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Conserved domains on  [gi|564370336|ref|XP_006245767|]
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pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X1 [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) ...
202-393 4.23e-20

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: 92.27  E-value: 4.23e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564370336 202 RVPCNtmfgSQHQMDVAFLEKLIKDDVERGRLPLLLVANAGTAAVGHTDKIGRLKELCEQYGIWLHVEGvnlatlALGyv 281
Cdd:cd06450  121 LVPVD----EDGRMDPEALEAAIDEDKAEGLNPIMVVATAGTTDTGAIDPLEEIADLAEKYDLWLHVDA------AYG-- 188
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564370336 282 sSSVLAATK----------CDSMTLTPGLWLGLPAVPAVTLYkhddpaltliagltsnkpadklRALPLWLSLQYLGLDG 351
Cdd:cd06450  189 -GFLLPFPEprhldfgierVDSISVDPHKYGLVPLGCSAVLV----------------------RALKLWATLRRFGRDG 245
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 564370336 352 IVGRIKHACQLSQRLQESLKKVDHIKILVEDELssPVVVFRF 393
Cdd:cd06450  246 YGEHIDRIVDLAKYLAELIRADPGFELLGEPNL--SLVCFRL 285
 
Name Accession Description Interval E-value
DOPA_deC_like cd06450
DOPA decarboxylase family. This family belongs to pyridoxal phosphate (PLP)-dependent ...
202-393 4.23e-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: 92.27  E-value: 4.23e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564370336 202 RVPCNtmfgSQHQMDVAFLEKLIKDDVERGRLPLLLVANAGTAAVGHTDKIGRLKELCEQYGIWLHVEGvnlatlALGyv 281
Cdd:cd06450  121 LVPVD----EDGRMDPEALEAAIDEDKAEGLNPIMVVATAGTTDTGAIDPLEEIADLAEKYDLWLHVDA------AYG-- 188
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564370336 282 sSSVLAATK----------CDSMTLTPGLWLGLPAVPAVTLYkhddpaltliagltsnkpadklRALPLWLSLQYLGLDG 351
Cdd:cd06450  189 -GFLLPFPEprhldfgierVDSISVDPHKYGLVPLGCSAVLV----------------------RALKLWATLRRFGRDG 245
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 564370336 352 IVGRIKHACQLSQRLQESLKKVDHIKILVEDELssPVVVFRF 393
Cdd:cd06450  246 YGEHIDRIVDLAKYLAELIRADPGFELLGEPNL--SLVCFRL 285
GadA COG0076
Glutamate or tyrosine decarboxylase or a related PLP-dependent protein [Amino acid transport ...
163-393 9.05e-16

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: 80.49  E-value: 9.05e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564370336 163 DGFNVLYNKKPIIYLSAAARPglgpylCNQ-----LGLPfpcLCRVPcntMFGSQHQMDVAFLEKLIKDDVERGrlplLL 237
Cdd:COG0076  148 LAESGKPGGKPNIVCSETAHF------SFEkaaryLGLG---LRRVP---TVPTDYRIDVDALEEAIDENTIGG----VV 211
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564370336 238 VANAGTAAVGHTDKIGRLKELCEQYGIWLHVEGvnlatlALGyvsSSVLAATKC-----------DSMTLTPGLWLGLPA 306
Cdd:COG0076  212 VGTAGTTDTGSIDDIEELADIAEEYGIWLHVDA------AFG---GFLLPFLEPdgrwdfglegvDSITVDGHKYGLAPI 282
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564370336 307 VPAVTLYK----------HDDPALT----LIAGLTSNKPADklRALPLWLSLQYLGLDGIVGRIKHACQLSQRLQESLKK 372
Cdd:COG0076  283 GCGVVLFRdeealrriliFADYYLPgggiPNFTILGSRPGR--QALALYANLRRLGREGYRKLLDRTLELARYLAEELEK 360
                        250       260
                 ....*....|....*....|.
gi 564370336 373 VDHIKILVEDELssPVVVFRF 393
Cdd:COG0076  361 LGDFELVNEPEL--PIVAFRL 379
Pyridoxal_deC pfam00282
Pyridoxal-dependent decarboxylase conserved domain;
170-392 2.53e-10

Pyridoxal-dependent decarboxylase conserved domain;


