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Conserved domains on  [gi|582839497|gb|EWB25725|]
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tRNA dihydrouridine synthase B [Staphylococcus aureus W16001]

Protein Classification

tRNA dihydrouridine synthase( domain architecture ID 11414563)

tRNA dihydrouridine synthase catalyzes the synthesis of dihydrouridine, a modified base found in the D-loop of most tRNAs

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
DusA COG0042
tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]; ...
8-314 3.91e-97

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: 289.69  E-value: 3.91e-97
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582839497   8 ELPRPFFiLAPMEDVTDIVFRHVVSEAARpDVFFTEFTNTESFCHpeGIHSVRGRLTFSEDEHPMVAHIWGDKPEQFRET 87
Cdd:COG0042    4 ELPNPLI-LAPMAGVTDRPFRRLCRELGA-GLLYTEMVSARALLH--GNRKTRRLLDFDPEEHPVAVQLFGSDPEELAEA 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582839497  88 SIQLAKMGFKGIDLNMGCPVANVAKKGKGSGLILRPDVAAEIIQATK-AGGLPVSVKTRLGYYEIDE-WKDWLKHVFEQD 165
Cdd:COG0042   80 ARIAEELGADEIDINMGCPVKKVTKGGAGAALLRDPELVAEIVKAVVeAVDVPVTVKIRLGWDDDDEnALEFARIAEDAG 159
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582839497 166 IANLSIHLRTRKEMSKVDAHWELIEAIKNlrdeiAPNTLLTINGDIPDRKTGLELAEKYGIDGVMIGRGIFHNPFAFEKE 245
Cdd:COG0042  160 AAALTVHGRTREQRYKGPADWDAIARVKE-----AVSIPVIGNGDIFSPEDAKRMLEETGCDGVMIGRGALGNPWLFREI 234
                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 582839497 246 PREHTSKELLDL-LRLHLSLFNKY------EKDEIRQFKSLRRFFKIYVRGIRGASELRHQLMNTQSIAEARALLD 314
Cdd:COG0042  235 DAYLAGGEAPPPsLEEVLELLLEHlellleFYGERRGLRRMRKHLLWYFKGLPGARELRRRLSKAKSLAELLELLE 310
 
Name Accession Description Interval E-value
DusA COG0042
tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]; ...
8-314 3.91e-97

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: 289.69  E-value: 3.91e-97
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582839497   8 ELPRPFFiLAPMEDVTDIVFRHVVSEAARpDVFFTEFTNTESFCHpeGIHSVRGRLTFSEDEHPMVAHIWGDKPEQFRET 87
Cdd:COG0042    4 ELPNPLI-LAPMAGVTDRPFRRLCRELGA-GLLYTEMVSARALLH--GNRKTRRLLDFDPEEHPVAVQLFGSDPEELAEA 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582839497  88 SIQLAKMGFKGIDLNMGCPVANVAKKGKGSGLILRPDVAAEIIQATK-AGGLPVSVKTRLGYYEIDE-WKDWLKHVFEQD 165
Cdd:COG0042   80 ARIAEELGADEIDINMGCPVKKVTKGGAGAALLRDPELVAEIVKAVVeAVDVPVTVKIRLGWDDDDEnALEFARIAEDAG 159
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582839497 166 IANLSIHLRTRKEMSKVDAHWELIEAIKNlrdeiAPNTLLTINGDIPDRKTGLELAEKYGIDGVMIGRGIFHNPFAFEKE 245
Cdd:COG0042  160 AAALTVHGRTREQRYKGPADWDAIARVKE-----AVSIPVIGNGDIFSPEDAKRMLEETGCDGVMIGRGALGNPWLFREI 234
                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 582839497 246 PREHTSKELLDL-LRLHLSLFNKY------EKDEIRQFKSLRRFFKIYVRGIRGASELRHQLMNTQSIAEARALLD 314
Cdd:COG0042  235 DAYLAGGEAPPPsLEEVLELLLEHlellleFYGERRGLRRMRKHLLWYFKGLPGARELRRRLSKAKSLAELLELLE 310
DUS_like_FMN cd02801
Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze ...
14-250 3.11e-80

