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Conserved domains on  [gi|489336524|ref|WP_003243741|]
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MULTISPECIES: tRNA dihydrouridine synthase DusB [Bacillus]

Protein Classification

tRNA-dihydrouridine synthase( domain architecture ID 11489538)

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
nifR3_yhdG TIGR00737
putative TIM-barrel protein, nifR3 family; This model represents one branch of COG0042 ...
 4-323 0e+00

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: 534.25  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489336524    4 IGDIQLKNRVVLAPMAGVCNSAFRLTVKEFGAGLVCAEMVSDKAILYNNARTMGMLYIDEREKPLSLQIFGGKKETLVEA 83
Cdd:TIGR00737   1 IGNIQLKSRVVLAPMAGVTDSPFRRLVAEYGAGLTVCEMVSSEAIVYDSQRTMRLLDIAEDETPISVQLFGSDPDTMAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489336524   84 AKfVDQNTTADIIDINMGCPVPKITKCDAGAKWLLDPDKIYEMVSAVVDAVNKPVTVKMRMGWDEDHIFAVKNAQAVERA 163
Cdd:TIGR00737  81 AK-INEELGADIIDINMGCPVPKITKKGAGSALLRDPDLIGKIVKAVVDAVDIPVTVKIRIGWDDAHINAVEAARIAEDA 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489336524  164 GGKAVALHGRTRVQMYEGTANWDIIKEVKQSVSIPVIGNGDVKTPQDAKRMLDETGVDGVMIGRAALGNPWMIYRTVQYL 243
Cdd:TIGR00737 160 GAQAVTLHGRTRAQGYSGEANWDIIARVKQAVRIPVIGNGDIFSPEDAKAMLETTGCDGVMIGRGALGNPWLFRQIEQYL 239

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489336524  244 ETGKLKEEPQVREKMAVCKLHLDRLIDLKGENVAVREMRKHAAWYLKGVKGNANVRNEINHCETREEFVQLLDAFTVEVE 323
Cdd:TIGR00737 240 TTGKYKPPPTFAEKLDAILRHLQLLADYYGESKGLRIARKHIAWYLKGFPGNAALRQTLNHASSFQEVKQLLDDFFETVG 319
 
Name Accession Description Interval E-value
nifR3_yhdG TIGR00737
putative TIM-barrel protein, nifR3 family; This model represents one branch of COG0042 ...
 4-323 0e+00

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: 534.25  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489336524    4 IGDIQLKNRVVLAPMAGVCNSAFRLTVKEFGAGLVCAEMVSDKAILYNNARTMGMLYIDEREKPLSLQIFGGKKETLVEA 83
Cdd:TIGR00737   1 IGNIQLKSRVVLAPMAGVTDSPFRRLVAEYGAGLTVCEMVSSEAIVYDSQRTMRLLDIAEDETPISVQLFGSDPDTMAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489336524   84 AKfVDQNTTADIIDINMGCPVPKITKCDAGAKWLLDPDKIYEMVSAVVDAVNKPVTVKMRMGWDEDHIFAVKNAQAVERA 163
Cdd:TIGR00737  81 AK-INEELGADIIDINMGCPVPKITKKGAGSALLRDPDLIGKIVKAVVDAVDIPVTVKIRIGWDDAHINAVEAARIAEDA 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489336524  164 GGKAVALHGRTRVQMYEGTANWDIIKEVKQSVSIPVIGNGDVKTPQDAKRMLDETGVDGVMIGRAALGNPWMIYRTVQYL 243
Cdd:TIGR00737 160 GAQAVTLHGRTRAQGYSGEANWDIIARVKQAVRIPVIGNGDIFSPEDAKAMLETTGCDGVMIGRGALGNPWLFRQIEQYL 239

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489336524  244 ETGKLKEEPQVREKMAVCKLHLDRLIDLKGENVAVREMRKHAAWYLKGVKGNANVRNEINHCETREEFVQLLDAFTVEVE 323
Cdd:TIGR00737 240 TTGKYKPPPTFAEKLDAILRHLQLLADYYGESKGLRIARKHIAWYLKGFPGNAALRQTLNHASSFQEVKQLLDDFFETVG 319
DusA COG0042
tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]; ...
 5-316 1.18e-164

