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Conserved domains on  [gi|26452531|dbj|BAC43350|]
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unknown protein [Arabidopsis thaliana]

Protein Classification

tRNA-dihydrouridine synthase family protein( domain architecture ID 10120048)

tRNA-dihydrouridine synthase family protein such as tRNA-dihydrouridine synthase, which catalyzes the synthesis of dihydrouridine, a modified base found in the D-loop of most tRNAs

CATH:  3.20.20.70
EC:  1.3.1.-
Gene Ontology:  GO:0017150|GO:0008033|GO:0050660|GO:0016491
PubMed:  30149704|34798057|12003496
SCOP:  4000080

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DUS_like_FMN cd02801
Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze ...
 19-211 6.09e-76

Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also in some archaea. Most dihydrouridines are found in the D loop of t-RNAs. The role of dihydrouridine in tRNA is currently unknown, but may increase conformational flexibility of the tRNA. It is likely that different family members have different substrate specificities, which may overlap. 1VHN, a putative flavin oxidoreductase, has high sequence similarity to DUS. The enzymatic mechanism of 1VHN is not known at the present.


:

Pssm-ID: 239200 [Multi-domain]  Cd Length: 231  Bit Score: 231.23  E-value: 6.09e-76
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 26452531  19 FVEKGTDNVVFSTCDEEKSRVVFQMGTSDAVRALKASEIVCN-DVATIDINMGCPKAFSIQGGMGAALLSKPELIHDILA 97
Cdd:cd02801  37 LLRGNRKRLRLLTRNPEERPLIVQLGGSDPETLAEAAKIVEElGADGIDLNMGCPSPKVTKGGAGAALLKDPELVAEIVR 116

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 26452531  98 TLKRNLDVPVTCKIRLLKS-PADTVELARRIEKLGVPALAVHGRKIADRPRDPAKWDEIADVVAALSIPVIANGDVLEYD 176
Cdd:cd02801 117 AVREAVPIPVTVKIRLGWDdEEETLELAKALEDAGASALTVHGRTREQRYSGPADWDYIAEIKEAVSIPVIANGDIFSLE 196

                       170       180       190
                ....*....|....*....|....*....|....*
gi 26452531 177 DFSRIKTATGAASVMVARGAMWNASIFSPKGKSHW 211
Cdd:cd02801 197 DALRCLEQTGVDGVMIGRGALGNPWLFREIKELLE 231
 
Name Accession Description Interval E-value
DUS_like_FMN cd02801
Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze ...
 19-211 6.09e-76

Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also in some archaea. Most dihydrouridines are found in the D loop of t-RNAs. The role of dihydrouridine in tRNA is currently unknown, but may increase conformational flexibility of the tRNA. It is likely that different family members have different substrate specificities, which may overlap. 1VHN, a putative flavin oxidoreductase, has high sequence similarity to DUS. The enzymatic mechanism of 1VHN is not known at the present.


Pssm-ID: 239200 [Multi-domain]  Cd Length: 231  Bit Score: 231.23  E-value: 6.09e-76
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 26452531  19 FVEKGTDNVVFSTCDEEKSRVVFQMGTSDAVRALKASEIVCN-DVATIDINMGCPKAFSIQGGMGAALLSKPELIHDILA 97
Cdd:cd02801  37 LLRGNRKRLRLLTRNPEERPLIVQLGGSDPETLAEAAKIVEElGADGIDLNMGCPSPKVTKGGAGAALLKDPELVAEIVR 116

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 26452531  98 TLKRNLDVPVTCKIRLLKS-PADTVELARRIEKLGVPALAVHGRKIADRPRDPAKWDEIADVVAALSIPVIANGDVLEYD 176
Cdd:cd02801 117 AVREAVPIPVTVKIRLGWDdEEETLELAKALEDAGASALTVHGRTREQRYSGPADWDYIAEIKEAVSIPVIANGDIFSLE 196