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: 243.56  E-value: 3.11e-80
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582839497  14 FILAPMEDVTDIVFRHVVSEAArPDVFFTEFTNTESFCHPEgiHSVRGRLTFSEDEHPMVAHIWGDKPEQFRETSIQLAK 93
Cdd:cd02801    2 LILAPMVGVTDLPFRLLCRRYG-ADLVYTEMISAKALLRGN--RKRLRLLTRNPEERPLIVQLGGSDPETLAEAAKIVEE 78
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582839497  94 MGFKGIDLNMGCPVANVAKKGKGSGLILRPDVAAEIIQATK-AGGLPVSVKTRLGYYEIDEWKDWLKHVFEQDIANLSIH 172
Cdd:cd02801   79 LGADGIDLNMGCPSPKVTKGGAGAALLKDPELVAEIVRAVReAVPIPVTVKIRLGWDDEEETLELAKALEDAGASALTVH 158
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 582839497 173 LRTRKEMSKVDAHWELIEAIKNlrdeiAPNTLLTINGDIPDRKTGLELAEKYGIDGVMIGRGIFHNPFAFEKEPREHT 250
Cdd:cd02801  159 GRTREQRYSGPADWDYIAEIKE-----AVSIPVIANGDIFSLEDALRCLEQTGVDGVMIGRGALGNPWLFREIKELLE 231
Dus pfam01207
Dihydrouridine synthase (Dus); Members of this family catalyze the reduction of the 5,6-double ...
15-316 3.21e-50

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: 169.04  E-value: 3.21e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582839497   15 ILAPMEDVTDIVFRHVVSEAARPDVFFTEFTNTESFCHPEgiHSVRGRLTFSEDEHPMVAHIWGDKPEQFRETSIQLAKM 94
Cdd:pfam01207   1 LLAPMAGVTDLPFRRLVREYGAGDLVYTEMVTAKAQLRPE--KVRIRMLSELEEPTPLAVQLGGSDPALLAEAAKLVEDR 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582839497   95 GFKGIDLNMGCPVANVAKKGKGSGLILRPDVAAEIIQAT-KAGGLPVSVKTRLGyyeIDEWKDWL----KHVFEQDIANL 169
Cdd:pfam01207  79 GADGIDINMGCPSKKVTRGGGGAALLRNPDLVAQIVKAVvKAVGIPVTVKIRIG---WDDSHENAveiaKIVEDAGAQAL 155
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582839497  170 SIHLRTRKEMSKVDAHWeliEAIKNLRDEIapNTLLTINGDIPDRKTGLELAEKYGIDGVMIGRGIFHNPFAFEkepREH 249
Cdd:pfam01207 156 TVHGRTRAQNYEGTADW---DAIKQVKQAV--SIPVIANGDITDPEDAQRCLAYTGADGVMIGRGALGNPWLFA---EQH 227
                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 582839497  250 TSKELLDLLRLHLSLF-----NKYE--KDEIRQFKSLRRFFKI---YVRGIRGASELRHQLMNTQSIAEARALLDEF 316
Cdd:pfam01207 228 TVKTGEFGPSPPLAEEaekvlRHLPylEEFLGEDKGLRHARKHlawYLKGFPGAAELRRELNDVFDPVEALINLDAA 304
nifR3_yhdG TIGR00737
putative TIM-barrel protein, nifR3 family; This model represents one branch of COG0042 ...
15-317 2.17e-44

