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Conserved domains on  [gi|157823503|ref|NP_001100790|]
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pyridoxal phosphate homeostasis protein [Rattus norvegicus]

Protein Classification

YggS family pyridoxal phosphate enzyme( domain architecture ID 10160097)

YggS family pyridoxal phosphate enzyme is a pyridoxal 5-phosphate (PLP)-dependent enzyme; similar to human pyridoxal phosphate homeostasis protein, which may be involved in intracellular homeostatic regulation of pyridoxal 5'-phosphate (PLP), the active form of vitamin B6

Gene Ontology:  GO:0030170

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PLPDE_III_YBL036c_euk cd06822
Pyridoxal 5-phosphate (PLP)-binding TIM barrel domain of Type III PLP-Dependent Enzymes, ...
 17-248 8.40e-147

Pyridoxal 5-phosphate (PLP)-binding TIM barrel domain of Type III PLP-Dependent Enzymes, Eukaryotic YBL036c-like proteins; This subfamily contains mostly uncharacterized eukaryotic proteins with similarity to the yeast hypothetical protein YBL036c, which is homologous to a Pseudomonas aeruginosa gene that is co-transcribed with a known proline biosynthetic gene. YBL036c is a single domain monomeric protein with a typical TIM barrel fold. It binds the PLP cofactor and has been shown to exhibit amino acid racemase activity. The YBL036c structure is similar to the N-terminal domain of the fold type III PLP-dependent enzymes, bacterial alanine racemase and eukaryotic ornithine decarboxylase, which are two-domain dimeric proteins. The lack of a second domain in YBL036c may explain limited D- to L-alanine racemase or non-specific racemase activity. Some members of this subfamily are also referred to as PROSC (Proline synthetase co-transcribed bacterial homolog).


:

Pssm-ID: 143496  Cd Length: 227  Bit Score: 410.05  E-value: 8.40e-147
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157823503  17 LRAVNERVQQSVARRPRGLPAIQPRLVAVSKTKPTEMVIEAYGHGQRTFGENYVQELLEKASNPTLlsscpEIKWHFIGH 96
Cdd:cd06822    1 LIANLKRIRQAVKRASKKLPASKPRLVAVSKTKPAELIKEAYDAGQRHFGENYVQELIEKAPDLPI-----DIKWHFIGH 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157823503  97 LQKQNVNKLMAVPNLSMLETIDSVKLADKVNSSWQKKGSPERLKVMVQINTSGEDSKHGLLPSETVAVVEHIKASCPNLE 176
Cdd:cd06822   76 LQSNKVKKLLKVPNLYMVETVDSEKLADKLNKAWEKLGEREPLKVMVQVNTSGEESKSGLEPSEAVELVKHIIEECPNLK 155

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 157823503 177 FVGLMTIGSFGHDLSQGPNPDFQRLLSLRQELCEKLGLPVEQVELSMGMSVDFQHAIEVGSTNIRVGSTIFG 248
Cdd:cd06822  156 FSGLMTIGSFGYSLSSGPNPDFLCLVDCRKKVCEKLGINPDDLELSMGMSADFEHAIEMGSTNVRVGSAIFG 227
 
Name Accession Description Interval E-value
PLPDE_III_YBL036c_euk cd06822
Pyridoxal 5-phosphate (PLP)-binding TIM barrel domain of Type III PLP-Dependent Enzymes, ...
 17-248 8.40e-147

Pyridoxal 5-phosphate (PLP)-binding TIM barrel domain of Type III PLP-Dependent Enzymes, Eukaryotic YBL036c-like proteins; This subfamily contains mostly uncharacterized eukaryotic proteins with similarity to the yeast hypothetical protein YBL036c, which is homologous to a Pseudomonas aeruginosa gene that is co-transcribed with a known proline biosynthetic gene. YBL036c is a single domain monomeric protein with a typical TIM barrel fold. It binds the PLP cofactor and has been shown to exhibit amino acid racemase activity. The YBL036c structure is similar to the N-terminal domain of the fold type III PLP-dependent enzymes, bacterial alanine racemase and eukaryotic ornithine decarboxylase, which are two-domain dimeric proteins. The lack of a second domain in YBL036c may explain limited D- to L-alanine racemase or non-specific racemase activity. Some members of this subfamily are also referred to as PROSC (Proline synthetase co-transcribed bacterial homolog).


