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Conserved domains on  [gi|506294699|ref|WP_015814474|]
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saccharopine dehydrogenase family protein [Dyadobacter fermentans]

Protein Classification

saccharopine dehydrogenase family protein( domain architecture ID 11448323)

saccharopine dehydrogenase family protein such as saccharopine dehydrogenase, an enzyme of the alpha-aminoadipate pathway of lysine biosynthesis that catalyzes the reversible conversion of glutamate and alpha-aminoadipic-delta-semialdehyde to saccharopine

CATH:  3.30.360.10|3.40.50.720
EC:  1.5.1.-
Gene Ontology:  GO:0016646|GO:0070403|GO:0009085
PubMed:  11080625|30945211

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Lys9 COG1748
Saccharopine dehydrogenase, NADP-dependent [Amino acid transport and metabolism]; Saccharopine ...
 26-351 3.95e-110

Saccharopine dehydrogenase, NADP-dependent [Amino acid transport and metabolism]; Saccharopine dehydrogenase, NADP-dependent is part of the Pathway/BioSystem: Lysine biosynthesis


:

Pssm-ID: 441354 [Multi-domain]  Cd Length: 352  Bit Score: 325.25  E-value: 3.95e-110
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 506294699  26 VTGVDR----AQPAVAL--PFQVVTGDVNDSLFVESVLMGFDAVVSCMPYNLNLPIARQAHKSGIHYFDLTEDVPTTA-- 97
Cdd:COG1748    3 VTLADRslekAEALAASgpKVEAAQLDASDPEALAALIAGADLVINALPPYLNLTVAEACIEAGVHYVDLSEDEPETEak 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 506294699  98 -AIREMAQDSRSVLAPQCGLAPGFIGIVGMDLAKRFTKIRDIELRVGALPRYPNGLMGYSFTWSPAGVVNEYLNDAEVIH 176
Cdd:COG1748   83 lALDELAKEAGVTAIPGCGLAPGLSNVLAAYAADRFDEIDSIDIRVGGLPGYPSNPLNYGTTWSPEGVIREYTNPARAIE 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 506294699 177 NGVRKMVPSLEGTEMINIEGQ-EFEAFSTSGGLATMCETLEgKVDTLNYKTIRYPGHCSLMRFlLYELCLKDK------- 248
Cdd:COG1748  163 DGKWVEVPPLSERETIDFPGVgRYEAYNTDGELETLPETYP-GVKTVRFKTGRYPGHLNHLKV-LVDLGLTDDepveveg 240

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 506294699 249 -----RALVEEILTEAKP--PVQQDVVYVYAVVEGWKGDhlEREEFYRAYHPIEIDGQHWRAISWTTAASIASVVEMVAD 321
Cdd:COG1748  241 vevspRDVLKAILPDPLPlgPTDKDVVVIGVVVKGTKDG--KRETYVYNLVDHEDAETGSTAMAYTTGVPAAIAAELLLE 318

                        330       340       350
                 ....*....|....*....|....*....|..
gi 506294699 322 GVLPDRGFVRQEDILLDDFFKTLN--GWYFTQ 351
Cdd:COG1748  319 GKIPKPGVVNPEQLDPDPFLEELAkrGIPIEE 350
 
Name Accession Description Interval E-value
Lys9 COG1748
Saccharopine dehydrogenase, NADP-dependent [Amino acid transport and metabolism]; Saccharopine ...
 26-351 3.95e-110

Saccharopine dehydrogenase, NADP-dependent [Amino acid transport and metabolism]; Saccharopine dehydrogenase, NADP-dependent is part of the Pathway/BioSystem: Lysine biosynthesis