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: 461.10  E-value: 1.18e-164
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489336524   5 GDIQLKNRVVLAPMAGVCNSAFRLTVKEFGAGLVCAEMVSDKAILYNNARTMGMLYIDEREKPLSLQIFGGKKETLVEAA 84
Cdd:COG0042    1 GNLELPNPLILAPMAGVTDRPFRRLCRELGAGLLYTEMVSARALLHGNRKTRRLLDFDPEEHPVAVQLFGSDPEELAEAA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489336524  85 KFVDQNTtADIIDINMGCPVPKITKCDAGAKWLLDPDKIYEMVSAVVDAVNKPVTVKMRMGWDEDHIFAVKNAQAVERAG 164
Cdd:COG0042   81 RIAEELG-ADEIDINMGCPVKKVTKGGAGAALLRDPELVAEIVKAVVEAVDVPVTVKIRLGWDDDDENALEFARIAEDAG 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489336524 165 GKAVALHGRTRVQMYEGTANWDIIKEVKQSVSIPVIGNGDVKTPQDAKRMLDETGVDGVMIGRAALGNPWMIYRTVQYLE 244
Cdd:COG0042  160 AAALTVHGRTREQRYKGPADWDAIARVKEAVSIPVIGNGDIFSPEDAKRMLEETGCDGVMIGRGALGNPWLFREIDAYLA 239

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 489336524 245 TGKLkEEPQVREKMAVCKLHLDRLIDLKGENVAVREMRKHAAWYLKGVKGNANVRNEINHCETREEFVQLLD 316
Cdd:COG0042  240 GGEA-PPPSLEEVLELLLEHLELLLEFYGERRGLRRMRKHLLWYFKGLPGARELRRRLSKAKSLAELLELLE 310
Dus pfam01207
Dihydrouridine synthase (Dus); Members of this family catalyze the reduction of the 5,6-double ...
 14-323 1.39e-147

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: 417.88  E-value: 1.39e-147
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489336524   14 VLAPMAGVCNSAFRLTVKEFGAG-LVCAEMVSDKAILYNNARTMGMLYIDEREKPLSLQIFGGKKETLVEAAKFVDQNTt 92
Cdd:pfam01207   1 LLAPMAGVTDLPFRRLVREYGAGdLVYTEMVTAKAQLRPEKVRIRMLSELEEPTPLAVQLGGSDPALLAEAAKLVEDRG- 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489336524   93 ADIIDINMGCPVPKITKCDAGAKWLLDPDKIYEMVSAVVDAVNKPVTVKMRMGWDEDHIFAVKNAQAVERAGGKAVALHG 172
Cdd:pfam01207  80 ADGIDINMGCPSKKVTRGGGGAALLRNPDLVAQIVKAVVKAVGIPVTVKIRIGWDDSHENAVEIAKIVEDAGAQALTVHG 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489336524  173 RTRVQMYEGTANWDIIKEVKQSVSIPVIGNGDVKTPQDAKRMLDETGVDGVMIGRAALGNPWMIYRtVQYLETGKLKEEP 252
Cdd:pfam01207 160 RTRAQNYEGTADWDAIKQVKQAVSIPVIANGDITDPEDAQRCLAYTGADGVMIGRGALGNPWLFAE-QHTVKTGEFGPSP 238

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 489336524  253 QVREKMAVCKLHLDRLIDLKGENVAVREMRKHAAWYLKGVKGNANVRNEINHCETREEFVQLLDAFTVEVE 323
Cdd:pfam01207 239 PLAEEAEKVLRHLPYLEEFLGEDKGLRHARKHLAWYLKGFPGAAELRRELNDVFDPVEALINLDAALRAAN 309
DUS_like_FMN cd02801
Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze ...
 12-244 1.06e-115

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: 334.08  E-value: 1.06e-115
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489336524  12 RVVLAPMAGVCNSAFRLTVKEFGAGLVCAEMVSDKAILYNNARTMGMLYIDEREKPLSLQIFGGKKETLVEAAKFVdQNT 91
Cdd:cd02801    1 KLILAPMVGVTDLPFRLLCRRYGADLVYTEMISAKALLRGNRKRLRLLTRNPEERPLIVQLGGSDPETLAEAAKIV-EEL 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489336524  92 TADIIDINMGCPVPKITKCDAGAKWLLDPDKIYEMVSAVVDAVNKPVTVKMRMGWDEDhIFAVKNAQAVERAGGKAVALH 171
Cdd:cd02801   80 GADGIDLNMGCPSPKVTKGGAGAALLKDPELVAEIVRAVREAVPIPVTVKIRLGWDDE-EETLELAKALEDAGASALTVH 158