Pssm-ID: 143496  Cd Length: 227  Bit Score: 410.05  E-value: 8.40e-147
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157823503  17 LRAVNERVQQSVARRPRGLPAIQPRLVAVSKTKPTEMVIEAYGHGQRTFGENYVQELLEKASNPTLlsscpEIKWHFIGH 96
Cdd:cd06822    1 LIANLKRIRQAVKRASKKLPASKPRLVAVSKTKPAELIKEAYDAGQRHFGENYVQELIEKAPDLPI-----DIKWHFIGH 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157823503  97 LQKQNVNKLMAVPNLSMLETIDSVKLADKVNSSWQKKGSPERLKVMVQINTSGEDSKHGLLPSETVAVVEHIKASCPNLE 176
Cdd:cd06822   76 LQSNKVKKLLKVPNLYMVETVDSEKLADKLNKAWEKLGEREPLKVMVQVNTSGEESKSGLEPSEAVELVKHIIEECPNLK 155

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 157823503 177 FVGLMTIGSFGHDLSQGPNPDFQRLLSLRQELCEKLGLPVEQVELSMGMSVDFQHAIEVGSTNIRVGSTIFG 248
Cdd:cd06822  156 FSGLMTIGSFGYSLSSGPNPDFLCLVDCRKKVCEKLGINPDDLELSMGMSADFEHAIEMGSTNVRVGSAIFG 227
YggS COG0325
Pyridoxal 5'-phosphate homeostasis protein YggS, UPF0001 family [Coenzyme transport and ...
 17-251 1.80e-82

Pyridoxal 5'-phosphate homeostasis protein YggS, UPF0001 family [Coenzyme transport and metabolism];


Pssm-ID: 440094  Cd Length: 227  Bit Score: 247.26  E-value: 1.80e-82
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157823503  17 LRAVNERVQQSVARRPRGLPAIqpRLVAVSKTKPTEMVIEAYGHGQRTFGENYVQELLEKASnptLLSSCPeIKWHFIGH 96
Cdd:COG0325    8 LAAVRERIAAAAARAGRDPEEV--TLVAVSKTVPAEAIREAYAAGQRDFGENRVQEALEKIE---ALADLD-IEWHFIGH 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157823503  97 LQKQNVNKlmAVPNLSMLETIDSVKLADKVNSSWQKKGSPerLKVMVQINTSGEDSKHGLLPSETVAVVEHIKAsCPNLE 176
Cdd:COG0325   82 LQSNKVKY--VAELFDLIHSVDRLKLAEELNKRAAKAGRP--LDVLLQVNISGEESKSGVAPEELPALAEAIAA-LPNLR 156

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 157823503 177 FVGLMTIGSFGHDLSQgPNPDFQRLLSLRQELCEK-LGLPveqvELSMGMSVDFQHAIEVGSTNIRVGSTIFGERD 251
Cdd:COG0325  157 LRGLMTIAPLTEDPEE-VRPAFARLRELFDRLRAQgPGLD----ELSMGMSGDYEIAIEEGATMVRVGTAIFGARP 227
TIGR00044 TIGR00044
pyridoxal phosphate enzyme, YggS family; Members of this protein family include YggS from ...
 41-250 1.11e-55

pyridoxal phosphate enzyme, YggS family; Members of this protein family include YggS from Escherichia coli and YBL036C, an uncharacterized pyridoxal protein of Saccharomyces cerevisiae. [Unknown function, Enzymes of unknown specificity]