                       170       180       190
                ....*....|....*....|....*....|....*
gi 26452531 177 DFSRIKTATGAASVMVARGAMWNASIFSPKGKSHW 211
Cdd:cd02801 197 DALRCLEQTGVDGVMIGRGALGNPWLFREIKELLE 231
Dus pfam01207
Dihydrouridine synthase (Dus); Members of this family catalyze the reduction of the 5,6-double ...
 31-203 1.75e-49

Dihydrouridine synthase (Dus); Members of this family catalyze the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also in some archae. Most dihydrouridines are found in the D loop of t-RNAs. The role of dihydrouridine in tRNA is currently unknown, but may increase conformational flexibility of the tRNA. It is likely that different family members have different substrate specificities, which may overlap. Dus 1 from Saccharomyces cerevisiae acts on pre-tRNA-Phe, while Dus 2 acts on pre-tRNA-Tyr and pre-tRNA-Leu. Dus 1 is active as a single subunit, requiring NADPH or NADH, and is stimulated by the presence of FAD. Some family members may be targeted to the mitochondria and even have a role in mitochondria.


Pssm-ID: 426126  Cd Length: 309  Bit Score: 165.96  E-value: 1.75e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 26452531    31 TCDEEKSRVVFQMGTSDAVRALKASEIVCN-DVATIDINMGCPKAFSIQGGMGAALLSKPELIHDILATLKRNLDVPVTC 109
Cdd:pfam01207  48 SELEEPTPLAVQLGGSDPALLAEAAKLVEDrGADGIDINMGCPSKKVTRGGGGAALLRNPDLVAQIVKAVVKAVGIPVTV 127

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 26452531   110 KIRLL--KSPADTVELARRIEKLGVPALAVHGRKIADRPRDPAKWDEIADVVAALSIPVIANGDVLEYDDFSRIKTATGA 187
Cdd:pfam01207 128 KIRIGwdDSHENAVEIAKIVEDAGAQALTVHGRTRAQNYEGTADWDAIKQVKQAVSIPVIANGDITDPEDAQRCLAYTGA 207

                         170
                  ....*....|....*.
gi 26452531   188 ASVMVARGAMWNASIF 203
Cdd:pfam01207 208 DGVMIGRGALGNPWLF 223
DusA COG0042
tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]; ...
 33-197 1.38e-48

tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]; tRNA-dihydrouridine synthase is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 439812 [Multi-domain]  Cd Length: 310  Bit Score: 163.73  E-value: 1.38e-48
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 26452531  33 DEEKSRVVfQMGTSDAVRALKASEIVC-NDVATIDINMGCP--KafsIQ-GGMGAALLSKPELIHDILATLKRNLDVPVT 108
Cdd:COG0042  59 PEEHPVAV-QLFGSDPEELAEAARIAEeLGADEIDINMGCPvkK---VTkGGAGAALLRDPELVAEIVKAVVEAVDVPVT 134

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 26452531 109 CKIRLLKSPAD--TVELARRIEKLGVPALAVHGRKIADRPRDPAKWDEIADVVAALSIPVIANGDVLEYDDFSRIKTATG 186
Cdd:COG0042 135 VKIRLGWDDDDenALEFARIAEDAGAAALTVHGRTREQRYKGPADWDAIARVKEAVSIPVIGNGDIFSPEDAKRMLEETG 214

                       170
                ....*....|.
gi 26452531 187 AASVMVARGAM 197
Cdd:COG0042 215 CDGVMIGRGAL 225
nifR3_yhdG TIGR00737
putative TIM-barrel protein, nifR3 family; This model represents one branch of COG0042 ...
 33-204 3.18e-38

putative TIM-barrel protein, nifR3 family; This model represents one branch of COG0042 (Predicted TIM-barrel enzymes, possibly dehydrogenases, nifR3 family). This branch includes NifR3 itself, from Rhodobacter capsulatus. It excludes a broadly distributed but more sparsely populated subfamily that contains sll0926 from Synechocystis PCC6803, HI0634 from Haemophilus influenzae, and BB0225 from Borrelia burgdorferi. It also excludes a shorter and more distant archaeal subfamily.The function of nifR3, a member of this family, is unknown, but it is found in an operon with nitrogen-sensing two component regulators in Rhodobacter capsulatus.Members of this family show a distant relationship to alpha/beta (TIM) barrel enzymes such as dihydroorotate dehydrogenase and glycolate oxidase. [Unknown function, General]


