nucleotide 5'-monophosphate nucleosidase PpnN; PpnN (pyrimidine/purine nucleotide 5'-monophosphate nucleosidase), widely conserved in gamma proteobacteria, plays a role in purine homeostasis. It can bind the the stringent response alarmones ppGpp and pppGpp and then, because of allosteric changes, have a much higher rate of cleavage of preferred substrate GMP. PpnN was previously known in E. coli as YgdH.
The actual alignment was detected with superfamily member NF038390:
Pssm-ID: 468501 [Multi-domain] Cd Length: 450 Bit Score: 909.96 E-value: 0e+00
L-serine dehydratase, iron-sulfur-dependent, single chain form; This enzyme is also called ...
1108-1557
0e+00
L-serine dehydratase, iron-sulfur-dependent, single chain form; This enzyme is also called serine deaminase and L-serine dehydratase 1. L-serine ammonia-lyase converts serine into pyruvate in the gluconeogenesis pathway from serine. This enzyme is comprised of a single chain in Escherichia coli, Mycobacterium tuberculosis, and several other species, but has separate alpha and beta chains in Bacillus subtilis and related species. The beta and alpha chains are homologous to the N-terminal and C-terminal regions, respectively, but are rather deeply branched in a UPGMA tree. This enzyme requires iron and dithiothreitol for activation in vitro, and is a predicted 4Fe-4S protein. Escherichia coli Pseudomonas aeruginosa have two copies of this protein. [Energy metabolism, Amino acids and amines, Energy metabolism, Glycolysis/gluconeogenesis]
:
Pssm-ID: 273233 [Multi-domain] Cd Length: 450 Bit Score: 789.62 E-value: 0e+00
serine transporter; The Hydroxy/Aromatic Amino Acid Permease (HAAAP) Family- serine/threonine subfamily (TC 2.A.42.2) The HAAAP family includes well characterized aromatic amino acid:H+ symport permeases and hydroxy amino acid permeases. This subfamily is specific for hydroxy amino acid transporters and includes the serine permease, SdaC, of E. coli, and the threonine permease, TdcC, of E. coli.//added GO terms, none avaialbelf or ser/thr specifically [SS 2/6/05] [Transport and binding proteins, Amino acids, peptides and amines]
:
Pssm-ID: 273283 Cd Length: 397 Bit Score: 621.28 E-value: 0e+00
nucleotide 5'-monophosphate nucleosidase PpnN; PpnN (pyrimidine/purine nucleotide 5'-monophosphate nucleosidase), widely conserved in gamma proteobacteria, plays a role in purine homeostasis. It can bind the the stringent response alarmones ppGpp and pppGpp and then, because of allosteric changes, have a much higher rate of cleavage of preferred substrate GMP. PpnN was previously known in E. coli as YgdH.
Pssm-ID: 468501 [Multi-domain] Cd Length: 450 Bit Score: 909.96 E-value: 0e+00
L-serine dehydratase, iron-sulfur-dependent, single chain form; This enzyme is also called ...
1108-1557
0e+00
L-serine dehydratase, iron-sulfur-dependent, single chain form; This enzyme is also called serine deaminase and L-serine dehydratase 1. L-serine ammonia-lyase converts serine into pyruvate in the gluconeogenesis pathway from serine. This enzyme is comprised of a single chain in Escherichia coli, Mycobacterium tuberculosis, and several other species, but has separate alpha and beta chains in Bacillus subtilis and related species. The beta and alpha chains are homologous to the N-terminal and C-terminal regions, respectively, but are rather deeply branched in a UPGMA tree. This enzyme requires iron and dithiothreitol for activation in vitro, and is a predicted 4Fe-4S protein. Escherichia coli Pseudomonas aeruginosa have two copies of this protein. [Energy metabolism, Amino acids and amines, Energy metabolism, Glycolysis/gluconeogenesis]
Pssm-ID: 273233 [Multi-domain] Cd Length: 450 Bit Score: 789.62 E-value: 0e+00
serine transporter; The Hydroxy/Aromatic Amino Acid Permease (HAAAP) Family- serine/threonine subfamily (TC 2.A.42.2) The HAAAP family includes well characterized aromatic amino acid:H+ symport permeases and hydroxy amino acid permeases. This subfamily is specific for hydroxy amino acid transporters and includes the serine permease, SdaC, of E. coli, and the threonine permease, TdcC, of E. coli.//added GO terms, none avaialbelf or ser/thr specifically [SS 2/6/05] [Transport and binding proteins, Amino acids, peptides and amines]
Pssm-ID: 273283 Cd Length: 397 Bit Score: 621.28 E-value: 0e+00
7-cyano-7-deazaguanine reductase; This enzyme catalyzes the 4-electron reduction of the cyano ...