Pssm-ID: 129155 [Multi-domain]  Cd Length: 229  Bit Score: 178.88  E-value: 1.11e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157823503   41 RLVAVSKTKPTEMVIEAYGHGQRTFGENYVQELLEKASnptLLSSCPEIKWHFIGHLQKqNVNKLMaVPNLSMLETIDSV 120
Cdd:TIGR00044  30 KLLAVSKTKPASAIQEAYDAGQRAFGENYVQELVEKIR---HLEELGLLEWHFIGPLQS-NKSRLV-VENFDWCHTIDSL 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157823503  121 KLADKVNSSWQKKGSPerLKVMVQINTSGEDSKHGLLPSETVAVVEHIkASCPNLEFVGLMTIGSFGHDLSQGPNpDFQR 200
Cdd:TIGR00044 105 KIATKLNEQREALLPP--LNVLLQINISDEESKSGIQPEELLELAAQL-EELKHLKLRGLMTIGAPTDSYVDQEE-VFRQ 180

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 157823503  201 LLSLRQELceKLGLPVEQV-ELSMGMSVDFQHAIEVGSTNIRVGSTIFGER 250
Cdd:TIGR00044 181 MKVLFAQI--KQRSPHGTIdTLSMGMSDDFEEAIAAGATMVRIGTAIFGAR 229
Ala_racemase_N pfam01168
Alanine racemase, N-terminal domain;
41-251 6.14e-18

Alanine racemase, N-terminal domain;


Pssm-ID: 460095 [Multi-domain]  Cd Length: 220  Bit Score: 79.96  E-value: 6.14e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157823503   41 RLVAVSKTkptemviEAYGHG------------QRTFGENYVQELLEkasnptLLSSCPEIKWHFIGHLQKQNVnKLMAV 108
Cdd:pfam01168  22 KLMAVVKA-------NAYGHGavevaralleggADGFAVATLDEALE------LREAGITAPILVLGGFPPEEL-ALAAE 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157823503  109 PNLSMleTIDSVKLADKVNSSWQKKGSPerLKVMVQINTSGedSKHGLLPSETVAVVEHIKAsCPNLEFVGLMTIGSFGH 188
Cdd:pfam01168  88 YDLTP--TVDSLEQLEALAAAARRLGKP--LRVHLKIDTGM--GRLGFRPEEALALLARLAA-LPGLRLEGLMTHFACAD 160

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 157823503  189 DLSQGPNP-DFQRLLSLRQELcEKLGLPVEqvELSMGMSvdfqHAIEVGSTN---IRVGSTIFGERD 251
Cdd:pfam01168 161 EPDDPYTNaQLARFREAAAAL-EAAGLRPP--VVHLANS----AAILLHPLHfdmVRPGIALYGLSP 220
 
Name Accession Description Interval E-value
PLPDE_III_YBL036c_euk cd06822
Pyridoxal 5-phosphate (PLP)-binding TIM barrel domain of Type III PLP-Dependent Enzymes, ...
 17-248 8.40e-147

Pyridoxal 5-phosphate (PLP)-binding TIM barrel domain of Type III PLP-Dependent Enzymes, Eukaryotic YBL036c-like proteins; This subfamily contains mostly uncharacterized eukaryotic proteins with similarity to the yeast hypothetical protein YBL036c, which is homologous to a Pseudomonas aeruginosa gene that is co-transcribed with a known proline biosynthetic gene. YBL036c is a single domain monomeric protein with a typical TIM barrel fold. It binds the PLP cofactor and has been shown to exhibit amino acid racemase activity. The YBL036c structure is similar to the N-terminal domain of the fold type III PLP-dependent enzymes, bacterial alanine racemase and eukaryotic ornithine decarboxylase, which are two-domain dimeric proteins. The lack of a second domain in YBL036c may explain limited D- to L-alanine racemase or non-specific racemase activity. Some members of this subfamily are also referred to as PROSC (Proline synthetase co-transcribed bacterial homolog).


