The N-lobe of transferrin, a member of the type 2 periplasmic binding protein fold superfamily; ...
342-664
0e+00
The N-lobe of transferrin, a member of the type 2 periplasmic binding protein fold superfamily; Transferrins are iron-binding blood plasma glycoproteins that regulate the level of free iron in biological fluids. Vertebrate transferrins are made of a single polypeptide chain with a molecular weight of about 80 kDa. The polypeptide is folded into two homologous lobes (the N-lobe and C-lobe), and each lobe is further subdivided into two similar alpha helices and beta sheets domains separated by a deep cleft that forms the binding site for ferric iron. Thus, the transferrin protein contains two homologous metal-binding sites with high affinities for ferric iron. The modern transferrin proteins are thought to be evolved from an ancestral gene coding for a protein of 40 kDa containing a single binding site by means of a gene duplication event. Vertebrate transferrins are found in a variety of bodily fluids, including serum transferrins, ovotransferrins, lactoferrins, and melanotransferrins. Transferrin-like proteins are also found in the circulatory fluid of certain invertebrates. The transferrins have the same structural fold as the type 2 periplasmic-binding proteins, many of which are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor.
:
Pssm-ID: 270336 Cd Length: 324 Bit Score: 658.35 E-value: 0e+00
Arginase types I and II and arginase-like family; This family includes arginase, also known as ...
9-303
0e+00
Arginase types I and II and arginase-like family; This family includes arginase, also known as arginase-like amidino hydrolase family, and related proteins, found in bacteria, archaea and eykaryotes. Arginase is a binuclear Mn-dependent metalloenzyme and catalyzes hydrolysis of L-arginine to L-ornithine and urea (Arg, EC 3.5.3.1), the reaction being the fifth and final step in the urea cycle, providing the path for the disposal of nitrogenous compounds. Arginase controls cellular levels of arginine and ornithine which are involved in protein biosynthesis, and in production of creatine, polyamines, proline and nitric acid. In vertebrates, at least two isozymes have been identified: type I cytoplasmic or hepatic liver-type arginase and type II mitochondrial or non-hepatic arginase. Point mutations in human arginase gene lead to hyperargininemia with consequent mental disorders, retarded development and early death. Arginase is a therapeutic target to treat asthma, erectile dysfunction, atherosclerosis and cancer.
:
Pssm-ID: 212536 Cd Length: 294 Bit Score: 516.27 E-value: 0e+00
The N-lobe of transferrin, a member of the type 2 periplasmic binding protein fold superfamily; ...
342-664
0e+00
The N-lobe of transferrin, a member of the type 2 periplasmic binding protein fold superfamily; Transferrins are iron-binding blood plasma glycoproteins that regulate the level of free iron in biological fluids. Vertebrate transferrins are made of a single polypeptide chain with a molecular weight of about 80 kDa. The polypeptide is folded into two homologous lobes (the N-lobe and C-lobe), and each lobe is further subdivided into two similar alpha helices and beta sheets domains separated by a deep cleft that forms the binding site for ferric iron. Thus, the transferrin protein contains two homologous metal-binding sites with high affinities for ferric iron. The modern transferrin proteins are thought to be evolved from an ancestral gene coding for a protein of 40 kDa containing a single binding site by means of a gene duplication event. Vertebrate transferrins are found in a variety of bodily fluids, including serum transferrins, ovotransferrins, lactoferrins, and melanotransferrins. Transferrin-like proteins are also found in the circulatory fluid of certain invertebrates. The transferrins have the same structural fold as the type 2 periplasmic-binding proteins, many of which are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor.
Pssm-ID: 270336 Cd Length: 324 Bit Score: 658.35 E-value: 0e+00
Arginase types I and II and arginase-like family; This family includes arginase, also known as ...
9-303
0e+00
Arginase types I and II and arginase-like family; This family includes arginase, also known as arginase-like amidino hydrolase family, and related proteins, found in bacteria, archaea and eykaryotes. Arginase is a binuclear Mn-dependent metalloenzyme and catalyzes hydrolysis of L-arginine to L-ornithine and urea (Arg, EC 3.5.3.1), the reaction being the fifth and final step in the urea cycle, providing the path for the disposal of nitrogenous compounds. Arginase controls cellular levels of arginine and ornithine which are involved in protein biosynthesis, and in production of creatine, polyamines, proline and nitric acid. In vertebrates, at least two isozymes have been identified: type I cytoplasmic or hepatic liver-type arginase and type II mitochondrial or non-hepatic arginase. Point mutations in human arginase gene lead to hyperargininemia with consequent mental disorders, retarded development and early death. Arginase is a therapeutic target to treat asthma, erectile dysfunction, atherosclerosis and cancer.