Pssm-ID: 129820  Cd Length: 319  Bit Score: 137.11  E-value: 3.18e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 26452531    33 DEEKSRVVfQMGTSDAVRALKASEIVCNDVAT-IDINMGCPKAFSIQGGMGAALLSKPELIHDILATLKRNLDVPVTCKI 111
Cdd:TIGR00737  60 EDETPISV-QLFGSDPDTMAEAAKINEELGADiIDINMGCPVPKITKKGAGSALLRDPDLIGKIVKAVVDAVDIPVTVKI 138

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 26452531   112 RLLKSPA--DTVELARRIEKLGVPALAVHGRKIADRPRDPAKWDEIADVVAALSIPVIANGDVLEYDDFSRIKTATGAAS 189
Cdd:TIGR00737 139 RIGWDDAhiNAVEAARIAEDAGAQAVTLHGRTRAQGYSGEANWDIIARVKQAVRIPVIGNGDIFSPEDAKAMLETTGCDG 218

                         170
                  ....*....|....*
gi 26452531   190 VMVARGAMWNASIFS 204
Cdd:TIGR00737 219 VMIGRGALGNPWLFR 233
PRK10415 PRK10415
tRNA-dihydrouridine synthase B; Provisional
 33-203 3.32e-28

tRNA-dihydrouridine synthase B; Provisional


Pssm-ID: 182440  Cd Length: 321  Bit Score: 110.45  E-value: 3.32e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 26452531   33 DEEKSRVVfQMGTSDAVRALKASEI-VCNDVATIDINMGCPKAFSIQGGMGAALLSKPELIHDILATLKRNLDVPVTCKI 111
Cdd:PRK10415  62 DEPGIRTV-QIAGSDPKEMADAARInVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDLVKSILTEVVNAVDVPVTLKI 140

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 26452531  112 RLLKSPA--DTVELARRIEKLGVPALAVHGRKIADRPRDPAKWDEIADVVAALSIPVIANGDVLEYDDFSRIKTATGAAS 189
Cdd:PRK10415 141 RTGWAPEhrNCVEIAQLAEDCGIQALTIHGRTRACLFNGEAEYDSIRAVKQKVSIPVIANGDITDPLKARAVLDYTGADA 220

                        170
                 ....*....|....
gi 26452531  190 VMVARGAMWNASIF 203
Cdd:PRK10415 221 LMIGRAAQGRPWIF 234
 
Name Accession Description Interval E-value
DUS_like_FMN cd02801
Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze ...
 19-211 6.09e-76

Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also in some archaea. Most dihydrouridines are found in the D loop of t-RNAs. The role of dihydrouridine in tRNA is currently unknown, but may increase conformational flexibility of the tRNA. It is likely that different family members have different substrate specificities, which may overlap. 1VHN, a putative flavin oxidoreductase, has high sequence similarity to DUS. The enzymatic mechanism of 1VHN is not known at the present.


Pssm-ID: 239200 [Multi-domain]  Cd Length: 231  Bit Score: 231.23  E-value: 6.09e-76
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 26452531  19 FVEKGTDNVVFSTCDEEKSRVVFQMGTSDAVRALKASEIVCN-DVATIDINMGCPKAFSIQGGMGAALLSKPELIHDILA 97
Cdd:cd02801  37 LLRGNRKRLRLLTRNPEERPLIVQLGGSDPETLAEAAKIVEElGADGIDLNMGCPSPKVTKGGAGAALLKDPELVAEIVR 116

