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Conserved domains on  [gi|2247533201|ref|WP_250392041|]
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pyridoxal-dependent decarboxylase, partial [Escherichia coli]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
AAT_I super family cl18945
Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP) ...
 1-71 1.75e-43

Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH groups), and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), and D-amino acid superfamily (fold type IV) and Glycogen phophorylase family (fold type V).


The actual alignment was detected with superfamily member TIGR01788:

Pssm-ID: 450240  Cd Length: 431  Bit Score: 144.47  E-value: 1.75e-43
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2247533201   1 GVTYTGNYEFPQPLHDALDKFQADTGIDIDMHIDAASGGFLAPFVAPDIVWDFRLPRVKSISASGHKFGLA 71
Cdd:TIGR01788 195 GTTYTGEYEDVKALNDALDEYNAKTGWDIPIHVDAASGGFIAPFVYPDLEWDFRLPRVKSINVSGHKYGLV 265
 
Name Accession Description Interval E-value
Glu-decarb-GAD TIGR01788
glutamate decarboxylase; This model represents the pyridoxal phosphate-dependent glutamate ...
 1-71 1.75e-43

glutamate decarboxylase; This model represents the pyridoxal phosphate-dependent glutamate (alpha) decarboxylase found in bacteria (low and hi-GC gram positive, proteobacteria and cyanobacteria), plants, fungi and at least one archaon (Methanosarcina). The product of the enzyme is gamma-aminobutyrate (GABA).


Pssm-ID: 130848  Cd Length: 431  Bit Score: 144.47  E-value: 1.75e-43
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2247533201   1 GVTYTGNYEFPQPLHDALDKFQADTGIDIDMHIDAASGGFLAPFVAPDIVWDFRLPRVKSISASGHKFGLA 71
Cdd:TIGR01788 195 GTTYTGEYEDVKALNDALDEYNAKTGWDIPIHVDAASGGFIAPFVYPDLEWDFRLPRVKSINVSGHKYGLV 265
Pyridoxal_deC pfam00282
Pyridoxal-dependent decarboxylase conserved domain;
1-71 1.73e-21

Pyridoxal-dependent decarboxylase conserved domain;


Pssm-ID: 395219  Cd Length: 373  Bit Score: 85.16  E-value: 1.73e-21
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2247533201   1 GVTYTGNYEFPQPLHDALDKfqadtgIDIDMHIDAASGG--FLAPFVAPdivWDFRLPRVKSISASGHKFGLA 71
Cdd:pfam00282 207 GTTGSGAFDDLQELGDICAK------HNLWLHVDAAYGGsaFICPEFRH---WLFGIERADSITFNPHKWMLV 270
DOPA_deC_like cd06450
DOPA decarboxylase family. This family belongs to pyridoxal phosphate (PLP)-dependent ...
 1-71 2.73e-20

DOPA decarboxylase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to DOPA/tyrosine decarboxylase (DDC), histidine decarboxylase (HDC), and glutamate decarboxylase (GDC). DDC is active as a dimer and catalyzes the decarboxylation of tyrosine. GDC catalyzes the decarboxylation of glutamate and HDC catalyzes the decarboxylation of histidine.


Pssm-ID: 99743 [Multi-domain]  Cd Length: 345  Bit Score: 81.48  E-value: 2.73e-20
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2247533201   1 GVTYTGNYEFPQPLHDALDKFqadtgiDIDMHIDAASGGFLAPFVAPDIvWDFRLPRVKSISASGHKFGLA 71
Cdd:cd06450   157 GTTDTGAIDPLEEIADLAEKY------DLWLHVDAAYGGFLLPFPEPRH-LDFGIERVDSISVDPHKYGLV 220
GadA COG0076
Glutamate or tyrosine decarboxylase or a related PLP-dependent protein [Amino acid transport ...
 1-71 1.36e-11

Glutamate or tyrosine decarboxylase or a related PLP-dependent protein [Amino acid transport and metabolism]; Glutamate or tyrosine decarboxylase or a related PLP-dependent protein is part of the Pathway/BioSystem: Pantothenate/CoA biosynthesis


Pssm-ID: 439846 [Multi-domain]  Cd Length: 460  Bit Score: 57.53  E-value: 1.36e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2247533201   1 GVTYTGNYEfpqPLhDALDKFQADTGIDidMHIDAASGGFLAPfvAPDIVWDF-RLPRVKSISASGHKFGLA 71
Cdd:COG0076   229 GTTNTGAID---PL-AEIADIAREHGLW--LHVDAAYGGFALP--SPELRHLLdGIERADSITVDPHKWLYV 292
PRK02769 PRK02769
histidine decarboxylase; Provisional
 1-68 1.17e-05

histidine decarboxylase; Provisional


Pssm-ID: 235068 [Multi-domain]  Cd Length: 380  Bit Score: 40.80  E-value: 1.17e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2247533201   1 GVTYTGNYEFPQPLHDALDKFQADtgiDIDMHIDAASGGFLAPFVAPDIVWDFRLPrVKSISASGHKF 68
Cdd:PRK02769  169 GTTMTGAIDNIKEIQEILKKIGID---DYYIHADAALSGMILPFVNNPPPFSFADG-IDSIAISGHKF 232
 
Name Accession Description Interval E-value
Glu-decarb-GAD TIGR01788
glutamate decarboxylase; This model represents the pyridoxal phosphate-dependent glutamate ...
 1-71 1.75e-43

glutamate decarboxylase; This model represents the pyridoxal phosphate-dependent glutamate (alpha) decarboxylase found in bacteria (low and hi-GC gram positive, proteobacteria and cyanobacteria), plants, fungi and at least one archaon (Methanosarcina). The product of the enzyme is gamma-aminobutyrate (GABA).