Pssm-ID: 441354 [Multi-domain]  Cd Length: 352  Bit Score: 325.25  E-value: 3.95e-110
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 506294699  26 VTGVDR----AQPAVAL--PFQVVTGDVNDSLFVESVLMGFDAVVSCMPYNLNLPIARQAHKSGIHYFDLTEDVPTTA-- 97
Cdd:COG1748    3 VTLADRslekAEALAASgpKVEAAQLDASDPEALAALIAGADLVINALPPYLNLTVAEACIEAGVHYVDLSEDEPETEak 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 506294699  98 -AIREMAQDSRSVLAPQCGLAPGFIGIVGMDLAKRFTKIRDIELRVGALPRYPNGLMGYSFTWSPAGVVNEYLNDAEVIH 176
Cdd:COG1748   83 lALDELAKEAGVTAIPGCGLAPGLSNVLAAYAADRFDEIDSIDIRVGGLPGYPSNPLNYGTTWSPEGVIREYTNPARAIE 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 506294699 177 NGVRKMVPSLEGTEMINIEGQ-EFEAFSTSGGLATMCETLEgKVDTLNYKTIRYPGHCSLMRFlLYELCLKDK------- 248
Cdd:COG1748  163 DGKWVEVPPLSERETIDFPGVgRYEAYNTDGELETLPETYP-GVKTVRFKTGRYPGHLNHLKV-LVDLGLTDDepveveg 240

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 506294699 249 -----RALVEEILTEAKP--PVQQDVVYVYAVVEGWKGDhlEREEFYRAYHPIEIDGQHWRAISWTTAASIASVVEMVAD 321
Cdd:COG1748  241 vevspRDVLKAILPDPLPlgPTDKDVVVIGVVVKGTKDG--KRETYVYNLVDHEDAETGSTAMAYTTGVPAAIAAELLLE 318

                        330       340       350
                 ....*....|....*....|....*....|..
gi 506294699 322 GVLPDRGFVRQEDILLDDFFKTLN--GWYFTQ 351
Cdd:COG1748  319 GKIPKPGVVNPEQLDPDPFLEELAkrGIPIEE 350
Sacchrp_dh_C pfam16653
Saccharopine dehydrogenase C-terminal domain; This family comprises the C-terminal domain of ...
 115-331 7.30e-27

Saccharopine dehydrogenase C-terminal domain; This family comprises the C-terminal domain of saccharopine dehydrogenase. In some organizms this enzyme is found as a bifunctional polypeptide with lysine ketoglutarate reductase. The saccharopine dehydrogenase can also function as a saccharopine reductase.


Pssm-ID: 465219  Cd Length: 255  Bit Score: 106.61  E-value: 7.30e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 506294699  115 GLAPGFIGIVGM----DLAKRFTKIRDIELRVGALP--RYPNGLMGYSFTWSPAGVVNEYLNDAEVIHNGVRKMVPSLEG 188
Cdd:pfam16653   1 GLDPGIDHMFAIkaidDVNAKGGKIESFLSYCGGLPapETSDNPLGYKFSWSPEGVLREGTNPARYWEDGKEVEVPGSEL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 506294699  189 TEMINI-EGQEFEAFSTSGGLATmcETLEG--KVDTLNYKTIRYPGHCSLMRFlLYELCLKDKRALVEEILTEAKPPVQ- 264
Cdd:pfam16653  81 MEPIYIrPGFAFEGYPNRDSLPH--EELYSlpEAKTLYRGTLRYPGFDEAIKS-LVELGLLSEEPKVSLEWLLFSGPLDv 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 506294699  265 ---------------QDVVYVYAVVEGWKGDHlereefyRAYHPIEIdGQHWR----AISWTTAASIASVVEMVADGVLP 325
Cdd:pfam16653 158 laalledklslgpgeRDMVVLQHEFDGKKGER-------RTYTLVDY-GDHEEvgpsAMARTVGVPAAIAALLILDGKIK 229


                  ....*.
gi 506294699  326 DRGFVR 331
Cdd:pfam16653 230 NKGVVN 235
PLN02819 PLN02819
lysine-ketoglutarate reductase/saccharopine dehydrogenase
 43-197 1.06e-06

lysine-ketoglutarate reductase/saccharopine dehydrogenase


Pssm-ID: 215439 [Multi-domain]  Cd Length: 1042  Bit Score: 50.57  E-value: 1.06e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 506294699   43 VTGDVNDSLFVESVLMGFDAVVSCMPYNLNLPIARQAHKSGIHYFDLTEDVPTTAAIREMAQDSRSVLAPQCGLAPGFIG 122
Cdd:PLN02819  632 VQLDVSDSESLLKYVSQVDVVISLLPASCHAVVAKACIELKKHLVTASYVSEEMSALDSKAKEAGITILCEMGLDPGIDH 711