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 26452531  98 TLKRNLDVPVTCKIRLLKS-PADTVELARRIEKLGVPALAVHGRKIADRPRDPAKWDEIADVVAALSIPVIANGDVLEYD 176
Cdd:cd02801 117 AVREAVPIPVTVKIRLGWDdEEETLELAKALEDAGASALTVHGRTREQRYSGPADWDYIAEIKEAVSIPVIANGDIFSLE 196

                       170       180       190
                ....*....|....*....|....*....|....*
gi 26452531 177 DFSRIKTATGAASVMVARGAMWNASIFSPKGKSHW 211
Cdd:cd02801 197 DALRCLEQTGVDGVMIGRGALGNPWLFREIKELLE 231
Dus pfam01207
Dihydrouridine synthase (Dus); Members of this family catalyze the reduction of the 5,6-double ...
 31-203 1.75e-49

Dihydrouridine synthase (Dus); Members of this family catalyze the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also in some archae. Most dihydrouridines are found in the D loop of t-RNAs. The role of dihydrouridine in tRNA is currently unknown, but may increase conformational flexibility of the tRNA. It is likely that different family members have different substrate specificities, which may overlap. Dus 1 from Saccharomyces cerevisiae acts on pre-tRNA-Phe, while Dus 2 acts on pre-tRNA-Tyr and pre-tRNA-Leu. Dus 1 is active as a single subunit, requiring NADPH or NADH, and is stimulated by the presence of FAD. Some family members may be targeted to the mitochondria and even have a role in mitochondria.


Pssm-ID: 426126  Cd Length: 309  Bit Score: 165.96  E-value: 1.75e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 26452531    31 TCDEEKSRVVFQMGTSDAVRALKASEIVCN-DVATIDINMGCPKAFSIQGGMGAALLSKPELIHDILATLKRNLDVPVTC 109
Cdd:pfam01207  48 SELEEPTPLAVQLGGSDPALLAEAAKLVEDrGADGIDINMGCPSKKVTRGGGGAALLRNPDLVAQIVKAVVKAVGIPVTV 127

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 26452531   110 KIRLL--KSPADTVELARRIEKLGVPALAVHGRKIADRPRDPAKWDEIADVVAALSIPVIANGDVLEYDDFSRIKTATGA 187
Cdd:pfam01207 128 KIRIGwdDSHENAVEIAKIVEDAGAQALTVHGRTRAQNYEGTADWDAIKQVKQAVSIPVIANGDITDPEDAQRCLAYTGA 207

                         170
                  ....*....|....*.
gi 26452531   188 ASVMVARGAMWNASIF 203
Cdd:pfam01207 208 DGVMIGRGALGNPWLF 223
DusA COG0042
tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]; ...
 33-197 1.38e-48

tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]; tRNA-dihydrouridine synthase is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 439812 [Multi-domain]  Cd Length: 310  Bit Score: 163.73  E-value: 1.38e-48
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 26452531  33 DEEKSRVVfQMGTSDAVRALKASEIVC-NDVATIDINMGCP--KafsIQ-GGMGAALLSKPELIHDILATLKRNLDVPVT 108
Cdd:COG0042  59 PEEHPVAV-QLFGSDPEELAEAARIAEeLGADEIDINMGCPvkK---VTkGGAGAALLRDPELVAEIVKAVVEAVDVPVT 134

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 26452531 109 CKIRLLKSPAD--TVELARRIEKLGVPALAVHGRKIADRPRDPAKWDEIADVVAALSIPVIANGDVLEYDDFSRIKTATG 186
Cdd:COG0042 135 VKIRLGWDDDDenALEFARIAEDAGAAALTVHGRTREQRYKGPADWDAIARVKEAVSIPVIGNGDIFSPEDAKRMLEETG 214

