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Conserved domains on  [gi|1958659286|ref|XP_038942167|]
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pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X5 [Rattus norvegicus]

Protein Classification

PLP-dependent aminotransferase family protein( domain architecture ID 139552)

PLP-dependent aminotransferase family protein may combine pyridoxal phosphate with an alpha-amino acid to form a Schiff base or aldimine intermediate, which then acts as the substrate in a reaction such as a transamination, racemization, or decarboxylation

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) ...
194-371 5.58e-18

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 cd06450:

Pssm-ID: 450240 [Multi-domain]  Cd Length: 345  Bit Score: 86.10  E-value: 5.58e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958659286 194 DVAFLEKLIKDDVERGRLPLLLVANAGTAAVGHTDKIGRLKELCEQYGIWLHVEGvnlatlALGyvsSSVLAATK----- 268
Cdd:cd06450   131 DPEALEAAIDEDKAEGLNPIMVVATAGTTDTGAIDPLEEIADLAEKYDLWLHVDA------AYG---GFLLPFPEprhld 201
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958659286 269 -----CDSMTLTPGLWLGLPAVPAVTLYkhddpaltliagltsnkpadklRALPLWLSLQYLGLDGIVGRIKHACQLSQR 343
Cdd:cd06450   202 fgierVDSISVDPHKYGLVPLGCSAVLV----------------------RALKLWATLRRFGRDGYGEHIDRIVDLAKY 259
                         170       180
                  ....*....|....*....|....*...
gi 1958659286 344 LQESLKKVDHIKILVEDELssPVVVFRF 371
Cdd:cd06450   260 LAELIRADPGFELLGEPNL--SLVCFRL 285
 
Name Accession Description Interval E-value
DOPA_deC_like cd06450
DOPA decarboxylase family. This family belongs to pyridoxal phosphate (PLP)-dependent ...
194-371 5.58e-18

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: 86.10  E-value: 5.58e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958659286 194 DVAFLEKLIKDDVERGRLPLLLVANAGTAAVGHTDKIGRLKELCEQYGIWLHVEGvnlatlALGyvsSSVLAATK----- 268
Cdd:cd06450   131 DPEALEAAIDEDKAEGLNPIMVVATAGTTDTGAIDPLEEIADLAEKYDLWLHVDA------AYG---GFLLPFPEprhld 201
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958659286 269 -----CDSMTLTPGLWLGLPAVPAVTLYkhddpaltliagltsnkpadklRALPLWLSLQYLGLDGIVGRIKHACQLSQR 343
Cdd:cd06450   202 fgierVDSISVDPHKYGLVPLGCSAVLV----------------------RALKLWATLRRFGRDGYGEHIDRIVDLAKY 259
                         170       180
                  ....*....|....*....|....*...
gi 1958659286 344 LQESLKKVDHIKILVEDELssPVVVFRF 371
Cdd:cd06450   260 LAELIRADPGFELLGEPNL--SLVCFRL 285
GadA COG0076
Glutamate or tyrosine decarboxylase or a related PLP-dependent protein [Amino acid transport ...
194-371 9.79e-14

Glutamate or tyrosine decarboxylase or a related PLP-dependent protein [Amino acid transport and metabolism];


Pssm-ID: 223154 [Multi-domain]  Cd Length: 460  Bit Score: 74.33  E-value: 9.79e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958659286 194 DVAFLEKLIKDDVERGrlplLLVANAGTAAVGHTDKIGRLKELCEQYGIWLHVEGvnlatlALGyvsSSVLAATKC---- 269
Cdd:COG0076   194 DVDALEEAIDENTIGG----VVVGTAGTTDTGSIDDIEELADIAEEYGIWLHVDA------AFG---GFLLPFLEPdgrw 260
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958659286 270 -------DSMTLTPGLWLGLPAVPAVTLYK----------HDDPALT----LIAGLTSNKPADklRALPLWLSLQYLGLD 328
Cdd:COG0076   261 dfglegvDSITVDGHKYGLAPIGCGVVLFRdeealrriliFADYYLPgggiPNFTILGSRPGR--QALALYANLRRLGRE 338
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 1958659286 329 GIVGRIKHACQLSQRLQESLKKVDHIKILVEDELssPVVVFRF 371
Cdd:COG0076   339 GYRKLLDRTLELARYLAEELEKLGDFELVNEPEL--PIVAFRL 379
Pyridoxal_deC pfam00282
Pyridoxal-dependent decarboxylase conserved domain;
198-370 1.46e-09