Pssm-ID: 143496  Cd Length: 227  Bit Score: 410.05  E-value: 8.40e-147
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157823503  17 LRAVNERVQQSVARRPRGLPAIQPRLVAVSKTKPTEMVIEAYGHGQRTFGENYVQELLEKASNPTLlsscpEIKWHFIGH 96
Cdd:cd06822    1 LIANLKRIRQAVKRASKKLPASKPRLVAVSKTKPAELIKEAYDAGQRHFGENYVQELIEKAPDLPI-----DIKWHFIGH 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157823503  97 LQKQNVNKLMAVPNLSMLETIDSVKLADKVNSSWQKKGSPERLKVMVQINTSGEDSKHGLLPSETVAVVEHIKASCPNLE 176
Cdd:cd06822   76 LQSNKVKKLLKVPNLYMVETVDSEKLADKLNKAWEKLGEREPLKVMVQVNTSGEESKSGLEPSEAVELVKHIIEECPNLK 155

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 157823503 177 FVGLMTIGSFGHDLSQGPNPDFQRLLSLRQELCEKLGLPVEQVELSMGMSVDFQHAIEVGSTNIRVGSTIFG 248
Cdd:cd06822  156 FSGLMTIGSFGYSLSSGPNPDFLCLVDCRKKVCEKLGINPDDLELSMGMSADFEHAIEMGSTNVRVGSAIFG 227
PLPDE_III_YBL036c_like cd00635
Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, YBL036c-like proteins; This family ...
 17-248 1.33e-82

Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, YBL036c-like proteins; This family contains mostly uncharacterized proteins, widely distributed among eukaryotes, bacteria and archaea, that bear similarity to the yeast hypothetical protein YBL036c, which is homologous to a Pseudomonas aeruginosa gene that is co-transcribed with a known proline biosynthetic gene. YBL036c is a single domain monomeric protein with a typical TIM barrel fold. It binds the PLP cofactor and has been shown to exhibit amino acid racemase activity. The YBL036c structure is similar to the N-terminal domain of the fold type III PLP-dependent enzymes, bacterial alanine racemase and eukaryotic ornithine decarboxylase, which are two-domain dimeric proteins. The lack of a second domain in YBL036c may explain limited D- to L-alanine racemase or non-specific racemase activity.


Pssm-ID: 143483  Cd Length: 222  Bit Score: 247.38  E-value: 1.33e-82
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157823503  17 LRAVNERVQQSVARRPRGLPAIqpRLVAVSKTKPTEMVIEAYGHGQRTFGENYVQELLEKAsnpTLLSScPEIKWHFIGH 96
Cdd:cd00635    5 LEEVRERIAAAAERAGRDPDEV--TLVAVSKTVPAEAIREAIEAGQRDFGENRVQEALDKA---EELPD-PDIEWHFIGH 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157823503  97 LQKqnvNKL-MAVPNLSMLETIDSVKLADKVNSSWQKKGSPerLKVMVQINTSGEDSKHGLLPSETVAVVEHIkASCPNL 175
Cdd:cd00635   79 LQT---NKVkYAVRLFDLIHSVDSLKLAEELNKRAEKEGRV--LDVLVQVNIGGEESKSGVAPEELEELLEEI-AALPNL 152

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 157823503 176 EFVGLMTIGSFGHDLSQgPNPDFQRLLSLRQELCEKLGLPVEqvELSMGMSVDFQHAIEVGSTNIRVGSTIFG 248
Cdd:cd00635  153 RIRGLMTIAPLTEDPEE-VRPYFRELRELRDELGAKGGVNLK--ELSMGMSGDFEIAIEEGATLVRIGTAIFG 222
YggS COG0325
Pyridoxal 5'-phosphate homeostasis protein YggS, UPF0001 family [Coenzyme transport and ...
 17-251 1.80e-82

Pyridoxal 5'-phosphate homeostasis protein YggS, UPF0001 family [Coenzyme transport and metabolism];


Pssm-ID: 440094  Cd Length: 227  Bit Score: 247.26  E-value: 1.80e-82
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157823503  17 LRAVNERVQQSVARRPRGLPAIqpRLVAVSKTKPTEMVIEAYGHGQRTFGENYVQELLEKASnptLLSSCPeIKWHFIGH 96
Cdd:COG0325    8 LAAVRERIAAAAARAGRDPEEV--TLVAVSKTVPAEAIREAYAAGQRDFGENRVQEALEKIE---ALADLD-IEWHFIGH 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157823503  97 LQKQNVNKlmAVPNLSMLETIDSVKLADKVNSSWQKKGSPerLKVMVQINTSGEDSKHGLLPSETVAVVEHIKAsCPNLE 176
Cdd:COG0325   82 LQSNKVKY--VAELFDLIHSVDRLKLAEELNKRAAKAGRP--LDVLLQVNISGEESKSGVAPEELPALAEAIAA-LPNLR 156

