SII-SWORD/CoKE huggingface dataset:
YhdP (YhdP)
Type: Family

This entry describes YhdP and related proteins present in the Proteobacteria.

Intermembrane phospholipid transporter YhdP is involved in maintaining lipid homeostasis in the outer membrane of Gram-negative bacteria. It likely transports phospholipids between the inner and outer membranes, providing a bridge-like structure that shields the lipids as they traverse the periplasm. Phosphate-containing molecules are thought to be captured along a hydrophobic groove that extends throughout the protein, excluding the extreme N-terminal. YhdP also appears to influence the levels of cyclic enterobacterial common antigen, a soluble molecule located in the periplasm. Along with TamB and YdbH, YhdP performs an essential function in supporting bacterial growth and outer membrane stability, though these proteins are redundant but not functionally equivalent. The transport activity of YhdP is thought to be biased towards phospholipids with saturated fatty acids, whereas TamB may preferentially handle more unsaturated phospholipids. Despite their differences, any one of these three proteins is sufficient to sustain growth under normal conditions . This protein is predicted to be related to AsmA proteins .
Glycogen debranching enzyme, GlgX type (Glycogen_debranch_GlgX)
Type: Family

This entry represents the glycogen debranching enzyme GlgX found in Escherichia coli, as well as its equivalogs in other prokaryotic species. This enzyme encodes an isoamylase-type debranching enzyme with high specificity for hydrolysis of chains consisting of three or four glucose residues, and is classed as family 13 of glycosyl hydrolases . GlgX is not required for glycogen biosynthesis, but instead acts as a debranching enzyme for glycogen catabolism. This entry distinguishes GlgX from pullanases and other related proteins that also operate on alpha-1,6-glycosidic linkages .

O-Glycosyl hydrolases (

) are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families . This classification is available on the CAZy (CArbohydrate-Active EnZymes) website.
Pullulanase, extracellular (Pullulan_Gpos)
Type: Domain

Pullulan is an unusual, industrially important polysaccharide in which short alpha-1,4 chains (maltotriose) are connected in alpha-1,6 linkages. Enzymes that cleave alpha-1,6 linkages in pullulan and release maltotriose are called pullulanases although pullulan itself may not be the natural substrate. In contrast, a glycogen debranching enzyme such GlgX, homologous to this family, can release glucose at alpha,1-6 linkages from glycogen first subjected to limit degradation by phosphorylase. Characterised members of this family include a surface-located pullulanase from Streptococcus pneumoniae and an extracellular bifunctional amylase/pullulanase with C-terminal pullulanase activity .
Alpha-1,6-glucosidases, pullulanase-type (Pullul_strch)
Type: Domain

Members of this protein family include secreted (or membrane-anchored) pullulanases of Gram-negative bacteria and pullulanase-type starch debranching enzymes of plants. Both enzymes hydrolyze alpha-1,6 glycosidic linkages. Pullulan is an unusual, industrially important polysaccharide in which short alpha-1,4 chains (maltotriose) are connected in alpha-1,6 linkages. Enzymes that cleave alpha-1,6 linkages in pullulan and release maltotriose are called pullulanases although pullulan itself may not be the natural substrate. This family is closely homologous to, but architecturally different from the pullulanases of Gram-positive bacteria (

).
Pullulanase, type I (PulA_typeI)
Type: Domain

Pullulan is an unusual, industrially important polysaccharide in which short alpha-1,4 chains (maltotriose) are connected in alpha-1,6 linkages. Enzymes that cleave alpha-1,6 linkages in pullulan and release maltotriose are called pullulanases although pullulan itself may not be the natural substrate. This family consists of pullulanases related to the entries in

and

but having a different domain architecture with shorter sequences. Members are called type I pullulanases .
Type III secretion system, needle protein (T3SS_needle_YscF)
Type: Family

Type III secretion systems translocate proteins, usually virulence factors, out across both inner and outer membranes of certain Gram-negative bacteria and further across the plasma membrane and into the cytoplasm of the host cell. This protein, termed YscF in Yersinia, and EscF, PscF, EprI, etc. in other systems, forms the needle of the injection apparatus . The structure of PscF has been revealed .
Coenzyme PQQ biosynthesis protein B (PQQ_synth_PqqB)
Type: Family