                       170
                ....*....|.
gi 26452531 187 AASVMVARGAM 197
Cdd:COG0042 215 CDGVMIGRGAL 225
nifR3_yhdG TIGR00737
putative TIM-barrel protein, nifR3 family; This model represents one branch of COG0042 ...
 33-204 3.18e-38

putative TIM-barrel protein, nifR3 family; This model represents one branch of COG0042 (Predicted TIM-barrel enzymes, possibly dehydrogenases, nifR3 family). This branch includes NifR3 itself, from Rhodobacter capsulatus. It excludes a broadly distributed but more sparsely populated subfamily that contains sll0926 from Synechocystis PCC6803, HI0634 from Haemophilus influenzae, and BB0225 from Borrelia burgdorferi. It also excludes a shorter and more distant archaeal subfamily.The function of nifR3, a member of this family, is unknown, but it is found in an operon with nitrogen-sensing two component regulators in Rhodobacter capsulatus.Members of this family show a distant relationship to alpha/beta (TIM) barrel enzymes such as dihydroorotate dehydrogenase and glycolate oxidase. [Unknown function, General]


Pssm-ID: 129820  Cd Length: 319  Bit Score: 137.11  E-value: 3.18e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 26452531    33 DEEKSRVVfQMGTSDAVRALKASEIVCNDVAT-IDINMGCPKAFSIQGGMGAALLSKPELIHDILATLKRNLDVPVTCKI 111
Cdd:TIGR00737  60 EDETPISV-QLFGSDPDTMAEAAKINEELGADiIDINMGCPVPKITKKGAGSALLRDPDLIGKIVKAVVDAVDIPVTVKI 138

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 26452531   112 RLLKSPA--DTVELARRIEKLGVPALAVHGRKIADRPRDPAKWDEIADVVAALSIPVIANGDVLEYDDFSRIKTATGAAS 189
Cdd:TIGR00737 139 RIGWDDAhiNAVEAARIAEDAGAQAVTLHGRTRAQGYSGEANWDIIARVKQAVRIPVIGNGDIFSPEDAKAMLETTGCDG 218

                         170
                  ....*....|....*
gi 26452531   190 VMVARGAMWNASIFS 204
Cdd:TIGR00737 219 VMIGRGALGNPWLFR 233
PRK10415 PRK10415
tRNA-dihydrouridine synthase B; Provisional
 33-203 3.32e-28

tRNA-dihydrouridine synthase B; Provisional


Pssm-ID: 182440  Cd Length: 321  Bit Score: 110.45  E-value: 3.32e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 26452531   33 DEEKSRVVfQMGTSDAVRALKASEI-VCNDVATIDINMGCPKAFSIQGGMGAALLSKPELIHDILATLKRNLDVPVTCKI 111
Cdd:PRK10415  62 DEPGIRTV-QIAGSDPKEMADAARInVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDLVKSILTEVVNAVDVPVTLKI 140

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 26452531  112 RLLKSPA--DTVELARRIEKLGVPALAVHGRKIADRPRDPAKWDEIADVVAALSIPVIANGDVLEYDDFSRIKTATGAAS 189
Cdd:PRK10415 141 RTGWAPEhrNCVEIAQLAEDCGIQALTIHGRTRACLFNGEAEYDSIRAVKQKVSIPVIANGDITDPLKARAVLDYTGADA 220

                        170
                 ....*....|....
gi 26452531  190 VMVARGAMWNASIF 203
Cdd:PRK10415 221 LMIGRAAQGRPWIF 234
PRK10550 PRK10550
tRNA dihydrouridine(16) synthase DusC;
65-197 3.66e-19

tRNA dihydrouridine(16) synthase DusC;


Pssm-ID: 236713  Cd Length: 312  Bit Score: 85.63  E-value: 3.66e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 26452531   65 IDINMGCPKAFSIQGGMGAALLSKPELIHDILATLKRNL--DVPVTCKIRL-LKSPADTVELARRIEKLGVPALAVHGRK 141
Cdd:PRK10550  92 VDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAMREAVpaHLPVTVKVRLgWDSGERKFEIADAVQQAGATELVVHGRT 171