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 157823503 177 FVGLMTIGSFGHDLSQgPNPDFQRLLSLRQELCEK-LGLPveqvELSMGMSVDFQHAIEVGSTNIRVGSTIFGERD 251
Cdd:COG0325  157 LRGLMTIAPLTEDPEE-VRPAFARLRELFDRLRAQgPGLD----ELSMGMSGDYEIAIEEGATMVRVGTAIFGARP 227
PLPDE_III_Yggs_like cd06824
Pyridoxal 5-phosphate (PLP)-binding TIM barrel domain of Type III PLP-Dependent Enzymes, ...
 17-249 1.14e-60

Pyridoxal 5-phosphate (PLP)-binding TIM barrel domain of Type III PLP-Dependent Enzymes, Yggs-like proteins; This subfamily contains mainly uncharacterized proteobacterial proteins with similarity to the hypothetical Escherichia coli protein YggS, a homolog of yeast YBL036c, which is homologous to a Pseudomonas aeruginosa gene that is co-transcribed with a known proline biosynthetic gene. Like yeast YBL036c, Yggs is a single domain monomeric protein with a typical TIM-barrel fold. Its structure, which shows a covalently-bound PLP cofactor, is similar to the N-terminal domain of the fold type III PLP-dependent enzymes, bacterial alanine racemase and eukaryotic ornithine decarboxylase, which are two-domain dimeric proteins. YggS has not been characterized extensively and its biological function is still unkonwn.


Pssm-ID: 143497  Cd Length: 224  Bit Score: 191.64  E-value: 1.14e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157823503  17 LRAVNERVQQSVARRPRGLPAIQprLVAVSKTKPTEMVIEAYGHGQRTFGENYVQELLEKAsnpTLLSSCPEIKWHFIGH 96
Cdd:cd06824    6 LAQVKQRIAQAAKQAGRDPSSVQ--LLAVSKTKPADAIREAYAAGQRHFGENYVQEALEKI---EALRDLQDIEWHFIGP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157823503  97 LQKqNVNKLMAvPNLSMLETIDSVKLADKVNSswQKKGSPERLKVMVQINTSGEDSKHGLLPSETVAVVEHIkASCPNLE 176
Cdd:cd06824   81 IQS-NKTKLIA-ENFDWVHSVDRLKIAKRLND--QRPAGLPPLNVCIQVNISGEDSKSGVAPEDAAELAEAI-SQLPNLR 155

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 157823503 177 FVGLMTIGSFGHDLSQgPNPDFQRLLSLRQELcEKLGLPVEqvELSMGMSVDFQHAIEVGSTNIRVGSTIFGE 249
Cdd:cd06824  156 LRGLMAIPAPTDDEAA-QRAAFKRLRQLFDQL-KKQYPDLD--TLSMGMSGDLEAAIAAGSTMVRIGTAIFGA 224
TIGR00044 TIGR00044
pyridoxal phosphate enzyme, YggS family; Members of this protein family include YggS from ...
 41-250 1.11e-55

pyridoxal phosphate enzyme, YggS family; Members of this protein family include YggS from Escherichia coli and YBL036C, an uncharacterized pyridoxal protein of Saccharomyces cerevisiae. [Unknown function, Enzymes of unknown specificity]