This entry describes coenzyme PQQ biosynthesis protein B, a gene required for the biosynthesis of pyrrolo-quinoline-quinone (coenzyme PQQ). PQQ is required for some glucose dehydrogenases and alcohol dehydrogenases. Note that this gene appears to be required for PQQ in biosynthesis in Methylobacterium extorquens (under the name pqqG) and in Klebsiella pneumoniae but that the equivalent pqqV in Acinetobacter calcoaceticus is not necessary for heterologous expression of PQQ biosynthesis in Escherichia coli. Based on this latter finding, it is suggested that PqqB might be a transporter or a PQQ-dependent enzyme rather than a PQQ biosynthesis enzyme .
Coenzyme PQQ biosynthesis protein E, bacteria (PQQ_synth_PqqE_bac)
Type: Family

Coenzyme PQQ biosynthesis protein E is required for the biosynthesis of pyrrolo-quinoline-quinone (coenzyme PQQ). PqqE is also known as PqqA peptide cyclase, as it carries out, in conjunction with PqqD, the radical-mediated formation of a new carbon-carbon bond between two amino acid side chains on PqqA .
Coenzyme PQQ biosynthesis protein PqqF (PQQ_synth_PqqF)
Type: Family

In the subset of species that make coenzyme PQQ (pyrrolo-quinoline-quinone), this peptidase is found in the PQQ biosynthesis region and is thought to act as a protease on PqqA (

), a probable peptide precursor of the coenzyme. PQQ is required for some glucose dehydrogenases and alcohol dehydrogenases .
Coenzyme PQQ biosynthesis protein C (PqqC)
Type: Family

This entry describes the coenzyme PQQ (pyrrolo-quinoline-quinone) biosynthesis protein PqqC. Pyrroloquinoline quinone (PQQ) is the prosthetic group of several bacterial enzymes, including methanol dehydrogenase of methylotrophs and the glucose dehydrogenase of a number of bacteria . PQQC is an oxidase whose reaction involves a ring closure and eight-electron oxidation of its substrate (AHQQ) to produce PQQ . This entry does not include related proteins likely to be functionally distinct from PqqC, such as homologues found in the Chlamydias.
Cyd operon protein YbgE (Cyd_oper_YbgE)
Type: Family

This entry describes a small protein of unknown function, about 100 amino acids in length, essentially always found in an operon with CydAB, subunits of the cytochrome d terminal oxidase. It appears to be an integral membrane protein. It is found so far only in the Proteobacteria .
Phosphopantothenoylcysteine decarboxylase (CoaC_strep)
Type: Family

In most bacteria, a single bifunctional protein catalyses phosphopantothenoylcysteine decarboxylase and phosphopantothenate--cysteine ligase activities, sequential steps in coenzyme A biosynthesis. These activities reside in separate proteins encoded by tandem genes in some bacterial lineages. This entry describes proteins from the genera Streptococcus and Enterococcus homologous to the N-terminal region of

, corresponding to phosphopantothenoylcysteine decarboxylase activity .
Phosphopantothenate--cysteine ligase (CoaB_strep)
Type: Family

In most bacteria, a single bifunctional protein catalyses phosphopantothenoylcysteine decarboxylase and phosphopantothenate--cysteine ligase activities, sequential steps in coenzyme A biosynthesis. These activities reside in separate proteins encoded by tandem genes in some bacterial lineages. This entry describes proteins from the genera Streptococcus and Enterococcus homologous to the C-terminal region of

, corresponding to phosphopantothenate--cysteine ligase activity .
Sodium/pantothenate symporter (Na/pantothenate_symporter)
Type: Family

Pantothenate (vitamin B5) is a precursor of coenzyme A and is made from aspartate and 2-oxoisovalerate in most bacteria. However, some pathogens must import pantothenate. This entry describes PanF, a sodium/pantothenate symporter. Several species that have this transporter appear to lack all enzymes of pantothenate biosynthesis, namely Haemophilus influenzae, Pasteurella multocida, Fusobacterium nucleatum, and Borrelia burgdorferi (Lyme disease spirochete) .
Type II secretion system protein GspF (T2SS_GspF)
Type: Family

GspF is the inner membrane component of the type II secretion system (T2SS). It interacts with GspE, a cytoplasmic hexameric ATPase of the T2SS .

