trypanosoma brucei cilia and flagella associated protein 410 (CFAP410) and related proteins. This domain is involved in oligomerisation and self-associates to form a tetrameric helical bundle composed of a dimer of two interlocking dimers.
S-layer protein, domain II (SlpA_D2)
Type: Domain

This domain is found in S-layer protein (SlpA) from Lactobacillus acidophilus and similar sequences. This domain is involved in the self-assembly and dimerisation of the S-layer. It adopts an α/β structure consisting of a curved mixed β-sheet and two α-helices packed on it. It has a partial structural similarity to the cadherin ectodomains comprising the curved β-sheet and differs significantly in the central part that adopts an α-helical conformation instead of extended β .
S-layer protein, N-terminal domain (SlpA_N)
Type: Domain

This entry represents the N-terminal domain of S-layer protein SlpA from Lactobacillus amylovorus and related proteins. This domain adopts unusual topology composed of β-strands arranged in a barrel-sandwich fold .
NACHT-associated inactive Restriction Endonuclease 2 domain (NA-iREase2_dom)
Type: Domain

This entry represents a predicted sensor domain in bacterial NACHT conflict systems. It is likely to bind a ligand which could contribute to activation of enzymatic domains additionally fused to the N terminus of the NACHT module .
MrpR, C-terminal catalytic domain (MrpR_C_cat)
Type: Domain

This family includes the MrpR protein from Bacillus subtilis (also known as SPbeta prophage-derived protein YopR), the master repressor of the lytic cycle of the temperate phage SPbeta. MrpR, a DNA-binding protein that has lost its recombinase function, shows a tyrosine recombinase fold with an N-terminal all-α domain

and a C-terminal catalytic domain (this entry) .
MrpR, N-terminal core-binding domain (MrpR_N_CB)
Type: Domain

This family includes the MrpR protein from Bacillus subtilis (also known as SPbeta prophage-derived protein YopR), the master repressor of the lytic cycle of the temperate phage SPbeta. MrpR, a DNA-binding protein that has lost its recombinase function, shows a tyrosine recombinase fold with an N-terminal core-binding (CB) domain with four α-helices (this entry) and a C-terminal catalytic domain (

) .
Tag1, middle barrel-like domain (Tag1_M)
Type: Domain

This entry represents the middle barrel-like domain of yeast Tag1 (also known as YLR173W). Tag1 is a vacuolar membrane protein involved in termination of autophagy. It regulates autophagy termination during persistent nitrogen starvation through Atg1p-mediated re-phosphorylation of Atg13p and PAS disassembly. It shows homology to LEA-2 domain, and together with TMEM106B from humans and Vac7 from yeast, are all predicted to be lipid transfer proteins . It was proposed that Tag1 is composed of 3 tandemly repeated LEA-2 domains .
Tag1, C-terminal domain (Tag1_C)
Type: Domain

This entry represents the C-terminal Ig-like domain of yeast Tag1 (also known as YLR173W). Tag1 is a vacuolar membrane protein involved in termination of autophagy. It regulates autophagy termination during persistent nitrogen starvation through Atg1p-mediated re-phosphorylation of Atg13p and PAS disassembly. It shows homology to LEA-2 domain, and together with TMEM106B from humans and Vac7 from yeast, are all predicted to be lipid transfer proteins . It was proposed that Tag1 is composed of 3 tandemly repeated LEA-2 domains .
Tag1, N-terminal domain (Tag1_N)
Type: Domain

This entry represents the N-terminal domain of yeast Tag1 (also known as YLR173W). Tag1 is a vacuolar membrane protein involved in termination of autophagy. It regulates autophagy termination during persistent nitrogen starvation through Atg1p-mediated re-phosphorylation of Atg13p and PAS disassembly. It shows homology to LEA-2 domain, and together with TMEM106B from humans and Vac7 from yeast, are all predicted to be lipid transfer proteins . Tag1 has 3 tandemly repeated LEA-2 domains .
Cobalt-zinc-cadmium resistance protein CzcI (CzcI)
Type: Family

This entry represents a group of proteins from betaproteobacteria, including Cobalt-zinc-cadmium resistance protein CzcI from Cupriavidus metallidurans. CzcI is a component of the czc cation-efflux system that confers resistance to cobalt, zinc and cadmium . This protein may have a regulatory function.
BapA/Bap-like, C-terminal domain (BapA_Bap-like_C)
Type: Domain

This entry represents a conserved C-terminal region shared by a number of large adhesins of Gram-negative genera mainly from gammaproteobacteria. Most members of this entry have repeat domains N-terminal to the region described here, including bacterial Ig-like domains. Notable members of the family include biofilm-associated protein BapA of Salmonella (

, ) and biofilm-associated Ig-like repeat protein Bap from Acinetobacter baumannii (

, ).
3-coathanger stack domain (GCX_COOH)
Type: Domain

This entry represents a domain which is frequently found as C-terminal of a larger protein, typically with Gly-Cys-Xaa(-Xaa) as the last three (or four) amino acids, or just upstream from type IX secretion system (T9SS) C-terminal sorting signal domain. In

from Spirosoma taeanense, a member of this group, this domain is predicted to adopt all-β structure for with the backbone resembling a stack of three wire coathangers, the first of which is the most poorly conserved.
Uncharacterised protein Aq_1974-like (Aq_1974-like)
Type: Family

This protein family includes the uncharacterised protein Aq_1974 from Aquifex aeolicus and similar sequences from Aquificales. This protein has a tryptophan content five times the average. Its structure is mainly α-helical with a small two-stranded β-sheet forming a fold named 'Aromatic Claw' .
Tailspike protein, C-terminal domain (G7C_C)
Type: Domain

This entry represents the Concanavalin-like C-terminal domain of Tail fibre protein from Escherichia phage vB_EcoP_G7C (

), also known as domain 6 (d6) of the tailspike receptor-binding protein (RBP) gp63.1. This domain is structurally similar to carbohydrate-binding domains and is putatively involved in substrate binding . This β-sandwich fold consists of two antiparallel β-sheets, each containing six strands (

).
Zonadhesin, first cohesin-like domain (Zona_CL1)
Type: Domain

This entry represents the first cohesin-like domain present in zonadhesin protein from Pichia pastoris .
Zonadhesin, second cohesin-like domain (Zona_CL2)
Type: Domain

This entry represents the second cohesin-like domain present in zonadhesin protein from Pichia pastoris .
Avirulence protein AvrPiz-t (AvrPiz-t)
Type: Family

This entry represents avirulence protein AvrPiz-t from Magnaporthe oryzae . It is predicted to be secreted and it can suppress programmed cell death (PCD) induced by BAX in tobacco which suggests that it might contribute to the pathogenicity of M.oryzae. This domain adopts a six-stranded β-sandwich

.
Glucosyltransferase Lgt1, N-terminal domain (Lgt1_N)
Type: Domain

This domain is found at the N-terminal end of Glucosyltransferase Lgt1 from Legionella pneumophila, which has been suggested to be involved in pathogenesis. This domain adopts a completely α-helical configuration . Members of this group are specific to Legionella species.