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 506294699  123 IVGM----DLAKRFTKIRDIELRVGALP--RYPNGLMGYSFTWSPAGVVNEYLNDAEVIHNGvrkmvpslegtEMINIEG 196
Cdd:PLN02819  712 MMAMkmidDAHERGGKVKSFTSYCGGLPspEAANNPLAYKFSWNPAGAIKAGQNPAVYKSNG-----------QIIHVDG 780


                  .
gi 506294699  197 Q 197
Cdd:PLN02819  781 E 781
BVR-B_like_SDR_a cd05244
biliverdin IX beta reductase (BVR-B, aka flavin reductase)-like proteins; atypical (a) SDRs; ...
 3-66 1.88e-03

biliverdin IX beta reductase (BVR-B, aka flavin reductase)-like proteins; atypical (a) SDRs; Human BVR-B catalyzes pyridine nucleotide-dependent production of bilirubin-IX beta during fetal development; in the adult BVR-B has flavin and ferric reductase activities. Human BVR-B catalyzes the reduction of FMN, FAD, and riboflavin. Recognition of flavin occurs mostly by hydrophobic interactions, accounting for the broad substrate specificity. Atypical SDRs are distinct from classical SDRs. BVR-B does not share the key catalytic triad, or conserved tyrosine typical of SDRs. The glycine-rich NADP-binding motif of BVR-B is GXXGXXG, which is similar but not identical to the pattern seen in extended SDRs. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Atypical SDRs include biliverdin IX beta reductase (BVR-B,aka flavin reductase), NMRa (a negative transcriptional regulator of various fungi), progesterone 5-beta-reductase like proteins, phenylcoumaran benzylic ether and pinoresinol-lariciresinol reductases, phenylpropene synthases, eugenol synthase, triphenylmethane reductase, isoflavone reductases, and others. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. In addition to the Rossmann fold core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.


Pssm-ID: 187555 [Multi-domain]  Cd Length: 207  Bit Score: 39.15  E-value: 1.88e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 506294699   3 KVLVIG-LGKVGSLVGTL-LSKRFLVTGVDRAQ---PAVALPFQVVTGDVNDSLFVESVLMGFDAVVSC 66
Cdd:cd05244    1 KIAIIGaTGRTGSAIVREaLARGHEVTALVRDPaklPAEHEKLKVVQGDVLDLEDVKEALEGQDAVISA 69
 
Name Accession Description Interval E-value
Lys9 COG1748
Saccharopine dehydrogenase, NADP-dependent [Amino acid transport and metabolism]; Saccharopine ...
 26-351 3.95e-110

Saccharopine dehydrogenase, NADP-dependent [Amino acid transport and metabolism]; Saccharopine dehydrogenase, NADP-dependent is part of the Pathway/BioSystem: Lysine biosynthesis


Pssm-ID: 441354 [Multi-domain]  Cd Length: 352  Bit Score: 325.25  E-value: 3.95e-110
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 506294699  26 VTGVDR----AQPAVAL--PFQVVTGDVNDSLFVESVLMGFDAVVSCMPYNLNLPIARQAHKSGIHYFDLTEDVPTTA-- 97
Cdd:COG1748    3 VTLADRslekAEALAASgpKVEAAQLDASDPEALAALIAGADLVINALPPYLNLTVAEACIEAGVHYVDLSEDEPETEak 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 506294699  98 -AIREMAQDSRSVLAPQCGLAPGFIGIVGMDLAKRFTKIRDIELRVGALPRYPNGLMGYSFTWSPAGVVNEYLNDAEVIH 176
Cdd:COG1748   83 lALDELAKEAGVTAIPGCGLAPGLSNVLAAYAADRFDEIDSIDIRVGGLPGYPSNPLNYGTTWSPEGVIREYTNPARAIE 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 506294699 177 NGVRKMVPSLEGTEMINIEGQ-EFEAFSTSGGLATMCETLEgKVDTLNYKTIRYPGHCSLMRFlLYELCLKDK------- 248
Cdd:COG1748  163 DGKWVEVPPLSERETIDFPGVgRYEAYNTDGELETLPETYP-GVKTVRFKTGRYPGHLNHLKV-LVDLGLTDDepveveg 240