7-229
4.45e-130
7-cyano-7-deazaguanine reductase; This enzyme catalyzes the 4-electron reduction of the cyano group of 7-cyano-7-deazaguanine (preQ0) to an amine. Although related to a large family of GTP cyclohydrolases (pfam01227), the relationship is structural and not germane to the catalytic mechanism. This mode represents the longer, gram-negative version of the enzyme as found in E. coli. The enzymatic step represents the first point at which the biosynthesis of queuosine in bacteria and eukaryotes is distinguished from the biosynthesis of archaeosine in archaea. [Transcription, RNA processing]
Pssm-ID: 274443 [Multi-domain] Cd Length: 275 Bit Score: 404.74 E-value: 4.45e-130
Serine dehydratase alpha chain; L-serine dehydratase (EC:4.2.1.13) is a found as a heterodimer ...
1289-1554
2.35e-110
Serine dehydratase alpha chain; L-serine dehydratase (EC:4.2.1.13) is a found as a heterodimer of alpha and beta chain or as a fusion of the two chains in a single protein. This enzyme catalyzes the deamination of serine to form pyruvate. This enzyme is part of the gluconeogenesis pathway.
Pssm-ID: 427238 Cd Length: 259 Bit Score: 350.17 E-value: 2.35e-110
Domain of unknown function (DUF3412); This presumed domain is functionally uncharacterized. ...
556-676
3.22e-79
Domain of unknown function (DUF3412); This presumed domain is functionally uncharacterized. This domain is found in bacteria. This domain is about 120 amino acids in length. This domain is found associated with pfam03641.
Pssm-ID: 463386 Cd Length: 121 Bit Score: 256.31 E-value: 3.22e-79
Nitrile reductase, 7-cyano-7-deazaguanine-reductase N-term; The QueF monomer is made up of two ...
20-130
1.27e-67
Nitrile reductase, 7-cyano-7-deazaguanine-reductase N-term; The QueF monomer is made up of two ferredoxin-like domains aligned together with their beta-sheets that have additional embellishments. This subunit is composed of a three-stranded beta-sheet and two alpha-helices. QueF reduces a nitrile bond to a primary amine. The two monomer units together create suitable substrate-binding pockets.
Pssm-ID: 464334 Cd Length: 111 Bit Score: 222.78 E-value: 1.27e-67
TIGR00730 family protein; This model represents one branch of a subfamily of proteins of ...
373-550
1.36e-07
TIGR00730 family protein; This model represents one branch of a subfamily of proteins of unknown function. Both PSI-BLAST and weak hits by this model show a low level of similarity to and suggest an evolutionary relationship of the subfamily to the DprA/Smf family of DNA-processing proteins involved in chromosomal transformation with foreign DNA. Both Aquifex aeolicus and Mycobacterium leprae have one member in each of two branches of this subfamily, suggesting that the branches may have distinct functions. [Hypothetical proteins, Conserved]
Pssm-ID: 129813 [Multi-domain] Cd Length: 178 Bit Score: 53.29 E-value: 1.36e-07
nucleotide 5'-monophosphate nucleosidase PpnN; PpnN (pyrimidine/purine nucleotide 5'-monophosphate nucleosidase), widely conserved in gamma proteobacteria, plays a role in purine homeostasis. It can bind the the stringent response alarmones ppGpp and pppGpp and then, because of allosteric changes, have a much higher rate of cleavage of preferred substrate GMP. PpnN was previously known in E. coli as YgdH.
Pssm-ID: 468501 [Multi-domain] Cd Length: 450 Bit Score: 909.96 E-value: 0e+00
L-serine dehydratase, iron-sulfur-dependent, single chain form; This enzyme is also called ...