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 26452531  142 IADRPRDPA-KWDEIADVVAALSIPVIANGDVLEYDDFSRIKTATGAASVMVARGAM 197
Cdd:PRK10550 172 KEDGYRAEHiNWQAIGEIRQRLTIPVIANGEIWDWQSAQQCMAITGCDAVMIGRGAL 228
PRK11815 PRK11815
tRNA dihydrouridine(20/20a) synthase DusA;
33-141 6.24e-08

tRNA dihydrouridine(20/20a) synthase DusA;


Pssm-ID: 236991 [Multi-domain]  Cd Length: 333  Bit Score: 52.83  E-value: 6.24e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 26452531   33 DEEKSRVVFQMGTSDAVRALKASEIvcndvAT------IDINMGCPkafS--IQGGM-GAALLSKPELIHDILATLKRNL 103
Cdd:PRK11815  61 DPEEHPVALQLGGSDPADLAEAAKL-----AEdwgydeINLNVGCP---SdrVQNGRfGACLMAEPELVADCVKAMKDAV 132

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 26452531  104 DVPVTCKIRL----LKSPADTVELARRIEKLGVPALAVHGRK 141
Cdd:PRK11815 133 SIPVTVKHRIgiddQDSYEFLCDFVDTVAEAGCDTFIVHARK 174
DHOD_1B_like cd04740
Dihydroorotate dehydrogenase (DHOD) class 1B FMN-binding domain. DHOD catalyzes the oxidation ...
 47-175 1.81e-06

Dihydroorotate dehydrogenase (DHOD) class 1B FMN-binding domain. DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine nucleotides. DHOD requires FMN as co-factor. DHOD divides into class 1 and class 2 based on their amino acid sequences and cellular location. Members of class 1 are cytosolic enzymes and multimers while class 2 enzymes are membrane associated and monomeric. The class 1 enzymes can be further divided into subtypes 1A and 1B which are homodimers and heterotetrameric proteins, respectively.


Pssm-ID: 240091 [Multi-domain]  Cd Length: 296  Bit Score: 48.31  E-value: 1.81e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 26452531  47 DAVRALKASEIVCndvatIDINMGCPKAfsiQGGmGAALLSKPELIHDILATLKRNLDVPVTCKIrllkSP--ADTVELA 124
Cdd:cd04740 106 EVAEKLADAGADA-----IELNISCPNV---KGG-GMAFGTDPEAVAEIVKAVKKATDVPVIVKL----TPnvTDIVEIA 172

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 26452531 125 RRIEKLGVPAL----AVHGRKIADRPRDPA-------------KwdEIA-----DVVAALSIPVIANG------DVLEY 175
Cdd:cd04740 173 RAAEEAGADGLtlinTLKGMAIDIETRKPIlgnvtgglsgpaiK--PIAlrmvyQVYKAVEIPIIGVGgiasgeDALEF 249
arch_FMN cd02911
Archeal FMN-binding domain. This family of archaeal proteins are part of the NAD(P)H-dependent ...
 51-196 3.33e-06

Archeal FMN-binding domain. This family of archaeal proteins are part of the NAD(P)H-dependent flavin oxidoreductase (oxidored) FMN-binding family that reduce a range of alternative electron acceptors. Most use FAD/FMN as a cofactor and NAD(P)H as electron donor. Some contain 4Fe-4S cluster to transfer electron from FAD to FMN. The specific function of this group is unknown.


Pssm-ID: 239237 [Multi-domain]  Cd Length: 233  Bit Score: 47.32  E-value: 3.33e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 26452531  51 ALKASEIVCNDVATIDINMGCPKAFSIQGGMGAALLSKPELIHDILATLKRnLDVPVTCKIRLlKSPADTVELARRIEKL 130
Cdd:cd02911  87 LLNAAALVAKNAAILEINAHCRQPEMVEAGAGEALLKDPERLSEFIKALKE-TGVPVSVKIRA-GVDVDDEELARLIEKA 164