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 506294699 249 -----RALVEEILTEAKP--PVQQDVVYVYAVVEGWKGDhlEREEFYRAYHPIEIDGQHWRAISWTTAASIASVVEMVAD 321
Cdd:COG1748  241 vevspRDVLKAILPDPLPlgPTDKDVVVIGVVVKGTKDG--KRETYVYNLVDHEDAETGSTAMAYTTGVPAAIAAELLLE 318

                        330       340       350
                 ....*....|....*....|....*....|..
gi 506294699 322 GVLPDRGFVRQEDILLDDFFKTLN--GWYFTQ 351
Cdd:COG1748  319 GKIPKPGVVNPEQLDPDPFLEELAkrGIPIEE 350
Sacchrp_dh_C pfam16653
Saccharopine dehydrogenase C-terminal domain; This family comprises the C-terminal domain of ...
 115-331 7.30e-27

Saccharopine dehydrogenase C-terminal domain; This family comprises the C-terminal domain of saccharopine dehydrogenase. In some organizms this enzyme is found as a bifunctional polypeptide with lysine ketoglutarate reductase. The saccharopine dehydrogenase can also function as a saccharopine reductase.


Pssm-ID: 465219  Cd Length: 255  Bit Score: 106.61  E-value: 7.30e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 506294699  115 GLAPGFIGIVGM----DLAKRFTKIRDIELRVGALP--RYPNGLMGYSFTWSPAGVVNEYLNDAEVIHNGVRKMVPSLEG 188
Cdd:pfam16653   1 GLDPGIDHMFAIkaidDVNAKGGKIESFLSYCGGLPapETSDNPLGYKFSWSPEGVLREGTNPARYWEDGKEVEVPGSEL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 506294699  189 TEMINI-EGQEFEAFSTSGGLATmcETLEG--KVDTLNYKTIRYPGHCSLMRFlLYELCLKDKRALVEEILTEAKPPVQ- 264
Cdd:pfam16653  81 MEPIYIrPGFAFEGYPNRDSLPH--EELYSlpEAKTLYRGTLRYPGFDEAIKS-LVELGLLSEEPKVSLEWLLFSGPLDv 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 506294699  265 ---------------QDVVYVYAVVEGWKGDHlereefyRAYHPIEIdGQHWR----AISWTTAASIASVVEMVADGVLP 325
Cdd:pfam16653 158 laalledklslgpgeRDMVVLQHEFDGKKGER-------RTYTLVDY-GDHEEvgpsAMARTVGVPAAIAALLILDGKIK 229


                  ....*.
gi 506294699  326 DRGFVR 331
Cdd:pfam16653 230 NKGVVN 235
Sacchrp_dh_NADP pfam03435
Saccharopine dehydrogenase NADP binding domain; This family contains the NADP binding domain ...
 4-108 5.49e-10

Saccharopine dehydrogenase NADP binding domain; This family contains the NADP binding domain of saccharopine dehydrogenase. In some organizms this enzyme is found as a bifunctional polypeptide with lysine ketoglutarate reductase. The saccharopine dehydrogenase can also function as a saccharopine reductase.


Pssm-ID: 397480 [Multi-domain]  Cd Length: 120  Bit Score: 56.44  E-value: 5.49e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 506294699    4 VLVIGLGKVGSLVGTLLSKRFL---VTGVDR--------AQPAVALPFQVVTGDV-NDSLFVESVLMGFDAVVSCMPYNL 71
Cdd:pfam03435   1 VLIIGAGSVGQGVAPLLARHFDvdrITVADRtlekaqalAAKLGGVRFIAVAVDAdNYEAVLAALLKEGDLVVNLSPPTL 80