The type II secretion system (T2SS) is one of several extracellular secretion systems in gram-negative bacteria. It delivers toxins and a range of hydrolytic enzymes including proteases, lipases and carbohydrate-active enzymes to the cell surface or extracellular space . T2SS systems are composed of 11 to 15 different proteins, which are generally called GspA to GspO and GspS. The T2SS spans the two bacterial membranes and ensures secretion of folded proteins across the outer membrane pore formed by GspD. The inner membrane complex contains GspC, GspL, GspM, and GspF. The cytoplasmic domains of GspL and GspF interact with an ATPase, GspE. GspE is thought to energize the formation of a short pseudopilus by several pilin-like proteins, GspG to GspK . GspD has been shown to interact with the inner membrane component GspC .
Sodium/proline symporter (Na/Pro_symporter)
Type: Family

This family consists of the sodium/proline symporter (proline permease) from a number of Gram-negative and Gram-positive bacteria and from the archaeal genus Methanosarcina. The Na+/proline transporter contributes to the use of L-proline as a nutrient and may supply cells with compatible solute during adaptation to osmotic stress .
TRAP transporter solute receptor, TAXI family (TRAP_TAXI)
Type: Family

Substrate-binding proteins (SBPs) are extracytoplasmic proteins involved in substrate recognition for several different bacterial transporters. This entry represents the TAXI family of the substrate-binding proteins. They are part of the TAXI-TRAP (tripartite ATP-independent periplasmic) transporter. Proteins in this family have been proposed to function as glutamine/glutamate specific uptake systems and a role in glutamate transport .

The tripartite ATP-independent periplasmic (TRAP) transporters are substrate-binding protein (SBP)-dependent secondary transporters found in prokaryotes. They consist of a substrate-binding protein (SBP) of the DctP or TAXI families and two integral membrane proteins that form the DctQ and DctM protein families .
TRAP C4-dicarboxylate transport system permease, fused DctM-DctQ (TRAP_DctM-Dct_fused)
Type: Family

In some species, the 12-transmembrane spanning (DctM) and 4-transmembrane spanning (DctQ) components of tripartite ATP-independent periplasmic (TRAP)-type transporters are fused. This entry describes such transporters, found in the archaea and in bacteria.
Carbamoyl dehydratase HypE (HypE)
Type: Family

This family includes carbamoyl dehydratase HypE (sometimes known as hydrogenase maturation protein HypE or HupE) which is involved in the maturation of [NiFe] hydrogenases. Along with HypF, it catalyzes the synthesis of the CN ligands of the active site iron of [NiFe]-hydrogenases . HypE dehydrates its own carbamoyl moiety in an ATP-dependent process to yield the enzyme thiocyanate. The N-terminal domain of HypE is related to the ATP-binding domains of the AIR synthases, selenophosphate synthetase (SelD), and FGAM synthase and is thought to bind ATP .
Phage major tail protein TP901-1 (Phgtail_TP901_1)
Type: Family

This entry describes the major tail protein (MTP) of the Siphoviridae and MTP genes in prophage regions of bacterial genomes. Homologues are also found in Gene Transfer Agents (GTA) , including ORFg9 (RCAP_rcc01691) of the GTA of Rhodobacter capsulatus (Rhodopseudomonas capsulata) [see Fig.1, in

]. The tail tube protein gp17.1* from bacteriophage SPP1 forms a sixfold helical, rigid tail tube which ejects of the phage DNA into the host when it binds to the entry receptor on the host cell surface, triggering structural rearrangements of the tail tube .
tRNA endonuclease-like domain superfamily (tRNA_endonuc-like_dom_sf)
Type: Homologous_superfamily

This superfamily represents a structural domain found in three types of endonucleases: TsnA endonuclease (N-terminal) , Hjc-type resolvase , and tRNA-intron endonuclease (C-terminal) (

) . These domains have a 3-layer α/β/α topology, which is similar in structure to a motif found in several restriction endonucleases.

TsnA endonuclease is a catalytic component of the Tn7 transposition system. Tn7 transposase is composed of four proteins: TnsA, TnsB, TnsC and TsnD. DNA breakage at the 5' end of the transposon is carried out by TnsA, and breakage and joining at the 3' end is carried out by TnsB. TnsC is the molecular switch that regulates transposition. The N-terminal domain of TnsA is catalytic.

Hjc is a type of Holliday junction resolvase. The Holliday junction is an essential intermediate of homologous recombination, comprising four-stranded DNA complexes that are formed during recombination and related DNA repair events. During homologous recombination, genetic information is physically exchanged between parental DNAs via crossing single strands of the same polarity within the four-way Holliday structure. Hjc is an archaeal endonuclease, which specifically resolves the junction DNA to produce two separate recombinant DNA duplexes. This process is terminated by the endonucleolytic activity of resolvases, which convert the four-way DNA back to two double strands.
His6/HISN3 (His6/HISN3)
Type: Family