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 489336524 172 GRTRVQMYEGTANWDIIKEVKQSVSIPVIGNGDVKTPQDAKRMLDETGVDGVMIGRAALGNPWMIYRTVQYLE 244
Cdd:cd02801  159 GRTREQRYSGPADWDYIAEIKEAVSIPVIANGDIFSLEDALRCLEQTGVDGVMIGRGALGNPWLFREIKELLE 231
PRK10415 PRK10415
tRNA-dihydrouridine synthase B; Provisional
 3-318 2.66e-83

tRNA-dihydrouridine synthase B; Provisional


Pssm-ID: 182440  Cd Length: 321  Bit Score: 254.90  E-value: 2.66e-83
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489336524   3 KIGDIQLKNRVVLAPMAGVCNSAFRLTVKEFGAGLVCAEMVSDKAILYNNART-MGMLYIDErekP--LSLQIFGGKKET 79
Cdd:PRK10415   2 RIGQYQLRNRLIAAPMAGITDRPFRTLCYEMGAGLTVSEMMSSNPQVWESDKSrLRMVHIDE---PgiRTVQIAGSDPKE 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489336524  80 LVEAAKfVDQNTTADIIDINMGCPVPKITKCDAGAKWLLDPDKIYEMVSAVVDAVNKPVTVKMRMGWDEDHIFAVKNAQA 159
Cdd:PRK10415  79 MADAAR-INVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDLVKSILTEVVNAVDVPVTLKIRTGWAPEHRNCVEIAQL 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489336524 160 VERAGGKAVALHGRTRVQMYEGTANWDIIKEVKQSVSIPVIGNGDVKTPQDAKRMLDETGVDGVMIGRAALGNPWmIYRT 239
Cdd:PRK10415 158 AEDCGIQALTIHGRTRACLFNGEAEYDSIRAVKQKVSIPVIANGDITDPLKARAVLDYTGADALMIGRAAQGRPW-IFRE 236

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489336524 240 VQ-YLETGKLKEEPQVREKMAVCKLHLDRLIDLKGENVAVREMRKHAAWYLKGVKGNANVRNEINHCETREEFVQLLDAF 318
Cdd:PRK10415 237 IQhYLDTGELLPPLPLAEVKRLLCAHVRELHDFYGPAKGYRIARKHVSWYLQEHAPNDQFRRTFNAIEDASEQLEALEAY 316
 
Name Accession Description Interval E-value
nifR3_yhdG TIGR00737
putative TIM-barrel protein, nifR3 family; This model represents one branch of COG0042 ...
 4-323 0e+00

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: 534.25  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489336524    4 IGDIQLKNRVVLAPMAGVCNSAFRLTVKEFGAGLVCAEMVSDKAILYNNARTMGMLYIDEREKPLSLQIFGGKKETLVEA 83
Cdd:TIGR00737   1 IGNIQLKSRVVLAPMAGVTDSPFRRLVAEYGAGLTVCEMVSSEAIVYDSQRTMRLLDIAEDETPISVQLFGSDPDTMAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489336524   84 AKfVDQNTTADIIDINMGCPVPKITKCDAGAKWLLDPDKIYEMVSAVVDAVNKPVTVKMRMGWDEDHIFAVKNAQAVERA 163
Cdd:TIGR00737  81 AK-INEELGADIIDINMGCPVPKITKKGAGSALLRDPDLIGKIVKAVVDAVDIPVTVKIRIGWDDAHINAVEAARIAEDA 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489336524  164 GGKAVALHGRTRVQMYEGTANWDIIKEVKQSVSIPVIGNGDVKTPQDAKRMLDETGVDGVMIGRAALGNPWMIYRTVQYL 243
Cdd:TIGR00737 160 GAQAVTLHGRTRAQGYSGEANWDIIARVKQAVRIPVIGNGDIFSPEDAKAMLETTGCDGVMIGRGALGNPWLFRQIEQYL 239

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489336524  244 ETGKLKEEPQVREKMAVCKLHLDRLIDLKGENVAVREMRKHAAWYLKGVKGNANVRNEINHCETREEFVQLLDAFTVEVE 323
Cdd:TIGR00737 240 TTGKYKPPPTFAEKLDAILRHLQLLADYYGESKGLRIARKHIAWYLKGFPGNAALRQTLNHASSFQEVKQLLDDFFETVG 319
DusA COG0042
tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]; ...
 5-316 1.18e-164