Pssm-ID: 212536 Cd Length: 294 Bit Score: 516.27 E-value: 0e+00
arginase; This model helps resolve arginases from known and putative agmatinases, ...
9-309
2.55e-170
arginase; This model helps resolve arginases from known and putative agmatinases, formiminoglutamases, and other related proteins of unknown specifity. The pathway from arginine to the polyamine putrescine may procede by hydrolysis to remove urea (arginase) followed by decarboxylation (ornithine decarboxylase), or by decarboxylation first (arginine decarboxylase) followed by removal of urea (agmatinase).
Pssm-ID: 162262 Cd Length: 300 Bit Score: 488.48 E-value: 2.55e-170
Arginase/agmatinase family enzyme [Amino acid transport and metabolism]; Arginase/agmatinase ...
2-306
4.76e-78
Arginase/agmatinase family enzyme [Amino acid transport and metabolism]; Arginase/agmatinase family enzyme is part of the Pathway/BioSystem: Urea cycle
Pssm-ID: 439781 [Multi-domain] Cd Length: 283 Bit Score: 250.51 E-value: 4.76e-78
The N-lobe of transferrin, a member of the type 2 periplasmic binding protein fold superfamily; ...
342-664
0e+00
The N-lobe of transferrin, a member of the type 2 periplasmic binding protein fold superfamily; Transferrins are iron-binding blood plasma glycoproteins that regulate the level of free iron in biological fluids. Vertebrate transferrins are made of a single polypeptide chain with a molecular weight of about 80 kDa. The polypeptide is folded into two homologous lobes (the N-lobe and C-lobe), and each lobe is further subdivided into two similar alpha helices and beta sheets domains separated by a deep cleft that forms the binding site for ferric iron. Thus, the transferrin protein contains two homologous metal-binding sites with high affinities for ferric iron. The modern transferrin proteins are thought to be evolved from an ancestral gene coding for a protein of 40 kDa containing a single binding site by means of a gene duplication event. Vertebrate transferrins are found in a variety of bodily fluids, including serum transferrins, ovotransferrins, lactoferrins, and melanotransferrins. Transferrin-like proteins are also found in the circulatory fluid of certain invertebrates. The transferrins have the same structural fold as the type 2 periplasmic-binding proteins, many of which are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor.
Pssm-ID: 270336 Cd Length: 324 Bit Score: 658.35 E-value: 0e+00
Arginase types I and II and arginase-like family; This family includes arginase, also known as ...
9-303
0e+00
Arginase types I and II and arginase-like family; This family includes arginase, also known as arginase-like amidino hydrolase family, and related proteins, found in bacteria, archaea and eykaryotes. Arginase is a binuclear Mn-dependent metalloenzyme and catalyzes hydrolysis of L-arginine to L-ornithine and urea (Arg, EC 3.5.3.1), the reaction being the fifth and final step in the urea cycle, providing the path for the disposal of nitrogenous compounds. Arginase controls cellular levels of arginine and ornithine which are involved in protein biosynthesis, and in production of creatine, polyamines, proline and nitric acid. In vertebrates, at least two isozymes have been identified: type I cytoplasmic or hepatic liver-type arginase and type II mitochondrial or non-hepatic arginase. Point mutations in human arginase gene lead to hyperargininemia with consequent mental disorders, retarded development and early death. Arginase is a therapeutic target to treat asthma, erectile dysfunction, atherosclerosis and cancer.
Pssm-ID: 212536 Cd Length: 294 Bit Score: 516.27 E-value: 0e+00
arginase; This model helps resolve arginases from known and putative agmatinases, ...
9-309
2.55e-170
arginase; This model helps resolve arginases from known and putative agmatinases, formiminoglutamases, and other related proteins of unknown specifity. The pathway from arginine to the polyamine putrescine may procede by hydrolysis to remove urea (arginase) followed by decarboxylation (ornithine decarboxylase), or by decarboxylation first (arginine decarboxylase) followed by removal of urea (agmatinase).
Pssm-ID: 162262 Cd Length: 300 Bit Score: 488.48 E-value: 2.55e-170
Arginase family; This family includes arginase, also known as arginase-like amidino hydrolase ...