His6 acts in the biosynthesis of histidine and has been characterised in Saccharomyces cerevisiae and Arabidopsis where it complements the Escherichia coli HisA gene. In eukaryotes, the gene is known as His6. In bacteria, this gene is found in Fibrobacter succinogenes (Bacteroides succinogenes), presumably due to lateral gene transfer from plants in the rumen gut. This entry also represents 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase HISN3 in plants.
Dihydrodipicolinate reductase, plant-type (Dihydrodipicolinate_Rdtase_pln)
Type: Family

Dihydrodipicolinate reductase is an enzyme found in bacteria and higher plants which is involved in the biosynthesis of diaminopimelic acid, a component of bacterial cell walls, and the essential amino acid L-lysine. It catalyses the the reduced pyridine nucleotide-dependent reduction of the alpha,beta-unsaturated cyclic imine, dihydrodipicolinate, to generate tetrahydrodipicolinate as shown below :

2,3-dihydrodipicolinate + NAD(P)H = 2,3,4,5-tetrahydrodipicolinate + NAD(P)(+)

As this enzyme is not found in mammals it is a potential target for the development of novel antibacterial and herbicidal compounds.

This narrow family includes genes from Arabidopsis and Fibrobacter succinogenes (Bacteroides succinogenes) (which probably recieved the gene from a plant via lateral gene transfer). The sequences are distantly related to the dihydrodipicolinate reductases from archaea. In Fibrobacter this gene is the only candidate DHPR in the genome.
Ribose 5-phosphate isomerase B, Actinobacteria-type (Rib-5-P_Isoase_Actino)
Type: Family

This family is a member of the RpiB/LacA/LacB family. It includes ribose 5-phosphate isomerases and D-erythrulose-4-phosphate isomerases . The only candidates for ribose 5-phosphate isomerase in the Actinobacteria are members of this family .

Ribose 5-phosphate isomerase (

) forms a homodimer and catalyses the interconversion of D-ribose 5-phosphate and D-ribulose 5-phosphate in the non-oxidative branch of the pentose phosphate pathway. This reaction permits the synthesis of ribose from other sugars, as well as the recycling of sugars from nucleotide breakdown. Two unrelated enzymes can catalyse this reaction: RpiA (found in most organisms) and RpiB (found in some bacteria and eukaryotes).
Transaldolase, Staphylococcus-type (Transald_staph-type)
Type: Family

This small family of proteins belong to the transaldolases. Coxiella and Staphylococcus lack members of the known transaldolase families and appear to require a transaldolase activity for completion of the pentose phosphate pathway.
Phosphate binding protein (Phos-bd)
Type: Family

Members of this family are phosphate-binding proteins. Most are found in phosphate ABC-transporter operons, but some are found in phosphate regulatory operons . This entry separates members from the phosphate ABC transporter phosphate binding proteins described by

.
Phosphoserine phosphatase/homoserine phosphotransferase bifunctional protein (HSK-PSP)
Type: Family

This protein is has been characterised as both a phosphoserine phosphatase and a phosphoserine:homoserine phosphotransferase . In Pseudomonas aeruginosa, where the characterisation was done, a second phosphoserine phosphatase (SerB) and a second homoserine kinase (thrB) are found, but in Fibrobacter succinogenes neither are present.
tRNA/tmRNA (uracil-C(5))-methyltransferase, TrmA (TrmA_MeTrfase)
Type: Family

This family consists of methyltransferases. The family member from Escherichia coli has been shown to have dual-specificity, catalysing the formation of 5-methyluridine at position 54 (m5U54) in all tRNAs, and that of position 341 (m5U341) in tmRNA (transfer-mRNA) . This enzyme is inhibited by adenosylhomocysteine .
Lysine biosynthesis enzyme LysX (LysX_arch)
Type: Family

The family of proteins found in this family include the characterised LysX from
Thermus thermophilus
which is part of a well-organised lysine biosynthesis gene cluster . LysX is believed to carry out an ATP-dependent acylation of the amino group of alpha-aminoadipate in the prokaryotic version of the fungal AAA lysine biosynthesis pathway. No species having a sequence in this family contains the elements of the more common diaminopimelate lysine biosythesis pathway, and none has been shown to be a lysine auxotroph. These sequences have mainly recieved the name of the related enzyme, "ribosomal protein bS6 modification protein RimK". RimK has been characterised in
Escherichia coli
, and acts by ATP-dependent condensation of bS6 with glutamate residues .
Fibrobacter succinogenes major paralogous domain (Fib_succ_major)
Type: Domain