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 506294699   72 NLPIARQAHKSGIHYFDltedvptTAAIREMAQDSRS 108
Cdd:pfam03435  81 SLDVLKACIETGVHYVD-------TSYLREAVLALHE 110
PLN02819 PLN02819
lysine-ketoglutarate reductase/saccharopine dehydrogenase
 43-197 1.06e-06

lysine-ketoglutarate reductase/saccharopine dehydrogenase


Pssm-ID: 215439 [Multi-domain]  Cd Length: 1042  Bit Score: 50.57  E-value: 1.06e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 506294699   43 VTGDVNDSLFVESVLMGFDAVVSCMPYNLNLPIARQAHKSGIHYFDLTEDVPTTAAIREMAQDSRSVLAPQCGLAPGFIG 122
Cdd:PLN02819  632 VQLDVSDSESLLKYVSQVDVVISLLPASCHAVVAKACIELKKHLVTASYVSEEMSALDSKAKEAGITILCEMGLDPGIDH 711

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 506294699  123 IVGM----DLAKRFTKIRDIELRVGALP--RYPNGLMGYSFTWSPAGVVNEYLNDAEVIHNGvrkmvpslegtEMINIEG 196
Cdd:PLN02819  712 MMAMkmidDAHERGGKVKSFTSYCGGLPspEAANNPLAYKFSWNPAGAIKAGQNPAVYKSNG-----------QIIHVDG 780


                  .
gi 506294699  197 Q 197
Cdd:PLN02819  781 E 781
YwnB COG2910
Putative NADH-flavin reductase [General function prediction only];
3-66 2.11e-06

Putative NADH-flavin reductase [General function prediction only];


Pssm-ID: 442154 [Multi-domain]  Cd Length: 205  Bit Score: 47.93  E-value: 2.11e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 506294699   3 KVLVIGL-GKVGSLVGTLLSKR-FLVTGVDRAQPAVALP---FQVVTGDVNDSLFVESVLMGFDAVVSC 66
Cdd:COG2910    1 KIAVIGAtGRVGSLIVREALARgHEVTALVRNPEKLPDEhpgLTVVVGDVLDPAAVAEALAGADAVVSA 69
WcaG COG0451
Nucleoside-diphosphate-sugar epimerase [Cell wall/membrane/envelope biogenesis];
3-64 2.69e-05

Nucleoside-diphosphate-sugar epimerase [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 440220 [Multi-domain]  Cd Length: 295  Bit Score: 45.35  E-value: 2.69e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 506294699   3 KVLVIG-LGKVGS-LVGTLLSKRFLVTGVDRAQPAVA-----LPFQVVTGDVNDSLFVESVLMGFDAVV 64
Cdd:COG0451    1 RILVTGgAGFIGShLARRLLARGHEVVGLDRSPPGAAnlaalPGVEFVRGDLRDPEALAAALAGVDAVV 69
TrkA_N pfam02254
TrkA-N domain; This domain is found in a wide variety of proteins. These proteins include ...
 4-68 9.13e-04

TrkA-N domain; This domain is found in a wide variety of proteins. These proteins include potassium channels, phosphoesterases, and various other transporters. This domain binds to NAD.


Pssm-ID: 426679 [Multi-domain]  Cd Length: 115  Bit Score: 38.66  E-value: 9.13e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 506294699    4 VLVIGLGKVGSLVGTLLSKRFLVTGVD----RAQPAVALPFQVVTGDVNDslfvESVLMG-----FDAVVSCMP 68
Cdd:pfam02254   1 IIIIGYGRVGRSLAEELSEGGDVVVIDkdeeRVEELREEGVPVVVGDATD----EEVLEEagieeADAVIAATG 70
BVR-B_like_SDR_a cd05244
biliverdin IX beta reductase (BVR-B, aka flavin reductase)-like proteins; atypical (a) SDRs; ...
 3-66 1.88e-03

biliverdin IX beta reductase (BVR-B, aka flavin reductase)-like proteins; atypical (a) SDRs; Human BVR-B catalyzes pyridine nucleotide-dependent production of bilirubin-IX beta during fetal development; in the adult BVR-B has flavin and ferric reductase activities. Human BVR-B catalyzes the reduction of FMN, FAD, and riboflavin. Recognition of flavin occurs mostly by hydrophobic interactions, accounting for the broad substrate specificity. Atypical SDRs are distinct from classical SDRs. BVR-B does not share the key catalytic triad, or conserved tyrosine typical of SDRs. The glycine-rich NADP-binding motif of BVR-B is GXXGXXG, which is similar but not identical to the pattern seen in extended SDRs. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Atypical SDRs include biliverdin IX beta reductase (BVR-B,aka flavin reductase), NMRa (a negative transcriptional regulator of various fungi), progesterone 5-beta-reductase like proteins, phenylcoumaran benzylic ether and pinoresinol-lariciresinol reductases, phenylpropene synthases, eugenol synthase, triphenylmethane reductase, isoflavone reductases, and others. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. In addition to the Rossmann fold core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.