1108-1557
0e+00
L-serine dehydratase, iron-sulfur-dependent, single chain form; This enzyme is also called serine deaminase and L-serine dehydratase 1. L-serine ammonia-lyase converts serine into pyruvate in the gluconeogenesis pathway from serine. This enzyme is comprised of a single chain in Escherichia coli, Mycobacterium tuberculosis, and several other species, but has separate alpha and beta chains in Bacillus subtilis and related species. The beta and alpha chains are homologous to the N-terminal and C-terminal regions, respectively, but are rather deeply branched in a UPGMA tree. This enzyme requires iron and dithiothreitol for activation in vitro, and is a predicted 4Fe-4S protein. Escherichia coli Pseudomonas aeruginosa have two copies of this protein. [Energy metabolism, Amino acids and amines, Energy metabolism, Glycolysis/gluconeogenesis]
Pssm-ID: 273233 [Multi-domain] Cd Length: 450 Bit Score: 789.62 E-value: 0e+00
serine transporter; The Hydroxy/Aromatic Amino Acid Permease (HAAAP) Family- serine/threonine subfamily (TC 2.A.42.2) The HAAAP family includes well characterized aromatic amino acid:H+ symport permeases and hydroxy amino acid permeases. This subfamily is specific for hydroxy amino acid transporters and includes the serine permease, SdaC, of E. coli, and the threonine permease, TdcC, of E. coli.//added GO terms, none avaialbelf or ser/thr specifically [SS 2/6/05] [Transport and binding proteins, Amino acids, peptides and amines]
Pssm-ID: 273283 Cd Length: 397 Bit Score: 621.28 E-value: 0e+00
7-cyano-7-deazaguanine reductase; This enzyme catalyzes the 4-electron reduction of the cyano ...
7-229
4.45e-130
7-cyano-7-deazaguanine reductase; This enzyme catalyzes the 4-electron reduction of the cyano group of 7-cyano-7-deazaguanine (preQ0) to an amine. Although related to a large family of GTP cyclohydrolases (pfam01227), the relationship is structural and not germane to the catalytic mechanism. This mode represents the longer, gram-negative version of the enzyme as found in E. coli. The enzymatic step represents the first point at which the biosynthesis of queuosine in bacteria and eukaryotes is distinguished from the biosynthesis of archaeosine in archaea. [Transcription, RNA processing]
Pssm-ID: 274443 [Multi-domain] Cd Length: 275 Bit Score: 404.74 E-value: 4.45e-130
Serine dehydratase alpha chain; L-serine dehydratase (EC:4.2.1.13) is a found as a heterodimer ...
1289-1554
2.35e-110
Serine dehydratase alpha chain; L-serine dehydratase (EC:4.2.1.13) is a found as a heterodimer of alpha and beta chain or as a fusion of the two chains in a single protein. This enzyme catalyzes the deamination of serine to form pyruvate. This enzyme is part of the gluconeogenesis pathway.
Pssm-ID: 427238 Cd Length: 259 Bit Score: 350.17 E-value: 2.35e-110
Domain of unknown function (DUF3412); This presumed domain is functionally uncharacterized. ...
556-676
3.22e-79
Domain of unknown function (DUF3412); This presumed domain is functionally uncharacterized. This domain is found in bacteria. This domain is about 120 amino acids in length. This domain is found associated with pfam03641.
Pssm-ID: 463386 Cd Length: 121 Bit Score: 256.31 E-value: 3.22e-79
Nitrile reductase, 7-cyano-7-deazaguanine-reductase N-term; The QueF monomer is made up of two ...
20-130
1.27e-67
Nitrile reductase, 7-cyano-7-deazaguanine-reductase N-term; The QueF monomer is made up of two ferredoxin-like domains aligned together with their beta-sheets that have additional embellishments. This subunit is composed of a three-stranded beta-sheet and two alpha-helices. QueF reduces a nitrile bond to a primary amine. The two monomer units together create suitable substrate-binding pockets.
Pssm-ID: 464334 Cd Length: 111 Bit Score: 222.78 E-value: 1.27e-67
Serine dehydratase beta chain; L-serine dehydratase (EC:4.2.1.13) is a found as a heterodimer ...
1118-1262
5.21e-66
Serine dehydratase beta chain; L-serine dehydratase (EC:4.2.1.13) is a found as a heterodimer of alpha and beta chain or as a fusion of the two chains in a single protein. This enzyme catalyzes the deamination of serine to form pyruvate. This enzyme is part of the gluconeogenesis pathway.
Pssm-ID: 427239 [Multi-domain] Cd Length: 146 Bit Score: 219.58 E-value: 5.21e-66
Pyrimidine/purine nucleotide 5'-monophosphate nucleosidases; This is an N-terminal domain ...
229-334
6.61e-64
Pyrimidine/purine nucleotide 5'-monophosphate nucleosidases; This is an N-terminal domain found in pyrimidine/purine nucleotide 5'-monophosphate nucleosidases (PpnN) in bacteria. PpnN catalyzes the hydrolysis of the N-glycosidic bond of diverse pyrimidine and purine nucleotide 5'-monophosphates, to form ribose 5-phosphate and the corresponding free base. It can use AMP, GMP, IMP, CMP, dTMP and UMP as substrates. It is found in association with pfam03641 and pfam11892.