Pssm-ID: 129155 [Multi-domain]  Cd Length: 229  Bit Score: 178.88  E-value: 1.11e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157823503   41 RLVAVSKTKPTEMVIEAYGHGQRTFGENYVQELLEKASnptLLSSCPEIKWHFIGHLQKqNVNKLMaVPNLSMLETIDSV 120
Cdd:TIGR00044  30 KLLAVSKTKPASAIQEAYDAGQRAFGENYVQELVEKIR---HLEELGLLEWHFIGPLQS-NKSRLV-VENFDWCHTIDSL 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157823503  121 KLADKVNSSWQKKGSPerLKVMVQINTSGEDSKHGLLPSETVAVVEHIkASCPNLEFVGLMTIGSFGHDLSQGPNpDFQR 200
Cdd:TIGR00044 105 KIATKLNEQREALLPP--LNVLLQINISDEESKSGIQPEELLELAAQL-EELKHLKLRGLMTIGAPTDSYVDQEE-VFRQ 180

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 157823503  201 LLSLRQELceKLGLPVEQV-ELSMGMSVDFQHAIEVGSTNIRVGSTIFGER 250
Cdd:TIGR00044 181 MKVLFAQI--KQRSPHGTIdTLSMGMSDDFEEAIAAGATMVRIGTAIFGAR 229
PLPDE_III cd06808
Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes; The fold type III PLP-dependent enzyme ...
 41-243 1.58e-18

Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes; The fold type III PLP-dependent enzyme family is predominantly composed of two-domain proteins with similarity to bacterial alanine racemases (AR) including eukaryotic ornithine decarboxylases (ODC), prokaryotic diaminopimelate decarboxylases (DapDC), biosynthetic arginine decarboxylases (ADC), carboxynorspermidine decarboxylases (CANSDC), and similar proteins. AR-like proteins contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. They exist as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. These proteins play important roles in the biosynthesis of amino acids and polyamine. The family also includes the single-domain YBL036c-like proteins, which contain a single PLP-binding TIM-barrel domain without any N- or C-terminal extensions. Due to the lack of a second domain, these proteins may possess only limited D- to L-alanine racemase activity or non-specific racemase activity.


Pssm-ID: 143484 [Multi-domain]  Cd Length: 211  Bit Score: 81.60  E-value: 1.58e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157823503  41 RLVAVSKTKPTEMVIEAYGHGQRTFGENYVQELLEKASnptllSSCPEIKWHFIGHLQKQNVNKLMAVPNLSMLeTIDSV 120
Cdd:cd06808   17 TLFAVVKANANPEVARTLAALGTGFDVASLGEALLLRA-----AGIPPEPILFLGPCKQVSELEDAAEQGVIVV-TVDSL 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157823503 121 KLADKVNSSWQKKGSPerLKVMVQINTSGEDSKHGLLPSETVAVVEHIKAsCPNLEFVGLMTIGSFGHDLSQGPNPDFQR 200
Cdd:cd06808   91 EELEKLEEAALKAGPP--ARVLLRIDTGDENGKFGVRPEELKALLERAKE-LPHLRLVGLHTHFGSADEDYSPFVEALSR 167

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 157823503 201 LLSLRQELcEKLGLPVEQVELSMGMSVD-FQHAIEVGSTNIRVG 243
Cdd:cd06808  168 FVAALDQL-GELGIDLEQLSIGGSFAILyLQELPLGTFIIVEPG 210
Ala_racemase_N pfam01168
Alanine racemase, N-terminal domain;
41-251 6.14e-18

Alanine racemase, N-terminal domain;


Pssm-ID: 460095 [Multi-domain]  Cd Length: 220  Bit Score: 79.96  E-value: 6.14e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157823503   41 RLVAVSKTkptemviEAYGHG------------QRTFGENYVQELLEkasnptLLSSCPEIKWHFIGHLQKQNVnKLMAV 108
Cdd:pfam01168  22 KLMAVVKA-------NAYGHGavevaralleggADGFAVATLDEALE------LREAGITAPILVLGGFPPEEL-ALAAE 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157823503  109 PNLSMleTIDSVKLADKVNSSWQKKGSPerLKVMVQINTSGedSKHGLLPSETVAVVEHIKAsCPNLEFVGLMTIGSFGH 188
Cdd:pfam01168  88 YDLTP--TVDSLEQLEALAAAARRLGKP--LRVHLKIDTGM--GRLGFRPEEALALLARLAA-LPGLRLEGLMTHFACAD 160