Pssm-ID: 187555 [Multi-domain]  Cd Length: 207  Bit Score: 39.15  E-value: 1.88e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 506294699   3 KVLVIG-LGKVGSLVGTL-LSKRFLVTGVDRAQ---PAVALPFQVVTGDVNDSLFVESVLMGFDAVVSC 66
Cdd:cd05244    1 KIAIIGaTGRTGSAIVREaLARGHEVTALVRDPaklPAEHEKLKVVQGDVLDLEDVKEALEGQDAVISA 69
YbjT COG0702
Uncharacterized conserved protein YbjT, contains NAD(P)-binding and DUF2867 domains [General ...
 3-87 1.98e-03

Uncharacterized conserved protein YbjT, contains NAD(P)-binding and DUF2867 domains [General function prediction only];


Pssm-ID: 440466 [Multi-domain]  Cd Length: 215  Bit Score: 39.06  E-value: 1.98e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 506294699   3 KVLVIG-LGKVGS-LVGTLLSKRFLVTGV----DRAQPAVALPFQVVTGDVNDSLFVESVLMGFDAVVSCMP-------- 68
Cdd:COG0702    1 KILVTGaTGFIGRrVVRALLARGHPVRALvrdpEKAAALAAAGVEVVQGDLDDPESLAAALAGVDAVFLLVPsgpggdfa 80

                         90       100
                 ....*....|....*....|.
gi 506294699  69 --YNLNLPIARQAHKSGIHYF 87
Cdd:COG0702   81 vdVEGARNLADAAKAAGVKRI 101
COG3268 COG3268
Uncharacterized conserved protein, related to short-chain dehydrogenases [Function unknown];
34-144 5.08e-03

Uncharacterized conserved protein, related to short-chain dehydrogenases [Function unknown];


Pssm-ID: 442499 [Multi-domain]  Cd Length: 368  Bit Score: 38.29  E-value: 5.08e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 506294699  34 PAVALPFQVVtgDVNDSLFVESVLMGFDAVVSCM-PY-NLNLPIARQAHKSGIHYFDLTEDVPttaAIREM-------AQ 104
Cdd:COG3268   50 GAADLPLRVA--DLDDPASLAALLAGTRVVLNTVgPFaRTGEPLVEACLAAGTHYLDLTGEPD---WVRRMidrydaaAR 124

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 506294699 105 DSRSVLAPQCGL--APGFIGiVGMdLAKRFTKIRDIELRVGA 144
Cdd:COG3268  125 AAGARIVPACGFdsVPSDLG-AAL-LQERLPEADRLTLAVRA 164
MurD COG0771
UDP-N-acetylmuramoylalanine-D-glutamate ligase [Cell wall/membrane/envelope biogenesis]; ...
 1-84 5.18e-03

UDP-N-acetylmuramoylalanine-D-glutamate ligase [Cell wall/membrane/envelope biogenesis]; UDP-N-acetylmuramoylalanine-D-glutamate ligase is part of the Pathway/BioSystem: Mureine biosynthesis


Pssm-ID: 440534 [Multi-domain]  Cd Length: 445  Bit Score: 38.52  E-value: 5.18e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 506294699   1 MQKVLVIGLGKVG-SLVGTLLSKRFLVTGVDRAQPAVALP-------FQVVTGDvndslFVESVLMGFDAVV-ScmP-YN 70
Cdd:COG0771    4 GKKVLVLGLGKSGlAAARLLAKLGAEVTVSDDRPAPELAAaeleapgVEVVLGE-----HPEELLDGADLVVkS--PgIP 76

                         90
                 ....*....|....
gi 506294699  71 LNLPIARQAHKSGI 84
Cdd:COG0771   77 PDHPLLKAARAAGI 90
 
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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