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Conserved domains on  [gi|2151495772|ref|WP_228941053|]
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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) ...
 1-84 4.76e-54

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: 172.59  E-value: 4.76e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2151495772   1 YTGNYEFPQPLHDALDKFQADTGIDIDMHIDAASGGFLAPFVAPDIVWDFRLPRVKSISASGHKFGLAPLGCGWVIWRDE 80
Cdd:TIGR01788 198 YTGEYEDVKALNDALDEYNAKTGWDIPIHVDAASGGFIAPFVYPDLEWDFRLPRVKSINVSGHKYGLVYPGVGWVIWRDE 277


                  ....
gi 2151495772  81 EALP 84
Cdd:TIGR01788 278 EALP 281
 
Name Accession Description Interval E-value
Glu-decarb-GAD TIGR01788
glutamate decarboxylase; This model represents the pyridoxal phosphate-dependent glutamate ...
 1-84 4.76e-54

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: 172.59  E-value: 4.76e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2151495772   1 YTGNYEFPQPLHDALDKFQADTGIDIDMHIDAASGGFLAPFVAPDIVWDFRLPRVKSISASGHKFGLAPLGCGWVIWRDE 80
Cdd:TIGR01788 198 YTGEYEDVKALNDALDEYNAKTGWDIPIHVDAASGGFIAPFVYPDLEWDFRLPRVKSINVSGHKYGLVYPGVGWVIWRDE 277


                  ....
gi 2151495772  81 EALP 84
Cdd:TIGR01788 278 EALP 281
Pyridoxal_deC pfam00282
Pyridoxal-dependent decarboxylase conserved domain;
1-84 1.25e-28

Pyridoxal-dependent decarboxylase conserved domain;


Pssm-ID: 395219  Cd Length: 373  Bit Score: 104.81  E-value: 1.25e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2151495772   1 YTGNYEFPQPLHDALDKfqadtgIDIDMHIDAASGG--FLAPFVAPdivWDFRLPRVKSISASGHKFGLAPLGCGWVIWR 78
Cdd:pfam00282 210 GSGAFDDLQELGDICAK------HNLWLHVDAAYGGsaFICPEFRH---WLFGIERADSITFNPHKWMLVLLDCSAVWVK 280


                  ....*.
gi 2151495772  79 DEEALP 84
Cdd:pfam00282 281 DKEALQ 286
DOPA_deC_like cd06450
DOPA decarboxylase family. This family belongs to pyridoxal phosphate (PLP)-dependent ...
 1-78 7.72e-26

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: 96.89  E-value: 7.72e-26
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2151495772   1 YTGNYEFPQPLHDALDKFqadtgiDIDMHIDAASGGFLAPFVAPDIvWDFRLPRVKSISASGHKFGLAPLGCGWVIWR 78
Cdd:cd06450   160 DTGAIDPLEEIADLAEKY------DLWLHVDAAYGGFLLPFPEPRH-LDFGIERVDSISVDPHKYGLVPLGCSAVLVR 230
GadA COG0076
Glutamate or tyrosine decarboxylase or a related PLP-dependent protein [Amino acid transport ...
 1-84 3.27e-19

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: 79.88  E-value: 3.27e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2151495772   1 YTGNYEfpqPLhDALDKFQADTGIDidMHIDAASGGFLAPfvAPDIVWDF-RLPRVKSISASGHKFGLAPLGCGWVIWRD 79
Cdd:COG0076   232 NTGAID---PL-AEIADIAREHGLW--LHVDAAYGGFALP--SPELRHLLdGIERADSITVDPHKWLYVPYGCGAVLVRD 303


                  ....*
gi 2151495772  80 EEALP 84
Cdd:COG0076   304 PELLR 308
PRK02769 PRK02769
histidine decarboxylase; Provisional
 20-76 2.20e-07

histidine decarboxylase; Provisional


Pssm-ID: 235068 [Multi-domain]  Cd Length: 380  Bit Score: 46.19  E-value: 2.20e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2151495772  20 ADTGI-DIDMHIDAASGGFLAPFVAPDIVWDFRLPrVKSISASGHKFGLAPLGCGWVI 76
Cdd:PRK02769  187 KKIGIdDYYIHADAALSGMILPFVNNPPPFSFADG-IDSIAISGHKFIGSPMPCGIVL 243
 
Name Accession Description Interval E-value
Glu-decarb-GAD TIGR01788
glutamate decarboxylase; This model represents the pyridoxal phosphate-dependent glutamate ...
 1-84 4.76e-54