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: 461.10  E-value: 1.18e-164
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489336524   5 GDIQLKNRVVLAPMAGVCNSAFRLTVKEFGAGLVCAEMVSDKAILYNNARTMGMLYIDEREKPLSLQIFGGKKETLVEAA 84
Cdd:COG0042    1 GNLELPNPLILAPMAGVTDRPFRRLCRELGAGLLYTEMVSARALLHGNRKTRRLLDFDPEEHPVAVQLFGSDPEELAEAA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489336524  85 KFVDQNTtADIIDINMGCPVPKITKCDAGAKWLLDPDKIYEMVSAVVDAVNKPVTVKMRMGWDEDHIFAVKNAQAVERAG 164
Cdd:COG0042   81 RIAEELG-ADEIDINMGCPVKKVTKGGAGAALLRDPELVAEIVKAVVEAVDVPVTVKIRLGWDDDDENALEFARIAEDAG 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489336524 165 GKAVALHGRTRVQMYEGTANWDIIKEVKQSVSIPVIGNGDVKTPQDAKRMLDETGVDGVMIGRAALGNPWMIYRTVQYLE 244
Cdd:COG0042  160 AAALTVHGRTREQRYKGPADWDAIARVKEAVSIPVIGNGDIFSPEDAKRMLEETGCDGVMIGRGALGNPWLFREIDAYLA 239

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 489336524 245 TGKLkEEPQVREKMAVCKLHLDRLIDLKGENVAVREMRKHAAWYLKGVKGNANVRNEINHCETREEFVQLLD 316
Cdd:COG0042  240 GGEA-PPPSLEEVLELLLEHLELLLEFYGERRGLRRMRKHLLWYFKGLPGARELRRRLSKAKSLAELLELLE 310
Dus pfam01207
Dihydrouridine synthase (Dus); Members of this family catalyze the reduction of the 5,6-double ...
 14-323 1.39e-147

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: 417.88  E-value: 1.39e-147
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489336524   14 VLAPMAGVCNSAFRLTVKEFGAG-LVCAEMVSDKAILYNNARTMGMLYIDEREKPLSLQIFGGKKETLVEAAKFVDQNTt 92
Cdd:pfam01207   1 LLAPMAGVTDLPFRRLVREYGAGdLVYTEMVTAKAQLRPEKVRIRMLSELEEPTPLAVQLGGSDPALLAEAAKLVEDRG- 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489336524   93 ADIIDINMGCPVPKITKCDAGAKWLLDPDKIYEMVSAVVDAVNKPVTVKMRMGWDEDHIFAVKNAQAVERAGGKAVALHG 172
Cdd:pfam01207  80 ADGIDINMGCPSKKVTRGGGGAALLRNPDLVAQIVKAVVKAVGIPVTVKIRIGWDDSHENAVEIAKIVEDAGAQALTVHG 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489336524  173 RTRVQMYEGTANWDIIKEVKQSVSIPVIGNGDVKTPQDAKRMLDETGVDGVMIGRAALGNPWMIYRtVQYLETGKLKEEP 252
Cdd:pfam01207 160 RTRAQNYEGTADWDAIKQVKQAVSIPVIANGDITDPEDAQRCLAYTGADGVMIGRGALGNPWLFAE-QHTVKTGEFGPSP 238

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 489336524  253 QVREKMAVCKLHLDRLIDLKGENVAVREMRKHAAWYLKGVKGNANVRNEINHCETREEFVQLLDAFTVEVE 323
Cdd:pfam01207 239 PLAEEAEKVLRHLPYLEEFLGEDKGLRHARKHLAWYLKGFPGAAELRRELNDVFDPVEALINLDAALRAAN 309
DUS_like_FMN cd02801
Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze ...
 12-244 1.06e-115

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: 334.08  E-value: 1.06e-115
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489336524  12 RVVLAPMAGVCNSAFRLTVKEFGAGLVCAEMVSDKAILYNNARTMGMLYIDEREKPLSLQIFGGKKETLVEAAKFVdQNT 91
Cdd:cd02801    1 KLILAPMVGVTDLPFRLLCRRYGADLVYTEMISAKALLRGNRKRLRLLTRNPEERPLIVQLGGSDPETLAEAAKIV-EEL 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489336524  92 TADIIDINMGCPVPKITKCDAGAKWLLDPDKIYEMVSAVVDAVNKPVTVKMRMGWDEDhIFAVKNAQAVERAGGKAVALH 171
Cdd:cd02801   80 GADGIDLNMGCPSPKVTKGGAGAALLKDPELVAEIVRAVREAVPIPVTVKIRLGWDDE-EETLELAKALEDAGASALTVH 158