8-303
6.47e-149
Arginase family; This family includes arginase, also known as arginase-like amidino hydrolase family, and related proteins. Arginase is a binuclear Mn-dependent metalloenzyme and catalyzes hydrolysis of L-arginine to L-ornithine and urea (Arg, EC 3.5.3.1), the reaction being the fifth and final step in the urea cycle, providing the path for the disposal of nitrogenous compounds. Arginase controls cellular levels of arginine and ornithine which are involved in protein biosynthesis, and in production of creatine, polyamines, proline and nitric acid. In vertebrates, at least two isozymes have been identified: type I (ARG1) cytoplasmic or hepatic liver-type arginase and type II (ARG2) mitochondrial or non-hepatic arginase. Point mutations in human arginase ARG1 gene lead to hyperargininemia with consequent mental disorders, retarded development and early death. Hyperargininemia is associated with a several-fold increase in the activity of the mitochondrial arginase (ARG2), causing persistent ureagenesis in patients. ARG2 overexpression plays a critical role in the pathophysiology of cholesterol mediated endothelial dysfunction. Thus, arginase is a therapeutic target to treat asthma, erectile dysfunction, atherosclerosis and cancer.
Pssm-ID: 212515 Cd Length: 290 Bit Score: 433.46 E-value: 6.47e-149
Transferrin family of the type 2 periplasmic-binding protein superfamily; Transferrins are ...
342-664
1.98e-121
Transferrin family of the type 2 periplasmic-binding protein superfamily; Transferrins are iron-binding blood plasma glycoproteins that regulate the level of free iron in biological fluids. Vertebrate transferrins are made of a single polypeptide chain with a molecular weight of about 80 kDa. The polypeptide is folded into two homologous lobes (the N-lobe and C-lobe), and each lobe is further subdivided into two similar alpha helical and beta sheet domains separated by a deep cleft that forms the binding site for ferric iron. Thus, the transferrin protein contains two homologous metal-binding sites with high affinities for ferric iron. The modern transferrin proteins are thought to be evolved from an ancestral gene coding for a protein of 40 kDa containing a single binding site by means of a gene duplication event. Vertebrate transferrins are found in a variety of bodily fluids, including serum transferrins, ovotransferrins, lactoferrins, and melanotransferrins. Transferrin-like proteins are also found in the circulatory fluid of certain invertebrates. The transferrins have the same structural fold as the type 2 periplasmic-binding proteins, many of which are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor.
Pssm-ID: 270247 Cd Length: 298 Bit Score: 363.65 E-value: 1.98e-121
Ureohydrolase superfamily includes arginase, formiminoglutamase, agmatinase and proclavaminate ...
10-301
9.12e-104
Ureohydrolase superfamily includes arginase, formiminoglutamase, agmatinase and proclavaminate amidinohydrolase (PAH); This family, also known as arginase-like amidino hydrolase family, includes Mn-dependent enzymes: arginase (Arg, EC 3.5.3.1), formimidoylglutamase (HutG, EC 3.5.3.8 ), agmatinase (SpeB, EC 3.5.3.11), guanidinobutyrase (Gbh, EC=3.5.3.7), proclavaminate amidinohydrolase (PAH, EC 3.5.3.22) and related proteins. These enzymes catalyze hydrolysis of amide bond. They are involved in control of cellular levels of arginine and ornithine (both involved in protein biosynthesis, and production of creatine, polyamines, proline and nitric acid), in histidine and arginine degradation, and in clavulanic acid biosynthesis.
Pssm-ID: 212511 [Multi-domain] Cd Length: 270 Bit Score: 317.06 E-value: 9.12e-104
The C-lobe of transferrin, a member of the type 2 periplasmic binding protein fold superfamily; ...
341-664
1.54e-103
The C-lobe of transferrin, a member of the type 2 periplasmic binding protein fold superfamily; Transferrins are iron-binding blood plasma glycoproteins that regulate the level of free iron in biological fluids. Vertebrate transferrins are made of a single polypeptide chain with a molecular weight of about 80 kDa. The polypeptide is folded into two homologous lobes (the N-lobe and C-lobe), and each lobe is further subdivided into two similar alpha helices and beta sheets domains separated by a deep cleft that forms the binding site for ferric iron. Thus, the transferrin protein contains two homologous metal-binding sites with high affinities for ferric iron. The modern transferrin proteins are thought to be evolved from an ancestral gene coding for a protein of 40 kDa containing a single binding site by means of a gene duplication event. Vertebrate transferrins are found in a variety of bodily fluids, including serum transferrins, ovotransferrins, lactoferrins, and melanotransferrins. Transferrin-like proteins are also found in the circulatory fluid of certain invertebrates. The transferrins have the same structural fold as the type 2 periplasmic-binding proteins, many of which are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor.