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: 172.59  E-value: 4.76e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2151495772   1 YTGNYEFPQPLHDALDKFQADTGIDIDMHIDAASGGFLAPFVAPDIVWDFRLPRVKSISASGHKFGLAPLGCGWVIWRDE 80
Cdd:TIGR01788 198 YTGEYEDVKALNDALDEYNAKTGWDIPIHVDAASGGFIAPFVYPDLEWDFRLPRVKSINVSGHKYGLVYPGVGWVIWRDE 277


                  ....
gi 2151495772  81 EALP 84
Cdd:TIGR01788 278 EALP 281
Pyridoxal_deC pfam00282
Pyridoxal-dependent decarboxylase conserved domain;
1-84 1.25e-28

Pyridoxal-dependent decarboxylase conserved domain;


Pssm-ID: 395219  Cd Length: 373  Bit Score: 104.81  E-value: 1.25e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2151495772   1 YTGNYEFPQPLHDALDKfqadtgIDIDMHIDAASGG--FLAPFVAPdivWDFRLPRVKSISASGHKFGLAPLGCGWVIWR 78
Cdd:pfam00282 210 GSGAFDDLQELGDICAK------HNLWLHVDAAYGGsaFICPEFRH---WLFGIERADSITFNPHKWMLVLLDCSAVWVK 280


                  ....*.
gi 2151495772  79 DEEALP 84
Cdd:pfam00282 281 DKEALQ 286
DOPA_deC_like cd06450
DOPA decarboxylase family. This family belongs to pyridoxal phosphate (PLP)-dependent ...
 1-78 7.72e-26

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: 96.89  E-value: 7.72e-26
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2151495772   1 YTGNYEFPQPLHDALDKFqadtgiDIDMHIDAASGGFLAPFVAPDIvWDFRLPRVKSISASGHKFGLAPLGCGWVIWR 78
Cdd:cd06450   160 DTGAIDPLEEIADLAEKY------DLWLHVDAAYGGFLLPFPEPRH-LDFGIERVDSISVDPHKYGLVPLGCSAVLVR 230
GadA COG0076
Glutamate or tyrosine decarboxylase or a related PLP-dependent protein [Amino acid transport ...
 1-84 3.27e-19

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: 79.88  E-value: 3.27e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2151495772   1 YTGNYEfpqPLhDALDKFQADTGIDidMHIDAASGGFLAPfvAPDIVWDF-RLPRVKSISASGHKFGLAPLGCGWVIWRD 79
Cdd:COG0076   232 NTGAID---PL-AEIADIAREHGLW--LHVDAAYGGFALP--SPELRHLLdGIERADSITVDPHKWLYVPYGCGAVLVRD 303


                  ....*
gi 2151495772  80 EEALP 84
Cdd:COG0076   304 PELLR 308
PRK02769 PRK02769
histidine decarboxylase; Provisional
 20-76 2.20e-07

histidine decarboxylase; Provisional


Pssm-ID: 235068 [Multi-domain]  Cd Length: 380  Bit Score: 46.19  E-value: 2.20e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2151495772  20 ADTGI-DIDMHIDAASGGFLAPFVAPDIVWDFRLPrVKSISASGHKFGLAPLGCGWVI 76
Cdd:PRK02769  187 KKIGIdDYYIHADAALSGMILPFVNNPPPFSFADG-IDSIAISGHKFIGSPMPCGIVL 243
PLN02263 PLN02263
serine decarboxylase
 28-80 6.89e-07

serine decarboxylase


Pssm-ID: 177904 [Multi-domain]  Cd Length: 470  Bit Score: 44.81  E-value: 6.89e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2151495772  28 MHIDAASGGFLAPFV--APDIVwdFRLPrVKSISASGHKFGLAPLGCGWVIWRDE 80
Cdd:PLN02263  266 IHCDGALFGLMMPFVkrAPKVT--FKKP-IGSVSVSGHKFVGCPMPCGVQITRME 317
PLN03032 PLN03032
serine decarboxylase; Provisional
 28-80 6.24e-06

serine decarboxylase; Provisional


Pssm-ID: 166673 [Multi-domain]  Cd Length: 374  Bit Score: 42.12  E-value: 6.24e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2151495772  28 MHIDAASGGFLAPFV--APDIVwdFRLPrVKSISASGHKFGLAPLGCGWVIWRDE 80
Cdd:PLN03032  199 IHCDGALFGLMMPFVsrAPEVT--FRKP-IGSVSVSGHKFLGCPMPCGVALTRKK 250
 
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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