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 157823503  189 DLSQGPNP-DFQRLLSLRQELcEKLGLPVEqvELSMGMSvdfqHAIEVGSTN---IRVGSTIFGERD 251
Cdd:pfam01168 161 EPDDPYTNaQLARFREAAAAL-EAAGLRPP--VVHLANS----AAILLHPLHfdmVRPGIALYGLSP 220
PLPDE_III_LS_D-TA_like cd06820
Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Low Specificity D-Threonine ...
 97-250 1.23e-06

Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Low Specificity D-Threonine Aldolase-like; This subfamily is composed of uncharacterized bacterial proteins with similarity to low specificity D-threonine aldolase (D-TA), which is a fold type III PLP-dependent enzyme that catalyzes the interconversion between D-threonine/D-allo-threonine and glycine plus acetaldehyde. Both PLP and divalent cations (eg. Mn2+) are required for catalytic activity. Low specificity D-TAs show similarity to bacterial alanine racemase (AR), which contains an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. AR exists as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. Based on its similarity to AR, it is possible that low specificity D-TAs also form dimers in solution. Experimental data show that the monomeric form of low specificity D-TAs exhibit full catalytic activity.


Pssm-ID: 143494 [Multi-domain]  Cd Length: 353  Bit Score: 48.85  E-value: 1.23e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157823503  97 LQKQNVNKLMAVP---NLSMleTIDSVKLADKVNSSWQKKGSPerLKVMVQINtSGEDSKHGLLPSETVAVVEHIkASCP 173
Cdd:cd06820   81 VGRQKLERLRALAervTLSV--GVDSAEVARGLAEVAEGAGRP--LEVLVEVD-SGMNRCGVQTPEDAVALARAI-ASAP 154

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157823503 174 NLEFVGLMTIGsfGHDLSQGPNP-----DFQRLLSLRQELcEKLGLPVEQVelSMGMSVDFQHAIEV-GSTNIRVGSTIF 247
Cdd:cd06820  155 GLRFRGIFTYP--GHSYAPGALEeaaadEAEALLAAAGIL-EEAGLEPPVV--SGGSTPTLWRSHEVpGITEIRPGTYIF 229


                 ...
gi 157823503 248 GER 250
Cdd:cd06820  230 NDA 232
LysA COG0019
Diaminopimelate decarboxylase [Amino acid transport and metabolism]; Diaminopimelate ...
 145-224 6.85e-05

Diaminopimelate decarboxylase [Amino acid transport and metabolism]; Diaminopimelate decarboxylase is part of the Pathway/BioSystem: Lysine biosynthesis


Pssm-ID: 439790 [Multi-domain]  Cd Length: 417  Bit Score: 43.60  E-value: 6.85e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157823503 145 INTSGEDSKHGLLPSETVAVVEHIKAScPNLEFVGLMTigsfgHDLSQGPNPD-----FQRLLSLRQELcEKLGLPVEqv 219
Cdd:COG0019  161 ISTGGKDSKFGIPLEDALEAYRRAAAL-PGLRLVGLHF-----HIGSQILDLEpfeeaLERLLELAEEL-RELGIDLE-- 231


                 ....*
gi 157823503 220 ELSMG 224
Cdd:COG0019  232 WLDLG 236
PLPDE_III_DapDC cd06828
Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; ...
 145-185 4.40e-03

Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Diaminopimelate decarboxylase (DapDC, EC 4.1.1.20) participates in the last step of lysine biosynthesis. It converts meso-2,6-diaminoheptanedioate to L-lysine. It is a fold type III PLP-dependent enzyme that contains an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain, similar to bacterial alanine racemases. DapDC exists as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. Homodimer formation and the presence of the PLP cofactor are required for catalytic activity.


Pssm-ID: 143501 [Multi-domain]  Cd Length: 373  Bit Score: 38.23  E-value: 4.40e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 157823503 145 INTSGEDSKHGLLPSETVAVVEHIKAScPNLEFVGL-MTIGS 185
Cdd:cd06828  138 ISTGGKDSKFGIPLEQALEAYRRAKEL-PGLKLVGLhCHIGS 178
 
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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