Pssm-ID: 270335 Cd Length: 331 Bit Score: 318.58 E-value: 1.54e-103
Arginase-like and histone-like hydrolases; Arginase-like/histone-like hydrolase superfamily ...
75-303
2.65e-82
Arginase-like and histone-like hydrolases; Arginase-like/histone-like hydrolase superfamily includes metal-dependent enzymes that belong to Arginase-like amidino hydrolase family and histone/histone-like deacetylase class I, II, IV family, respectively. These enzymes catalyze hydrolysis of amide bond. Arginases are known to be involved in control of cellular levels of arginine and ornithine, in histidine and arginine degradation and in clavulanic acid biosynthesis. Deacetylases play a role in signal transduction through histone and/or other protein modification and can repress/activate transcription of a number of different genes. They participate in different cellular processes including cell cycle regulation, DNA damage response, embryonic development, cytokine signaling important for immune response and post-translational control of the acetyl coenzyme A synthetase. Mammalian histone deacetyases are known to be involved in progression of different tumors. Specific inhibitors of mammalian histone deacetylases are an emerging class of promising novel anticancer drugs.
Pssm-ID: 212513 Cd Length: 217 Bit Score: 259.23 E-value: 2.65e-82
Arginase/agmatinase family enzyme [Amino acid transport and metabolism]; Arginase/agmatinase ...
2-306
4.76e-78
Arginase/agmatinase family enzyme [Amino acid transport and metabolism]; Arginase/agmatinase family enzyme is part of the Pathway/BioSystem: Urea cycle
Pssm-ID: 439781 [Multi-domain] Cd Length: 283 Bit Score: 250.51 E-value: 4.76e-78
Agmatinase-like family; Agmatinase subfamily currently includes metalloenzymes such as ...
8-304
6.93e-43
Agmatinase-like family; Agmatinase subfamily currently includes metalloenzymes such as agmatinase, guanidinobutyrase, guanidopropionase, formimidoylglutamase and proclavaminate amidinohydrolase. Agmatinase (agmatine ureohydrolase; SpeB; EC=3.5.3.11) is the key enzyme in the synthesis of polyamine putrescine; it catalyzes hydrolysis of agmatine to yield putrescine and urea. This enzyme has been found in bacteria, archaea and eukaryotes, requiring divalent Mn and sometimes Zn, Co or Ca for activity. In mammals, the highest level of agmatinase mRNA was found in liver and kidney. However, catabolism of agmatine via agmatinase apparently is a not major path; it is mostly catabolized via diamine oxidase. Agmatinase has been shown to be down-regulated in tumor renal cells. Guanidinobutyrase (Gbh, EC=3.5.3.7) catalyzes hydrolysis of 4-guanidinobutanoate to yield 4-aminobutanoate and urea in arginine degradation pathway. Activity has been shown for purified enzyme from Arthrobacter sp. KUJ 8602. Additionally, guanidinobutyrase is able to hydrolyze D-arginine, 3-guanidinopropionate, 5-guanidinovaleriate and L-arginine with much less affinity, having divalent Zn ions for catalysis. Proclavaminate amidinohydrolase (Pah, EC 3.5.3.22) hydrolyzes amidinoproclavaminate to yield proclavaminate and urea in clavulanic acid biosynthesis. Activity has been shown for purified enzyme from Streptomyces clavuligerus. Clavulanic acid is the effective inhibitor of beta-lactamases. This acid is used in combination with the penicillin amoxicillin to prevent antibiotic's beta-lactam rings from hydrolysis, thus keeping the antibiotics biologically active.
Pssm-ID: 212516 [Multi-domain] Cd Length: 275 Bit Score: 155.79 E-value: 6.93e-43
Agmatinase and related proteins; This family includes known and predicted bacterial and ...
8-283
4.09e-41
Agmatinase and related proteins; This family includes known and predicted bacterial and archaeal agmatinase (agmatine ureohydrolase; AUH; SpeB; EC=3.5.3.11), a binuclear manganese metalloenzyme that belongs to the ureohydrolase superfamily. It is a key enzyme in the synthesis of polyamine putrescine; it catalyzes hydrolysis of agmatine to yield urea and putrescine, the precursor for biosynthesis of higher polyamines, spermidine, and spermine. As compared to E. coli where two paths to putrescine exist, via decarboxylation of an amino acid, ornithine or arginine, a single path is found in Bacillus subtilis, where polyamine synthesis starts with agmatine; the speE and speB encode spermidine synthase and agmatinase, respectively. The level of agmatinase synthesis is very low, allowing strict control on the synthesis of putrescine and therefore, of all polyamines, consistent with polyamine levels in the cell. This subfamily belongs to the ureohydrolase superfamily, which includes arginase, agmatinase, proclavaminate amidinohydrolase, and formiminoglutamase.