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: 154.44  E-value: 2.17e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582839497   15 ILAPMEDVTDIVFRHVVSEAaRPDVFFTEFTNTES--FCHPegihSVRGRLTFSEDEHPMVAHIWGDKPEQFRETSIQLA 92
Cdd:TIGR00737  11 VLAPMAGVTDSPFRRLVAEY-GAGLTVCEMVSSEAivYDSQ----RTMRLLDIAEDETPISVQLFGSDPDTMAEAAKINE 85
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582839497   93 KMGFKGIDLNMGCPVANVAKKGKGSGLILRPDVAAEIIQAT-KAGGLPVSVKTRLGyyeIDE----WKDWLKHVFEQDIA 167
Cdd:TIGR00737  86 ELGADIIDINMGCPVPKITKKGAGSALLRDPDLIGKIVKAVvDAVDIPVTVKIRIG---WDDahinAVEAARIAEDAGAQ 162
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582839497  168 NLSIHLRTRKEMSKVDAHWELIEAIKNlrdeiapntLLTI----NGDIPDRKTGLELAEKYGIDGVMIGRGIFHNPFAFe 243
Cdd:TIGR00737 163 AVTLHGRTRAQGYSGEANWDIIARVKQ---------AVRIpvigNGDIFSPEDAKAMLETTGCDGVMIGRGALGNPWLF- 232
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582839497  244 KEPREH--TSKELLDLLRLHLSLFNKYEKDEIRQFKSLRRFFKI-------YVRGIRGASELRHQLMNTQSIAEARALLD 314
Cdd:TIGR00737 233 RQIEQYltTGKYKPPPTFAEKLDAILRHLQLLADYYGESKGLRIarkhiawYLKGFPGNAALRQTLNHASSFQEVKQLLD 312

                  ...
gi 582839497  315 EFE 317
Cdd:TIGR00737 313 DFF 315
PRK10550 PRK10550
tRNA dihydrouridine(16) synthase DusC;
15-239 2.09e-19

tRNA dihydrouridine(16) synthase DusC;


Pssm-ID: 236713  Cd Length: 312  Bit Score: 86.79  E-value: 2.09e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582839497  15 ILAPMEDVTDIVFRHVVSEAARPDVFFTEFTN-------TESF---ChPEGIHSVRgrltfSEDEHPMVAHIWGDKPEQF 84
Cdd:PRK10550   4 LLAPMEGVLDSLVRELLTEVNDYDLCITEFLRvvdqllpVKVFhrlC-PELHNASR-----TPSGTLVRIQLLGQYPQWL 77
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582839497  85 RETSIQLAKMGFKGIDLNMGCPVANVAKKGKGSGLILRPDVaaeIIQATKA------GGLPVSVKTRLGYYEIDEWKDWL 158
Cdd:PRK10550  78 AENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPEL---IYQGAKAmreavpAHLPVTVKVRLGWDSGERKFEIA 154
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582839497 159 KHVFEQDIANLSIHLRTRKEMSKVDA-HWELIEAIKNlrdeiapntLLTI----NGDIPDRKTGLELAEKYGIDGVMIGR 233
Cdd:PRK10550 155 DAVQQAGATELVVHGRTKEDGYRAEHiNWQAIGEIRQ---------RLTIpviaNGEIWDWQSAQQCMAITGCDAVMIGR 225

                 ....*.
gi 582839497 234 GIFHNP 239
Cdd:PRK10550 226 GALNIP 231
 
Name Accession Description Interval E-value
DusA COG0042
tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]; ...
8-314 3.91e-97

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: 289.69  E-value: 3.91e-97
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582839497   8 ELPRPFFiLAPMEDVTDIVFRHVVSEAARpDVFFTEFTNTESFCHpeGIHSVRGRLTFSEDEHPMVAHIWGDKPEQFRET 87
Cdd:COG0042    4 ELPNPLI-LAPMAGVTDRPFRRLCRELGA-GLLYTEMVSARALLH--GNRKTRRLLDFDPEEHPVAVQLFGSDPEELAEA 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582839497  88 SIQLAKMGFKGIDLNMGCPVANVAKKGKGSGLILRPDVAAEIIQATK-AGGLPVSVKTRLGYYEIDE-WKDWLKHVFEQD 165
Cdd:COG0042   80 ARIAEELGADEIDINMGCPVKKVTKGGAGAALLRDPELVAEIVKAVVeAVDVPVTVKIRLGWDDDDEnALEFARIAEDAG 159
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582839497 166 IANLSIHLRTRKEMSKVDAHWELIEAIKNlrdeiAPNTLLTINGDIPDRKTGLELAEKYGIDGVMIGRGIFHNPFAFEKE 245
Cdd:COG0042  160 AAALTVHGRTREQRYKGPADWDAIARVKE-----AVSIPVIGNGDIFSPEDAKRMLEETGCDGVMIGRGALGNPWLFREI 234
                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 582839497 246 PREHTSKELLDL-LRLHLSLFNKY------EKDEIRQFKSLRRFFKIYVRGIRGASELRHQLMNTQSIAEARALLD 314
Cdd:COG0042  235 DAYLAGGEAPPPsLEEVLELLLEHlellleFYGERRGLRRMRKHLLWYFKGLPGARELRRRLSKAKSLAELLELLE 310
DUS_like_FMN cd02801
Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze ...
14-250 3.11e-80