Pssm-ID: 395219  Cd Length: 373  Bit Score: 62.82  E-value: 2.53e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564370336  170 NKKPIIYLSAAARpglgpYLCNQLGLPFPCLCR-VPCNtmfgSQHQMDVAFLEKLIKDDVERGRLPLLLVANAGTAAVGH 248
Cdd:pfam00282 143 LAKLVAYTSDQAH-----SSIEKAALYGGVKLReIPSD----DNGKMRGMDLEKAIEEDKENGLIPFFVVATLGTTGSGA 213
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564370336  249 TDKIGRLKELCEQYGIWLHVEGVNLATLALG-YVSSSVLAATKCDSMTLTPGLWLGLPA------------------VPA 309
Cdd:pfam00282 214 FDDLQELGDICAKHNLWLHVDAAYGGSAFICpEFRHWLFGIERADSITFNPHKWMLVLLdcsavwvkdkealqqafqFNP 293
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564370336  310 VTLYKHDDPALTLIAGLTSNKpadKLRALPLWLSLQYLGLDGIVGRIKHACQLSQRLQESLKKVDHIKILVEDELssPVV 389
Cdd:pfam00282 294 LYLGHTDSAYDTGHKQIPLSR---RFRILKLWFVIRSLGVEGLQNQIRRHVELAQYLEALIRKDGRFEICAEVGL--GLV 368

                  ...
gi 564370336  390 VFR 392
Cdd:pfam00282 369 CFR 371
PLN02590 PLN02590
probable tyrosine decarboxylase
220-393 1.94e-04

probable tyrosine decarboxylase


Pssm-ID: 178200 [Multi-domain]  Cd Length: 539  Bit Score: 44.70  E-value: 1.94e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564370336 220 LEKLIKDDVERGRLPLLLVANAGTAAVGHTDKIGRLKELCEQYGIWLHVEGVNLATLALGYVSSSVLAATK-CDSMTLTP 298
Cdd:PLN02590 274 LEEAISHDLAKGFIPFFICATVGTTSSAAVDPLVPLGNIAKKYGIWLHVDAAYAGNACICPEYRKFIDGIEnADSFNMNA 353
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564370336 299 GLWLgLPAVPAVTLYKHDdpALTLIAGLTSNKP----------------------ADKLRALPLWLSLQYLGLDGIVGRI 356
Cdd:PLN02590 354 HKWL-FANQTCSPLWVKD--RYSLIDALKTNPEylefkvskkdtvvnykdwqislSRRFRSLKLWMVLRLYGSENLRNFI 430
                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 564370336 357 KHACQLSQRLQESLKKVDHIKILVEDELSspVVVFRF 393
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 ...
202-393 4.23e-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: 92.27  E-value: 4.23e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564370336 202 RVPCNtmfgSQHQMDVAFLEKLIKDDVERGRLPLLLVANAGTAAVGHTDKIGRLKELCEQYGIWLHVEGvnlatlALGyv 281
Cdd:cd06450  121 LVPVD----EDGRMDPEALEAAIDEDKAEGLNPIMVVATAGTTDTGAIDPLEEIADLAEKYDLWLHVDA------AYG-- 188
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564370336 282 sSSVLAATK----------CDSMTLTPGLWLGLPAVPAVTLYkhddpaltliagltsnkpadklRALPLWLSLQYLGLDG 351
Cdd:cd06450  189 -GFLLPFPEprhldfgierVDSISVDPHKYGLVPLGCSAVLV----------------------RALKLWATLRRFGRDG 245
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 564370336 352 IVGRIKHACQLSQRLQESLKKVDHIKILVEDELssPVVVFRF 393
Cdd:cd06450  246 YGEHIDRIVDLAKYLAELIRADPGFELLGEPNL--SLVCFRL 285
GadA COG0076
Glutamate or tyrosine decarboxylase or a related PLP-dependent protein [Amino acid transport ...
163-393 9.05e-16

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: 80.49  E-value: 9.05e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564370336 163 DGFNVLYNKKPIIYLSAAARPglgpylCNQ-----LGLPfpcLCRVPcntMFGSQHQMDVAFLEKLIKDDVERGrlplLL 237
Cdd:COG0076  148 LAESGKPGGKPNIVCSETAHF------SFEkaaryLGLG---LRRVP---TVPTDYRIDVDALEEAIDENTIGG----VV 211
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564370336 238 VANAGTAAVGHTDKIGRLKELCEQYGIWLHVEGvnlatlALGyvsSSVLAATKC-----------DSMTLTPGLWLGLPA 306
Cdd:COG0076  212 VGTAGTTDTGSIDDIEELADIAEEYGIWLHVDA------AFG---GFLLPFLEPdgrwdfglegvDSITVDGHKYGLAPI 282
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564370336 307 VPAVTLYK----------HDDPALT----LIAGLTSNKPADklRALPLWLSLQYLGLDGIVGRIKHACQLSQRLQESLKK 372
Cdd:COG0076  283 GCGVVLFRdeealrriliFADYYLPgggiPNFTILGSRPGR--QALALYANLRRLGREGYRKLLDRTLELARYLAEELEK 360
                        250       260
                 ....*....|....*....|.
gi 564370336 373 VDHIKILVEDELssPVVVFRF 393
Cdd:COG0076  361 LGDFELVNEPEL--PIVAFRL 379
Pyridoxal_deC pfam00282
Pyridoxal-dependent decarboxylase conserved domain;
170-392 2.53e-10