Pssm-ID: 212539 [Multi-domain] Cd Length: 263 Bit Score: 150.70 E-value: 4.09e-41
Agmatinase-like family includes proclavaminic acid amidinohydrolase; This agmatinase subfamily ...
8-281
4.88e-38
Agmatinase-like family includes proclavaminic acid amidinohydrolase; This agmatinase subfamily contains bacterial and fungal/metazoan enzymes, including proclavaminic acid amidinohydrolase (PAH, EC 3.5.3.22) and Pseudomonas aeruginosa guanidinobutyrase (GbuA) and guanidinopropionase (GpuA). PAH hydrolyzes amidinoproclavaminate to yield proclavaminate and urea in clavulanic acid biosynthesis. Clavulanic acid is an effective inhibitor of beta-lactamases and is used in combination with amoxicillin to prevent the beta-lactam rings of the antibiotic from hydrolysis and, thus keeping the antibiotic biologically active. GbuA hydrolyzes 4-guanidinobutyrate (4-GB) into 4-aminobutyrate and urea while GpuA hydrolyzes 3-guanidinopropionate (3-GP) into beta-alanine and urea. Mutation studies show that significant variations in two active site loops in these two enzymes may be important for substrate specificity. This subfamily belongs to the ureohydrolase superfamily, which includes arginase, agmatinase, proclavaminate amidinohydrolase, and formiminoglutamase.
Pssm-ID: 212538 [Multi-domain] Cd Length: 289 Bit Score: 143.00 E-value: 4.88e-38
Arginase-like amidino hydrolase family; This family includes arginase, also known as ...
10-283
8.38e-38
Arginase-like amidino hydrolase family; This family includes arginase, also known as arginase-like amidino hydrolase family, as well as arginase-like proteins and are found in bacteria, archaea and eykaryotes, but does not include metazoan arginases. Arginase is a binuclear Mn-dependent metalloenzyme and catalyzes hydrolysis of L-arginine to L-ornithine and urea (Arg, EC 3.5.3.1), the reaction being the fifth and final step in the urea cycle, providing the path for the disposal of nitrogenous compounds. Arginase controls cellular levels of arginine and ornithine which are involved in protein biosynthesis, and in production of creatine, polyamines, proline and nitric acid.
Pssm-ID: 212523 Cd Length: 272 Bit Score: 141.61 E-value: 8.38e-38
agmatinase; Members of this family include known and predicted examples of agmatinase ...
10-280
1.15e-23
agmatinase; Members of this family include known and predicted examples of agmatinase (agmatine ureohydrolase). The seed includes members of archaea, for which no definitive agmatinase sequence has yet been made available. However, archaeal sequences are phylogenetically close to the experimentally verified B. subtilis sequence. One species of Halobacterium has been demonstrated in vitro to produce agmatine from arginine, but no putrescine from ornithine, suggesting that arginine decarboxylase and agmatinase, rather than arginase and ornithine decarboxylase, lead from Arg to polyamine biosynthesis. Note: a history of early misannotation of members of this family is detailed in PUBMED:10931887.
Pssm-ID: 273514 [Multi-domain] Cd Length: 275 Bit Score: 101.37 E-value: 1.15e-23
Formimidoylglutamase or HutE; Formimidoylglutamase (N-formimidoyl-L-glutamate ...
9-282
1.25e-22
Formimidoylglutamase or HutE; Formimidoylglutamase (N-formimidoyl-L-glutamate formimidoylhydrolase; formiminoglutamase; N-formiminoglutamate hydrolase; N-formimino-L-glutamate formiminohydrolase; HutE; EC 3.5.3.8) is a metalloenzyme that catalyzes hydrolysis of N-formimidoyl-L-glutamate to L-glutamate and formamide. This enzyme is involved in histidine degradation, requiring Mn as a cofactor while glutathione may be required for maximal activity. In Pseudomonas PAO1, mutation studies show that histidine degradation proceeds via a 'four-step' pathway if the 'five-step' route is absent and vice versa; in the four-step pathway, formiminoglutaminase (HutE, EC 3.5.3.8) directly converts formiminoglutamate (FIGLU) to L-glutamate and formamide in a single step. Formiminoglutamase has traditionally also been referred to as HutG; however, formiminoglutamase is structurally and mechanistically unrelated to N-formyl-glutamate deformylase (also called HutG). Phylogenetic analysis has suggested that HutE was acquired by horizontal gene transfer from a Ralstonia-like ancestor.