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: 243.56  E-value: 3.11e-80
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582839497  14 FILAPMEDVTDIVFRHVVSEAArPDVFFTEFTNTESFCHPEgiHSVRGRLTFSEDEHPMVAHIWGDKPEQFRETSIQLAK 93
Cdd:cd02801    2 LILAPMVGVTDLPFRLLCRRYG-ADLVYTEMISAKALLRGN--RKRLRLLTRNPEERPLIVQLGGSDPETLAEAAKIVEE 78
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582839497  94 MGFKGIDLNMGCPVANVAKKGKGSGLILRPDVAAEIIQATK-AGGLPVSVKTRLGYYEIDEWKDWLKHVFEQDIANLSIH 172
Cdd:cd02801   79 LGADGIDLNMGCPSPKVTKGGAGAALLKDPELVAEIVRAVReAVPIPVTVKIRLGWDDEEETLELAKALEDAGASALTVH 158
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 582839497 173 LRTRKEMSKVDAHWELIEAIKNlrdeiAPNTLLTINGDIPDRKTGLELAEKYGIDGVMIGRGIFHNPFAFEKEPREHT 250
Cdd:cd02801  159 GRTREQRYSGPADWDYIAEIKE-----AVSIPVIANGDIFSLEDALRCLEQTGVDGVMIGRGALGNPWLFREIKELLE 231
Dus pfam01207
Dihydrouridine synthase (Dus); Members of this family catalyze the reduction of the 5,6-double ...
15-316 3.21e-50

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: 169.04  E-value: 3.21e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582839497   15 ILAPMEDVTDIVFRHVVSEAARPDVFFTEFTNTESFCHPEgiHSVRGRLTFSEDEHPMVAHIWGDKPEQFRETSIQLAKM 94
Cdd:pfam01207   1 LLAPMAGVTDLPFRRLVREYGAGDLVYTEMVTAKAQLRPE--KVRIRMLSELEEPTPLAVQLGGSDPALLAEAAKLVEDR 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582839497   95 GFKGIDLNMGCPVANVAKKGKGSGLILRPDVAAEIIQAT-KAGGLPVSVKTRLGyyeIDEWKDWL----KHVFEQDIANL 169
Cdd:pfam01207  79 GADGIDINMGCPSKKVTRGGGGAALLRNPDLVAQIVKAVvKAVGIPVTVKIRIG---WDDSHENAveiaKIVEDAGAQAL 155
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582839497  170 SIHLRTRKEMSKVDAHWeliEAIKNLRDEIapNTLLTINGDIPDRKTGLELAEKYGIDGVMIGRGIFHNPFAFEkepREH 249
Cdd:pfam01207 156 TVHGRTRAQNYEGTADW---DAIKQVKQAV--SIPVIANGDITDPEDAQRCLAYTGADGVMIGRGALGNPWLFA---EQH 227
                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 582839497  250 TSKELLDLLRLHLSLF-----NKYE--KDEIRQFKSLRRFFKI---YVRGIRGASELRHQLMNTQSIAEARALLDEF 316
Cdd:pfam01207 228 TVKTGEFGPSPPLAEEaekvlRHLPylEEFLGEDKGLRHARKHlawYLKGFPGAAELRRELNDVFDPVEALINLDAA 304
nifR3_yhdG TIGR00737
putative TIM-barrel protein, nifR3 family; This model represents one branch of COG0042 ...
15-317 2.17e-44