This domain of about 175 to 200 amino acids is found, in from one to five copies, in over 50 proteins in Fibrobacter succinogenes subsp. succinogenes S85, an obligate anaerobe of the rumen. Many members of this family have an apparent lipoprotein signal sequence. Conserved cysteine residues, suggestive of disulphide bond formation, are also consistent with an extracytoplasmic location for this domain. This domain can also be found in small numbers of proteins in Chlorobium tepidum and Bacteroides thetaiotaomicron.
Homocitrate synthase (Homocitrate_synth)
Type: Family

This entry includes the yeast LYS21 gene which carries out the first step of the alpha-aminoadipate (AAA) lysine biosynthesis pathway . A related pathway is found in Thermus thermophilus . This enzyme is closely related to 2-isopropylmalate synthase (LeuA) and citramalate synthase (CimA), both of which are present in the euryarchaeota. Some archaea have a separate homocitrate synthase (AksA) which also synthesizes longer homocitrate analogs .
Conserved hypothetical protein CHP02147 (CHP02147)
Type: Family

This family consists of the 40 members of a paralogous protein family in the rumen anaerobe Fibrobacter succinogenes S85, and a smaller number in Bdellovibrio bacteriovorus HD100. Member proteins are about 270 residues long and appear to lack signal sequences and transmembrane helices. The only perfectly conserved residue is a glycine in an otherwise poorly conserved region, suggesting members are not enzymes. The family is not characterised.
Fibro-slime (Fibro_Slime)
Type: Domain

This entry represents a conserved region of about 90 amino acids, shared in at least 4 distinct large putative proteins from the slime mold Dictyostelium discoideum (Slime mold) and 10 proteins from the rumen bacterium Fibrobacter succinogenes (Bacteroides succinogenes), and in no other species so far.
Alpha-maltose-1-phosphate synthase (M1P_synthase)
Type: Family

Alpha-glucan in mycobacteria is assembled intracellularly utilizing the building block alpha-maltose-1-phosphate (M1P). Mycobacterial GlgA was believed to be a glycogen synthase, but subsequent studies have shown that this enzyme is a M1P-producing glucosyltransferase, producing little or no classical glycogen in vivo. It has been rename to GlgM .
Isopentenyl-diphosphate delta-isomerase, type 1 (IsopentenylPP_isomerase_typ1)
Type: Family

This entry represents type 1 of two non-homologous families of the enzyme isopentenyl-diphosphate delta-isomerase (IPP isomerase;

). IPP isomerase is a member of the Nudix hydrolase superfamily, and is a key enzyme in the isoprenoid biosynthetic pathway. It catalyses the interconversion of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate. Dimethylallyl phosphate is the initial substrate for the biosynthesis of carotenoids and other long chain isoprenoids . IPP is an essential building block for many compounds, including enzyme cofactors, sterols, and prenyl groups. This enzyme interconverts isopentenyl diphosphate and dimethylallyl diphosphate. The enzyme requires one Mn2+ or Mg2+ ion in its active site to fold into an active conformation and also contains the Nudix motif, a highly conserved 23-residue block (GX5EX7REUXEEXGU, where U = I, L or V), that functions as a metal binding and catalytic site. The metal binding site is present within the active site and plays structural and catalytical roles. IPP isomerase is well represented in several bacteria, archaebacteria and eukaryotes, including fungi, mammals and plants. Despite sequence variations (mainly at the N terminus), the core structure is highly conserved .
Ribokinase (Ribokinase)
Type: Family

This entry describes ribokinase enzyme. Ribokinase catalyses the first step in ribose catabolism. This phosphorylation of ribose to ribose-5-phosphate using ATP traps ribose within the cell after uptake and prepares the sugar for use in the synthesis of nucleotides and histidine, and for entry into the pentose phosphate pathway . The rbsK gene encoding ribokinase typically is found with ribose transport genes . This entry also includes bifunctional ribokinase/ribose-5-phosphate isomerase A from Lactobacillus sanfranciscensis and deoxyribokinases.
Glutamyl-tRNA(Gln) amidotransferase subunit D (GatD)
Type: Family

GatD (Glutamyl-tRNA(Gln) amidotransferase subunit D) is found only in the Archaea. It is part of a heterodimer, with GatE (

), that acts as an amidotransferase on misacylated Glu-tRNA(Gln) to produce Gln-tRNA(Gln). This function is carried out in bacteria by the GatABC system, which acts both on Asp-tRNA(Asn) and Glu-tRNA(Gln). GatABC orthologues also exist in some archaea, where it coexist with GatDE; while other archaea only posses GatED and use an asparaginyl-tRNA synthetase to produce Asn-tRNA by direct acylation of the tRNA .