Pyridoxal-dependent decarboxylase conserved domain;


Pssm-ID: 395219  Cd Length: 373  Bit Score: 60.51  E-value: 1.46e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958659286 198 LEKLIKDDVERGRLPLLLVANAGTAAVGHTDKIGRLKELCEQYGIWLHVEGVNLATLALG-YVSSSVLAATKCDSMTLTP 276
Cdd:pfam00282 185 LEKAIEEDKENGLIPFFVVATLGTTGSGAFDDLQELGDICAKHNLWLHVDAAYGGSAFICpEFRHWLFGIERADSITFNP 264
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958659286 277 GLWLGLPA------------------VPAVTLYKHDDPALTLIAGLTSNKpadKLRALPLWLSLQYLGLDGIVGRIKHAC 338
Cdd:pfam00282 265 HKWMLVLLdcsavwvkdkealqqafqFNPLYLGHTDSAYDTGHKQIPLSR---RFRILKLWFVIRSLGVEGLQNQIRRHV 341
                         170       180       190
                  ....*....|....*....|....*....|..
gi 1958659286 339 QLSQRLQESLKKVDHIKILVEDELssPVVVFR 370
Cdd:pfam00282 342 ELAQYLEALIRKDGRFEICAEVGL--GLVCFR 371
PLN02590 PLN02590
probable tyrosine decarboxylase
198-371 1.87e-04

probable tyrosine decarboxylase


Pssm-ID: 178200 [Multi-domain]  Cd Length: 539  Bit Score: 44.70  E-value: 1.87e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958659286 198 LEKLIKDDVERGRLPLLLVANAGTAAVGHTDKIGRLKELCEQYGIWLHVEGVNLATLALGYVSSSVLAATK-CDSMTLTP 276
Cdd:PLN02590  274 LEEAISHDLAKGFIPFFICATVGTTSSAAVDPLVPLGNIAKKYGIWLHVDAAYAGNACICPEYRKFIDGIEnADSFNMNA 353
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958659286 277 GLWLgLPAVPAVTLYKHDdpALTLIAGLTSNKP----------------------ADKLRALPLWLSLQYLGLDGIVGRI 334
Cdd:PLN02590  354 HKWL-FANQTCSPLWVKD--RYSLIDALKTNPEylefkvskkdtvvnykdwqislSRRFRSLKLWMVLRLYGSENLRNFI 430
                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 1958659286 335 KHACQLSQRLQESLKKVDHIKILVEDELSspVVVFRF 371
Cdd:PLN02590  431 RDHVNLAKHFEDYVAQDPSFEVVTTRYFS--LVCFRL 465
 
Name Accession Description Interval E-value
DOPA_deC_like cd06450
DOPA decarboxylase family. This family belongs to pyridoxal phosphate (PLP)-dependent ...
194-371 5.58e-18

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: 86.10  E-value: 5.58e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958659286 194 DVAFLEKLIKDDVERGRLPLLLVANAGTAAVGHTDKIGRLKELCEQYGIWLHVEGvnlatlALGyvsSSVLAATK----- 268
Cdd:cd06450   131 DPEALEAAIDEDKAEGLNPIMVVATAGTTDTGAIDPLEEIADLAEKYDLWLHVDA------AYG---GFLLPFPEprhld 201
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958659286 269 -----CDSMTLTPGLWLGLPAVPAVTLYkhddpaltliagltsnkpadklRALPLWLSLQYLGLDGIVGRIKHACQLSQR 343
Cdd:cd06450   202 fgierVDSISVDPHKYGLVPLGCSAVLV----------------------RALKLWATLRRFGRDGYGEHIDRIVDLAKY 259
                         170       180
                  ....*....|....*....|....*...
gi 1958659286 344 LQESLKKVDHIKILVEDELssPVVVFRF 371
Cdd:cd06450   260 LAELIRADPGFELLGEPNL--SLVCFRL 285
GadA COG0076
Glutamate or tyrosine decarboxylase or a related PLP-dependent protein [Amino acid transport ...
194-371 9.79e-14