Pssm-ID: 212514 [Multi-domain] Cd Length: 262 Bit Score: 97.97 E-value: 1.25e-22
Agmatinase and related proteins; This family includes known and predicted bacterial agmatinase ...
8-282
7.84e-20
Agmatinase and related proteins; This family includes known and predicted bacterial agmatinase (agmatine ureohydrolase; AUH; SpeB; EC=3.5.3.11), a binuclear manganese metalloenzyme, belonging to the ureohydrolase superfamily. It is a key enzyme in the synthesis of polyamine putrescine; it catalyzes hydrolysis of agmatine to yield urea and putrescine, the precursor for biosynthesis of higher polyamines, spermidine, and spermine. Agmatinase from Deinococcus radiodurans shows approximately 33% of sequence identity to human mitochondrial agmatinase. An analysis of the evolutionary relationship among ureohydrolase superfamily enzymes indicates the pathway involving arginine decarboxylase and agmatinase evolved earlier than the arginase pathway of polyamine.
Pssm-ID: 212537 Cd Length: 274 Bit Score: 89.97 E-value: 7.84e-20
Type 2 periplasmic binding fold superfamily; This evolutionary model and hierarchy represent ...
342-592
1.02e-12
Type 2 periplasmic binding fold superfamily; This evolutionary model and hierarchy represent the ligand-binding domains found in solute binding proteins that serve as initial receptors in the transport, signal transduction and channel gating. The PBP2 proteins share the same architecture as periplasmic binding proteins type 1 (PBP1), but have a different topology. They are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The origin of PBP module can be traced across the distant phyla, including eukaryotes, archebacteria, and prokaryotes. The majority of PBP2 proteins are involved in the uptake of a variety of soluble substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the family includes ionotropic glutamate receptors and unorthodox sensor proteins involved in signal transduction. The substrate binding domain of the LysR transcriptional regulators and the oligopeptide-like transport systems also contain the type 2 periplasmic binding fold and thus they are significantly homologous to that of the PBP2; however, these two families are grouped into a separate hierarchy of the PBP2 superfamily due to the large number of protein sequences.
Pssm-ID: 270214 [Multi-domain] Cd Length: 196 Bit Score: 67.21 E-value: 1.02e-12
Substrate binding domain of phosphonate uptake system-like, a member of the type 2 ...
380-472
7.52e-06
Substrate binding domain of phosphonate uptake system-like, a member of the type 2 periplasmic-binding fold superfamily; This family includes alkylphosphonate binding domain PhnD. These domains are found in PhnD-like proteins that are predicted to function as initial receptors in hypophosphite, phosphonate, or phosphate ABC transport in archaea and eubacteria. PhnD is the periplasmic binding component of an ABC-type phosphonate uptake system (PhnCDE) that recognizes and binds phosphonate. PhnD belongs to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. The PBP2 have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap.
Pssm-ID: 270232 [Multi-domain] Cd Length: 253 Bit Score: 48.03 E-value: 7.52e-06
ABC transporter, phosphonate, periplasmic substrate-binding protein; This is a family of ...
380-651
2.02e-03
ABC transporter, phosphonate, periplasmic substrate-binding protein; This is a family of periplasmic proteins which are part of the transport system for alkylphosphonate uptake.
Pssm-ID: 432911 [Multi-domain] Cd Length: 243 Bit Score: 40.32 E-value: 2.02e-03
Database: CDSEARCH/cdd Low complexity filter: no Composition Based Adjustment: yes E-value threshold: 0.01
References:
Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
of the residues that compose this conserved feature have been mapped to the query sequence.
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non-specific hits
meet or exceed the RPS-BLAST threshold for statistical significance (default E-value cutoff of 0.01, or an E-value selected by user via the
advanced search options)
the domain superfamily to which the specific and non-specific hits belong
multi-domain models that were computationally detected and are likely to contain multiple single domains
Retrieve proteins that contain one or more of the domains present in the query sequence, using the Conserved Domain Architecture Retrieval Tool
(CDART).
Modify your query to search against a different database and/or use advanced search options