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 26452531 131 GVPALAVHgrkiADRPRDPAKWDEIADVVAALSIpvIANGDVLEYDDFSRIKTAtGAASVMVARGA 196
Cdd:cd02911 165 GADIIHVD----AMDPGNHADLKKIRDISTELFI--IGNNSVTTIESAKEMFSY-GADMVSVARAS 223
OYE_like_FMN_family cd02803
Old yellow enzyme (OYE)-like FMN binding domain. OYE was the first flavin-dependent enzyme ...
 94-196 8.59e-06

Old yellow enzyme (OYE)-like FMN binding domain. OYE was the first flavin-dependent enzyme identified, however its true physiological role remains elusive to this day. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a reducing agent with oxygens, quinones, and alpha,beta-unsaturated aldehydes and ketones, and can act as electron acceptors in the catalytic reaction. Members of OYE family include trimethylamine dehydrogenase, 2,4-dienoyl-CoA reductase, enoate reductase, pentaerythriol tetranitrate reductase, xenobiotic reductase, and morphinone reductase.


Pssm-ID: 239201 [Multi-domain]  Cd Length: 327  Bit Score: 46.41  E-value: 8.59e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 26452531  94 DILATLKRNL--DVPVTCKIRLLK------SPADTVELARRIEKLGVPALAV-------HGRKIADRPRDPAKWDEIADV 158
Cdd:cd02803 196 EIVAAVREAVgpDFPVGVRLSADDfvpgglTLEEAIEIAKALEEAGVDALHVsggsyesPPPIIPPPYVPEGYFLELAEK 275

                        90       100       110
                ....*....|....*....|....*....|....*....
gi 26452531 159 V-AALSIPVIANGDVLEYDDFSRIKTATGAASVMVARGA 196
Cdd:cd02803 276 IkKAVKIPVIAVGGIRDPEVAEEILAEGKADLVALGRAL 314
DHOD_DHPD_FMN cd02810
Dihydroorotate dehydrogenase (DHOD) and Dihydropyrimidine dehydrogenase (DHPD) FMN-binding ...
 65-199 1.23e-05

Dihydroorotate dehydrogenase (DHOD) and Dihydropyrimidine dehydrogenase (DHPD) FMN-binding domain. DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine nucleotides. DHOD requires FMN as co-factor. DHOD divides into class 1 and class 2 based on their amino acid sequences and cellular location. Members of class 1 are cytosolic enzymes and multimers while class 2 enzymes are membrane associated and monomeric. The class 1 enzymes can be further divided into subtypes 1A and 1B which are homodimers and heterotetrameric proteins, respectively. DHPD catalyzes the first step in pyrimidine degradation: the NADPH-dependent reduction of uracil and thymine to the corresponding 5,6-dihydropyrimidines. DHPD contains two FAD, two FMN and eight [4Fe-4S] clusters, arranged in two electron transfer chains that pass its homodimeric interface twice. Two of the Fe-S clusters show a hitherto unobserved coordination involving a glutamine residue.


Pssm-ID: 239204 [Multi-domain]  Cd Length: 289  Bit Score: 45.81  E-value: 1.23e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 26452531  65 IDINMGCPKAfsiqgGMGAALLSKPELIHDILATLKRNLDVPVTCKIRLLKSPADTVELARRIEKLGVPALAVHGRkIAD 144
Cdd:cd02810 128 LELNLSCPNV-----GGGRQLGQDPEAVANLLKAVKAAVDIPLLVKLSPYFDLEDIVELAKAAERAGADGLTAINT-ISG 201

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 26452531 145 RPRD------------------PAKW---DEIADVVAALS--IPVIANG------DVLEYDDfsriktaTGAASVMVARG 195
Cdd:cd02810 202 RVVDlktvgpgpkrgtgglsgaPIRPlalRWVARLAARLQldIPIIGVGgidsgeDVLEMLM-------AGASAVQVATA 274


                ....
gi 26452531 196 AMWN 199
Cdd:cd02810 275 LMWD 278
FadH COG1902
2,4-dienoyl-CoA reductase or related NADH-dependent reductase, Old Yellow Enzyme (OYE) family ...
 116-199 3.77e-04