Glutamate or tyrosine decarboxylase or a related PLP-dependent protein [Amino acid transport and metabolism];


Pssm-ID: 223154 [Multi-domain]  Cd Length: 460  Bit Score: 74.33  E-value: 9.79e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958659286 194 DVAFLEKLIKDDVERGrlplLLVANAGTAAVGHTDKIGRLKELCEQYGIWLHVEGvnlatlALGyvsSSVLAATKC---- 269
Cdd:COG0076   194 DVDALEEAIDENTIGG----VVVGTAGTTDTGSIDDIEELADIAEEYGIWLHVDA------AFG---GFLLPFLEPdgrw 260
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958659286 270 -------DSMTLTPGLWLGLPAVPAVTLYK----------HDDPALT----LIAGLTSNKPADklRALPLWLSLQYLGLD 328
Cdd:COG0076   261 dfglegvDSITVDGHKYGLAPIGCGVVLFRdeealrriliFADYYLPgggiPNFTILGSRPGR--QALALYANLRRLGRE 338
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 1958659286 329 GIVGRIKHACQLSQRLQESLKKVDHIKILVEDELssPVVVFRF 371
Cdd:COG0076   339 GYRKLLDRTLELARYLAEELEKLGDFELVNEPEL--PIVAFRL 379
Pyridoxal_deC pfam00282
Pyridoxal-dependent decarboxylase conserved domain;
198-370 1.46e-09

Pyridoxal-dependent decarboxylase conserved domain;


Pssm-ID: 395219  Cd Length: 373  Bit Score: 60.51  E-value: 1.46e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958659286 198 LEKLIKDDVERGRLPLLLVANAGTAAVGHTDKIGRLKELCEQYGIWLHVEGVNLATLALG-YVSSSVLAATKCDSMTLTP 276
Cdd:pfam00282 185 LEKAIEEDKENGLIPFFVVATLGTTGSGAFDDLQELGDICAKHNLWLHVDAAYGGSAFICpEFRHWLFGIERADSITFNP 264
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958659286 277 GLWLGLPA------------------VPAVTLYKHDDPALTLIAGLTSNKpadKLRALPLWLSLQYLGLDGIVGRIKHAC 338
Cdd:pfam00282 265 HKWMLVLLdcsavwvkdkealqqafqFNPLYLGHTDSAYDTGHKQIPLSR---RFRILKLWFVIRSLGVEGLQNQIRRHV 341
                         170       180       190
                  ....*....|....*....|....*....|..
gi 1958659286 339 QLSQRLQESLKKVDHIKILVEDELssPVVVFR 370
Cdd:pfam00282 342 ELAQYLEALIRKDGRFEICAEVGL--GLVCFR 371
PLN02590 PLN02590
probable tyrosine decarboxylase
198-371 1.87e-04

probable tyrosine decarboxylase


Pssm-ID: 178200 [Multi-domain]  Cd Length: 539  Bit Score: 44.70  E-value: 1.87e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958659286 198 LEKLIKDDVERGRLPLLLVANAGTAAVGHTDKIGRLKELCEQYGIWLHVEGVNLATLALGYVSSSVLAATK-CDSMTLTP 276
Cdd:PLN02590  274 LEEAISHDLAKGFIPFFICATVGTTSSAAVDPLVPLGNIAKKYGIWLHVDAAYAGNACICPEYRKFIDGIEnADSFNMNA 353
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958659286 277 GLWLgLPAVPAVTLYKHDdpALTLIAGLTSNKP----------------------ADKLRALPLWLSLQYLGLDGIVGRI 334
Cdd:PLN02590  354 HKWL-FANQTCSPLWVKD--RYSLIDALKTNPEylefkvskkdtvvnykdwqislSRRFRSLKLWMVLRLYGSENLRNFI 430
                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 1958659286 335 KHACQLSQRLQESLKKVDHIKILVEDELSspVVVFRF 371
Cdd:PLN02590  431 RDHVNLAKHFEDYVAQDPSFEVVTTRYFS--LVCFRL 465
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.20
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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