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: 154.44  E-value: 2.17e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582839497   15 ILAPMEDVTDIVFRHVVSEAaRPDVFFTEFTNTES--FCHPegihSVRGRLTFSEDEHPMVAHIWGDKPEQFRETSIQLA 92
Cdd:TIGR00737  11 VLAPMAGVTDSPFRRLVAEY-GAGLTVCEMVSSEAivYDSQ----RTMRLLDIAEDETPISVQLFGSDPDTMAEAAKINE 85
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582839497   93 KMGFKGIDLNMGCPVANVAKKGKGSGLILRPDVAAEIIQAT-KAGGLPVSVKTRLGyyeIDE----WKDWLKHVFEQDIA 167
Cdd:TIGR00737  86 ELGADIIDINMGCPVPKITKKGAGSALLRDPDLIGKIVKAVvDAVDIPVTVKIRIG---WDDahinAVEAARIAEDAGAQ 162
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582839497  168 NLSIHLRTRKEMSKVDAHWELIEAIKNlrdeiapntLLTI----NGDIPDRKTGLELAEKYGIDGVMIGRGIFHNPFAFe 243
Cdd:TIGR00737 163 AVTLHGRTRAQGYSGEANWDIIARVKQ---------AVRIpvigNGDIFSPEDAKAMLETTGCDGVMIGRGALGNPWLF- 232
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582839497  244 KEPREH--TSKELLDLLRLHLSLFNKYEKDEIRQFKSLRRFFKI-------YVRGIRGASELRHQLMNTQSIAEARALLD 314
Cdd:TIGR00737 233 RQIEQYltTGKYKPPPTFAEKLDAILRHLQLLADYYGESKGLRIarkhiawYLKGFPGNAALRQTLNHASSFQEVKQLLD 312

                  ...
gi 582839497  315 EFE 317
Cdd:TIGR00737 313 DFF 315
PRK10550 PRK10550
tRNA dihydrouridine(16) synthase DusC;
15-239 2.09e-19

tRNA dihydrouridine(16) synthase DusC;


Pssm-ID: 236713  Cd Length: 312  Bit Score: 86.79  E-value: 2.09e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582839497  15 ILAPMEDVTDIVFRHVVSEAARPDVFFTEFTN-------TESF---ChPEGIHSVRgrltfSEDEHPMVAHIWGDKPEQF 84
Cdd:PRK10550   4 LLAPMEGVLDSLVRELLTEVNDYDLCITEFLRvvdqllpVKVFhrlC-PELHNASR-----TPSGTLVRIQLLGQYPQWL 77
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582839497  85 RETSIQLAKMGFKGIDLNMGCPVANVAKKGKGSGLILRPDVaaeIIQATKA------GGLPVSVKTRLGYYEIDEWKDWL 158
Cdd:PRK10550  78 AENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPEL---IYQGAKAmreavpAHLPVTVKVRLGWDSGERKFEIA 154
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582839497 159 KHVFEQDIANLSIHLRTRKEMSKVDA-HWELIEAIKNlrdeiapntLLTI----NGDIPDRKTGLELAEKYGIDGVMIGR 233
Cdd:PRK10550 155 DAVQQAGATELVVHGRTKEDGYRAEHiNWQAIGEIRQ---------RLTIpviaNGEIWDWQSAQQCMAITGCDAVMIGR 225

                 ....*.
gi 582839497 234 GIFHNP 239
Cdd:PRK10550 226 GALNIP 231
PRK11815 PRK11815
tRNA dihydrouridine(20/20a) synthase DusA;
9-240 6.02e-19

tRNA dihydrouridine(20/20a) synthase DusA;


Pssm-ID: 236991 [Multi-domain]  Cd Length: 333  Bit Score: 85.96  E-value: 6.02e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582839497   9 LPRPFFIlAPMEDVTDivfRH------VVSEAARpdvFFTEFTNTESFchpegIHSVRGR-LTFSEDEHPMVAHIWGDKP 81
Cdd:PRK11815   9 PSRRFSV-APMMDWTD---RHcryfhrLLSRHAL---LYTEMVTTGAI-----IHGDRERlLAFDPEEHPVALQLGGSDP 76
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582839497  82 EQFREtSIQLA-KMGFKGIDLNMGCPVANVaKKGK-GSGLILRPDVAAEIIQATK-AGGLPVSVKTRLGYYEIDEW---K 155
Cdd:PRK11815  77 ADLAE-AAKLAeDWGYDEINLNVGCPSDRV-QNGRfGACLMAEPELVADCVKAMKdAVSIPVTVKHRIGIDDQDSYeflC 154
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582839497 156 DWLKHVFEQDIANLSIHlrTRK------------EMSKVDahWELIEAIKNLRdeiaPNTLLTINGDIpdrkTGLELAEK 223
Cdd:PRK11815 155 DFVDTVAEAGCDTFIVH--ARKawlkglspkenrEIPPLD--YDRVYRLKRDF----PHLTIEINGGI----KTLEEAKE 222
                        250
                 ....*....|....*....
gi 582839497 224 Y--GIDGVMIGRGIFHNPF 240
Cdd:PRK11815 223 HlqHVDGVMIGRAAYHNPY 241
PRK10415 PRK10415
tRNA-dihydrouridine synthase B; Provisional
14-244 1.63e-18