Pssm-ID: 434214 Cd Length: 109 Bit Score: 212.01 E-value: 6.61e-64
L-serine dehydratase, iron-sulfur-dependent, alpha subunit; This enzyme is also called serine ...
1277-1554
7.18e-50
L-serine dehydratase, iron-sulfur-dependent, alpha subunit; This enzyme is also called serine deaminase. L-serine dehydratase converts serine into pyruvate in the gluconeogenesis pathway from serine. This model describes the alpha chain of an iron-sulfur-dependent L-serine dehydratase, found in Bacillus subtilis. A fairly deep split in a UPGMA tree separates members of this family of alpha chains from the homologous region of single chain forms such as found in Escherichia coli. This family of enzymes is not homologous to the pyridoxal phosphate-dependent threonine deaminases and eukaryotic serine deaminases. [Energy metabolism, Amino acids and amines, Energy metabolism, Glycolysis/gluconeogenesis]
Pssm-ID: 129801 Cd Length: 294 Bit Score: 179.04 E-value: 7.18e-50
Possible lysine decarboxylase; The members of this family share a highly conserved motif ...
413-551
1.85e-34
Possible lysine decarboxylase; The members of this family share a highly conserved motif PGGXGTXXE that is probably functionally important. This family includes proteins annotated as lysine decarboxylases, although the evidence for this is not clear.
Pssm-ID: 397621 Cd Length: 130 Bit Score: 128.88 E-value: 1.85e-34
TIGR00730 family protein; This model represents one branch of a subfamily of proteins of ...
373-550
1.36e-07
TIGR00730 family protein; This model represents one branch of a subfamily of proteins of unknown function. Both PSI-BLAST and weak hits by this model show a low level of similarity to and suggest an evolutionary relationship of the subfamily to the DprA/Smf family of DNA-processing proteins involved in chromosomal transformation with foreign DNA. Both Aquifex aeolicus and Mycobacterium leprae have one member in each of two branches of this subfamily, suggesting that the branches may have distinct functions. [Hypothetical proteins, Conserved]
Pssm-ID: 129813 [Multi-domain] Cd Length: 178 Bit Score: 53.29 E-value: 1.36e-07
spore germination protein (amino acid permease); This model describes spore germination ...
705-949
4.88e-06
spore germination protein (amino acid permease); This model describes spore germination protein GerKB and paralogs from Bacillus subtilis, Clostridium tetani, and other known or predicted endospore-forming members of the Firmicutes (low-GC Gram positive bacteria). Members show some similarity to amino acid permeases. [Transport and binding proteins, Amino acids, peptides and amines]
Pssm-ID: 273333 Cd Length: 359 Bit Score: 50.75 E-value: 4.88e-06
L-serine dehydratase, iron-sulfur-dependent, beta subunit; This enzyme is also called serine ...
1109-1182
2.12e-04
L-serine dehydratase, iron-sulfur-dependent, beta subunit; This enzyme is also called serine deaminase. This model describes the beta chain of an iron-sulfur-dependent L-serine dehydratase, as in Bacillus subtilis. A fairly deep split in a UPGMA tree separates members of this family of beta chains from the homologous region of single chain forms such as found in E. coli. This family of enzymes is not homologous to the pyridoxal phosphate-dependent threonine deaminases and eukaryotic serine deaminases. [Energy metabolism, Amino acids and amines, Energy metabolism, Glycolysis/gluconeogenesis]
Pssm-ID: 129802 [Multi-domain] Cd Length: 208 Bit Score: 44.15 E-value: 2.12e-04
7-cyano-7-deazaguanine reductase; This enzyme catalyzes the 4-electron reduction of the cyano ...
188-228
9.33e-03
7-cyano-7-deazaguanine reductase; This enzyme catalyzes the 4-electron reduction of the cyano group of 7-cyano-7-deazaguanine (proQ1) to an amine. Although related to a large family of GTP cyclohydrolases (pfam01227), the relationship is structural and not germane to the catalytic mechanism. This mode represents the shorter, gram-positive version of the enzyme as found in B. subtilis. The enzymatic step represents the first point at which the biosynthesis of queuosine in bacteria and eukaryotes is distinguished from the biosynthesis of archaeosine in archaea.
Pssm-ID: 213775 [Multi-domain] Cd Length: 115 Bit Score: 37.69 E-value: 9.33e-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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