2,4-dienoyl-CoA reductase or related NADH-dependent reductase, Old Yellow Enzyme (OYE) family [Energy production and conversion];


Pssm-ID: 441506 [Multi-domain]  Cd Length: 365  Bit Score: 41.31  E-value: 3.77e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 26452531 116 SPADTVELARRIEKLGVPALAVHGRKIADRPRDPAKWDE------IADVVAALSIPVIANGDVLEYDDFSRIkTATGAAS 189
Cdd:COG1902 234 TLEESVELAKALEEAGVDYLHVSSGGYEPDAMIPTIVPEgyqlpfAARIRKAVGIPVIAVGGITTPEQAEAA-LASGDAD 312

                        90
                ....*....|.
gi 26452531 190 -VMVARGAMWN 199
Cdd:COG1902 313 lVALGRPLLAD 323
PRK07259 PRK07259
dihydroorotate dehydrogenase;
62-175 6.64e-04

dihydroorotate dehydrogenase;


Pssm-ID: 235982  Cd Length: 301  Bit Score: 40.52  E-value: 6.64e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 26452531   62 VATIDINMGCPKAfsiqGGMGAALLSKPELIHDILATLKRNLDVPVTCKIrllkSP--ADTVELARRIEKLGVPALA--- 136
Cdd:PRK07259 119 VDAIELNISCPNV----KHGGMAFGTDPELAYEVVKAVKEVVKVPVIVKL----TPnvTDIVEIAKAAEEAGADGLSlin 190

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 26452531  137 -VHGRKIADRPRDPA-------------KwdEIA-----DVVAALSIPVIANG------DVLEY 175
Cdd:PRK07259 191 tLKGMAIDIKTRKPIlanvtgglsgpaiK--PIAlrmvyQVYQAVDIPIIGMGgissaeDAIEF 252
PRK13585 PRK13585
1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide ...
 119-192 1.77e-03

1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase;


Pssm-ID: 184165  Cd Length: 241  Bit Score: 39.12  E-value: 1.77e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 26452531  119 DTVELARRIEKLGVPALA-----VHGRKIADRPrdpakwDEIADVVAALSIPVIANGDVLEYDDFSRIKTaTGAASVMV 192
Cdd:PRK13585 150 TPVEAAKRFEELGAGSILftnvdVEGLLEGVNT------EPVKELVDSVDIPVIASGGVTTLDDLRALKE-AGAAGVVV 221
OYE_YqiM_FMN cd02932
Old yellow enzyme (OYE) YqjM-like FMN binding domain. YqjM is involved in the oxidative stress ...
 116-199 4.81e-03

Old yellow enzyme (OYE) YqjM-like FMN binding domain. YqjM is involved in the oxidative stress response of Bacillus subtilis. Like the other OYE members, each monomer of YqjM contains FMN as a non-covalently bound cofactor and uses NADPH as a reducing agent. The YqjM enzyme exists as a homotetramer that is assembled as a dimer of catalytically dependent dimers, while other OYE members exist only as monomers or dimers. Moreover, the protein displays a shared active site architecture where an arginine finger at the COOH terminus of one monomer extends into the active site of the adjacent monomer and is directly involved in substrate recognition. Another remarkable difference in the binding of the ligand in YqjM is represented by the contribution of the NH2-terminal tyrosine instead of a COOH-terminal tyrosine in OYE and its homologs.


Pssm-ID: 239242 [Multi-domain]  Cd Length: 336  Bit Score: 37.86  E-value: 4.81e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 26452531 116 SPADTVELARRIEKLGVPALAV------HGRKIadrPRDPAKWDEIADVV-AALSIPVIANGDVLEYDDFSRIKTATGAA 188
Cdd:cd02932 239 DLEDSVELAKALKELGVDLIDVssggnsPAQKI---PVGPGYQVPFAERIrQEAGIPVIAVGLITDPEQAEAILESGRAD 315

                        90
                ....*....|.
gi 26452531 189 SVMVARGAMWN 199
Cdd:cd02932 316 LVALGRELLRN 326
 
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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