tRNA-dihydrouridine synthase B; Provisional


Pssm-ID: 182440  Cd Length: 321  Bit Score: 84.64  E-value: 1.63e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582839497  14 FILAPMEDVTDIVFRhVVSEAARPDVFFTEFTNTesfcHPEGIHSVRGRLTFSEDEHPMV--AHIWGDKPEQFRETSIQL 91
Cdd:PRK10415  12 LIAAPMAGITDRPFR-TLCYEMGAGLTVSEMMSS----NPQVWESDKSRLRMVHIDEPGIrtVQIAGSDPKEMADAARIN 86
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582839497  92 AKMGFKGIDLNMGCPVANVAKKGKGSGLILRPDVAAEIIQA-TKAGGLPVSVKTRLGY-------YEIDEWKDwlkhvfE 163
Cdd:PRK10415  87 VESGAQIIDINMGCPAKKVNRKLAGSALLQYPDLVKSILTEvVNAVDVPVTLKIRTGWapehrncVEIAQLAE------D 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582839497 164 QDIANLSIHLRTRKEMSKVDAHWELIEAIKNlrdeiAPNTLLTINGDIPDRKTGLELAEKYGIDGVMIGRGIFHNPFAFE 243
Cdd:PRK10415 161 CGIQALTIHGRTRACLFNGEAEYDSIRAVKQ-----KVSIPVIANGDITDPLKARAVLDYTGADALMIGRAAQGRPWIFR 235

                 .
gi 582839497 244 K 244
Cdd:PRK10415 236 E 236
DHOD_1B_like cd04740
Dihydroorotate dehydrogenase (DHOD) class 1B FMN-binding domain. DHOD catalyzes the oxidation ...
71-143 3.99e-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: 47.54  E-value: 3.99e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 582839497  71 PMVAHIWGDKPEQFRETSIQLAKMGFKGIDLNMGCPvaNVakKGKGSGLILRPDVAAEIIQATK-AGGLPVSVK 143
Cdd:cd04740   91 PVIASIAGSTVEEFVEVAEKLADAGADAIELNISCP--NV--KGGGMAFGTDPEAVAEIVKAVKkATDVPVIVK 160
arch_FMN cd02911
Archeal FMN-binding domain. This family of archaeal proteins are part of the NAD(P)H-dependent ...
99-147 5.42e-03

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: 37.69  E-value: 5.42e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 582839497  99 IDLNMGCPVANVAKKGKGSGLILRPDVAAEIIQATKAGGLPVSVKTRLG 147
Cdd:cd02911  101 LEINAHCRQPEMVEAGAGEALLKDPERLSEFIKALKETGVPVSVKIRAG 149
DHOD_DHPD_FMN cd02810
Dihydroorotate dehydrogenase (DHOD) and Dihydropyrimidine dehydrogenase (DHPD) FMN-binding ...
68-150 6.34e-03

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: 37.72  E-value: 6.34e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582839497  68 DEHPMVAHIWGDKPEQFRETSIQLAKMGFKGIDLNMGCPvaNVakkGKGSGLILRPDVAAEIIQATKAG-GLPVSVKtrL 146
Cdd:cd02810   97 PGQPLIASVGGSSKEDYVELARKIERAGAKALELNLSCP--NV---GGGRQLGQDPEAVANLLKAVKAAvDIPLLVK--L 169

                 ....
gi 582839497 147 GYYE 150
Cdd:cd02810  170 SPYF 173
 
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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