Pyridoxal-dependent decarboxylase conserved domain;


Pssm-ID: 395219  Cd Length: 373  Bit Score: 62.82  E-value: 2.53e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564370336  170 NKKPIIYLSAAARpglgpYLCNQLGLPFPCLCR-VPCNtmfgSQHQMDVAFLEKLIKDDVERGRLPLLLVANAGTAAVGH 248
Cdd:pfam00282 143 LAKLVAYTSDQAH-----SSIEKAALYGGVKLReIPSD----DNGKMRGMDLEKAIEEDKENGLIPFFVVATLGTTGSGA 213
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564370336  249 TDKIGRLKELCEQYGIWLHVEGVNLATLALG-YVSSSVLAATKCDSMTLTPGLWLGLPA------------------VPA 309
Cdd:pfam00282 214 FDDLQELGDICAKHNLWLHVDAAYGGSAFICpEFRHWLFGIERADSITFNPHKWMLVLLdcsavwvkdkealqqafqFNP 293
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564370336  310 VTLYKHDDPALTLIAGLTSNKpadKLRALPLWLSLQYLGLDGIVGRIKHACQLSQRLQESLKKVDHIKILVEDELssPVV 389
Cdd:pfam00282 294 LYLGHTDSAYDTGHKQIPLSR---RFRILKLWFVIRSLGVEGLQNQIRRHVELAQYLEALIRKDGRFEICAEVGL--GLV 368

                  ...
gi 564370336  390 VFR 392
Cdd:pfam00282 369 CFR 371
PLN02590 PLN02590
probable tyrosine decarboxylase
220-393 1.94e-04

probable tyrosine decarboxylase


Pssm-ID: 178200 [Multi-domain]  Cd Length: 539  Bit Score: 44.70  E-value: 1.94e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564370336 220 LEKLIKDDVERGRLPLLLVANAGTAAVGHTDKIGRLKELCEQYGIWLHVEGVNLATLALGYVSSSVLAATK-CDSMTLTP 298
Cdd:PLN02590 274 LEEAISHDLAKGFIPFFICATVGTTSSAAVDPLVPLGNIAKKYGIWLHVDAAYAGNACICPEYRKFIDGIEnADSFNMNA 353
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564370336 299 GLWLgLPAVPAVTLYKHDdpALTLIAGLTSNKP----------------------ADKLRALPLWLSLQYLGLDGIVGRI 356
Cdd:PLN02590 354 HKWL-FANQTCSPLWVKD--RYSLIDALKTNPEylefkvskkdtvvnykdwqislSRRFRSLKLWMVLRLYGSENLRNFI 430
                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 564370336 357 KHACQLSQRLQESLKKVDHIKILVEDELSspVVVFRF 393
Cdd:PLN02590 431 RDHVNLAKHFEDYVAQDPSFEVVTTRYFS--LVCFRL 465
PLN02880 PLN02880
tyrosine decarboxylase
192-368 8.38e-04

tyrosine decarboxylase


Pssm-ID: 215475 [Multi-domain]  Cd Length: 490  Bit Score: 42.59  E-value: 8.38e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564370336 192 QLGLPFPCLCRV---PCNTMFGSQHQMdvafLEKLIKDDVERGRLPLLLVANAGTAAVGHTDKIGRLKELCEQYGIWLHV 268
Cdd:PLN02880 199 QIAGIHPENCRLlktDSSTNYALAPEL----LSEAISTDLSSGLIPFFLCATVGTTSSTAVDPLLELGKIAKSNGMWFHV 274
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564370336 269 EGvnlatlalGYVSSSVL---------AATKCDSMTLTPGLWLgLPAVPAVTLYKHDDPAltLIAGLTS------NKPAD 333
Cdd:PLN02880 275 DA--------AYAGSACIcpeyrhyidGVEEADSFNMNAHKWF-LTNFDCSLLWVKDRNA--LIQSLSTnpeflkNKASQ 343
                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|.
gi 564370336 334 ----------------KLRALPLWLSLQYLGLDGIVGRIKHACQLSQRLQE 368
Cdd:PLN02880 344 ansvvdykdwqiplgrRFRSLKLWMVLRLYGVENLQSYIRNHIKLAKEFEQ 394
 
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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