Pssm-ID: 130848  Cd Length: 431  Bit Score: 144.47  E-value: 1.75e-43
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2247533201   1 GVTYTGNYEFPQPLHDALDKFQADTGIDIDMHIDAASGGFLAPFVAPDIVWDFRLPRVKSISASGHKFGLA 71
Cdd:TIGR01788 195 GTTYTGEYEDVKALNDALDEYNAKTGWDIPIHVDAASGGFIAPFVYPDLEWDFRLPRVKSINVSGHKYGLV 265
Pyridoxal_deC pfam00282
Pyridoxal-dependent decarboxylase conserved domain;
1-71 1.73e-21

Pyridoxal-dependent decarboxylase conserved domain;


Pssm-ID: 395219  Cd Length: 373  Bit Score: 85.16  E-value: 1.73e-21
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2247533201   1 GVTYTGNYEFPQPLHDALDKfqadtgIDIDMHIDAASGG--FLAPFVAPdivWDFRLPRVKSISASGHKFGLA 71
Cdd:pfam00282 207 GTTGSGAFDDLQELGDICAK------HNLWLHVDAAYGGsaFICPEFRH---WLFGIERADSITFNPHKWMLV 270
DOPA_deC_like cd06450
DOPA decarboxylase family. This family belongs to pyridoxal phosphate (PLP)-dependent ...
 1-71 2.73e-20

DOPA decarboxylase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to DOPA/tyrosine decarboxylase (DDC), histidine decarboxylase (HDC), and glutamate decarboxylase (GDC). DDC is active as a dimer and catalyzes the decarboxylation of tyrosine. GDC catalyzes the decarboxylation of glutamate and HDC catalyzes the decarboxylation of histidine.


Pssm-ID: 99743 [Multi-domain]  Cd Length: 345  Bit Score: 81.48  E-value: 2.73e-20
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2247533201   1 GVTYTGNYEFPQPLHDALDKFqadtgiDIDMHIDAASGGFLAPFVAPDIvWDFRLPRVKSISASGHKFGLA 71
Cdd:cd06450   157 GTTDTGAIDPLEEIADLAEKY------DLWLHVDAAYGGFLLPFPEPRH-LDFGIERVDSISVDPHKYGLV 220
GadA COG0076
Glutamate or tyrosine decarboxylase or a related PLP-dependent protein [Amino acid transport ...
 1-71 1.36e-11

Glutamate or tyrosine decarboxylase or a related PLP-dependent protein [Amino acid transport and metabolism]; Glutamate or tyrosine decarboxylase or a related PLP-dependent protein is part of the Pathway/BioSystem: Pantothenate/CoA biosynthesis


Pssm-ID: 439846 [Multi-domain]  Cd Length: 460  Bit Score: 57.53  E-value: 1.36e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2247533201   1 GVTYTGNYEfpqPLhDALDKFQADTGIDidMHIDAASGGFLAPfvAPDIVWDF-RLPRVKSISASGHKFGLA 71
Cdd:COG0076   229 GTTNTGAID---PL-AEIADIAREHGLW--LHVDAAYGGFALP--SPELRHLLdGIERADSITVDPHKWLYV 292
PRK02769 PRK02769
histidine decarboxylase; Provisional
 1-68 1.17e-05

histidine decarboxylase; Provisional


Pssm-ID: 235068 [Multi-domain]  Cd Length: 380  Bit Score: 40.80  E-value: 1.17e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2247533201   1 GVTYTGNYEFPQPLHDALDKFQADtgiDIDMHIDAASGGFLAPFVAPDIVWDFRLPrVKSISASGHKF 68
Cdd:PRK02769  169 GTTMTGAIDNIKEIQEILKKIGID---DYYIHADAALSGMILPFVNNPPPFSFADG-IDSIAISGHKF 232
PLN02263 PLN02263
serine decarboxylase
 31-68 1.38e-03

serine decarboxylase


Pssm-ID: 177904 [Multi-domain]  Cd Length: 470  Bit Score: 34.79  E-value: 1.38e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 2247533201  31 MHIDAASGGFLAPFV--APDIVwdFRLPrVKSISASGHKF 68
Cdd:PLN02263  266 IHCDGALFGLMMPFVkrAPKVT--FKKP-IGSVSVSGHKF 302
PLN03032 PLN03032
serine decarboxylase; Provisional
 31-68 2.97e-03

serine decarboxylase; Provisional


Pssm-ID: 166673 [Multi-domain]  Cd Length: 374  Bit Score: 34.03  E-value: 2.97e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 2247533201  31 MHIDAASGGFLAPFV--APDIVwdFRLPrVKSISASGHKF 68
Cdd:PLN03032  199 IHCDGALFGLMMPFVsrAPEVT--FRKP-IGSVSVSGHKF 235
TST_Repeats cd01445
Thiosulfate sulfurtransferases (TST) contain 2 copies of the Rhodanese Homology Domain. Only ...
 3-55 5.94e-03

Thiosulfate sulfurtransferases (TST) contain 2 copies of the Rhodanese Homology Domain. Only the second repeat contains the catalytically active Cys residue. The role of the 1st repeat is uncertain, but believed to be involved in protein interaction. This CD aligns the 1st and 2nd repeats.


Pssm-ID: 238722 [Multi-domain]  Cd Length: 138  Bit Score: 32.84  E-value: 5.94e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2247533201   3 TYTGNYEFPQPLHDALDKFQADTGIDIDMHIDAASGGFLAPFVAPDIVWDFRL 55
Cdd:cd01445    68 DEAGFEESMEPSEAEFAAMFEAKGIDLDKHLIATDGDDLGGFTACHIALAARL 120
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options: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.
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