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 489336524 172 GRTRVQMYEGTANWDIIKEVKQSVSIPVIGNGDVKTPQDAKRMLDETGVDGVMIGRAALGNPWMIYRTVQYLE 244
Cdd:cd02801  159 GRTREQRYSGPADWDYIAEIKEAVSIPVIANGDIFSLEDALRCLEQTGVDGVMIGRGALGNPWLFREIKELLE 231
PRK10415 PRK10415
tRNA-dihydrouridine synthase B; Provisional
 3-318 2.66e-83

tRNA-dihydrouridine synthase B; Provisional


Pssm-ID: 182440  Cd Length: 321  Bit Score: 254.90  E-value: 2.66e-83
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489336524   3 KIGDIQLKNRVVLAPMAGVCNSAFRLTVKEFGAGLVCAEMVSDKAILYNNART-MGMLYIDErekP--LSLQIFGGKKET 79
Cdd:PRK10415   2 RIGQYQLRNRLIAAPMAGITDRPFRTLCYEMGAGLTVSEMMSSNPQVWESDKSrLRMVHIDE---PgiRTVQIAGSDPKE 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489336524  80 LVEAAKfVDQNTTADIIDINMGCPVPKITKCDAGAKWLLDPDKIYEMVSAVVDAVNKPVTVKMRMGWDEDHIFAVKNAQA 159
Cdd:PRK10415  79 MADAAR-INVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDLVKSILTEVVNAVDVPVTLKIRTGWAPEHRNCVEIAQL 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489336524 160 VERAGGKAVALHGRTRVQMYEGTANWDIIKEVKQSVSIPVIGNGDVKTPQDAKRMLDETGVDGVMIGRAALGNPWmIYRT 239
Cdd:PRK10415 158 AEDCGIQALTIHGRTRACLFNGEAEYDSIRAVKQKVSIPVIANGDITDPLKARAVLDYTGADALMIGRAAQGRPW-IFRE 236

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489336524 240 VQ-YLETGKLKEEPQVREKMAVCKLHLDRLIDLKGENVAVREMRKHAAWYLKGVKGNANVRNEINHCETREEFVQLLDAF 318
Cdd:PRK10415 237 IQhYLDTGELLPPLPLAEVKRLLCAHVRELHDFYGPAKGYRIARKHVSWYLQEHAPNDQFRRTFNAIEDASEQLEALEAY 316
PRK10550 PRK10550
tRNA dihydrouridine(16) synthase DusC;
12-244 1.54e-35

tRNA dihydrouridine(16) synthase DusC;


Pssm-ID: 236713  Cd Length: 312  Bit Score: 131.09  E-value: 1.54e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489336524  12 RVVLAPMAGVCNSAFR----------LTVKEFGAglVCAEMVSDKAI------LYNNARTmgmlyidEREKPLSLQIFGG 75
Cdd:PRK10550   2 RVLLAPMEGVLDSLVRelltevndydLCITEFLR--VVDQLLPVKVFhrlcpeLHNASRT-------PSGTLVRIQLLGQ 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489336524  76 KKETLVE-AAKFVDQNTTAdiIDINMGCPVPKITKCDAGAKWLLDPDKIYEMVSAVVDAV--NKPVTVKMRMGWDE-DHI 151
Cdd:PRK10550  73 YPQWLAEnAARAVELGSWG--VDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAMREAVpaHLPVTVKVRLGWDSgERK 150

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489336524 152 FAVknAQAVERAGGKAVALHGRTRVQMYEGTA-NWDIIKEVKQSVSIPVIGNGDVKTPQDAKRMLDETGVDGVMIGRAAL 230
Cdd:PRK10550 151 FEI--ADAVQQAGATELVVHGRTKEDGYRAEHiNWQAIGEIRQRLTIPVIANGEIWDWQSAQQCMAITGCDAVMIGRGAL 228

                        250
                 ....*....|....
gi 489336524 231 GNPwMIYRTVQYLE 244
Cdd:PRK10550 229 NIP-NLSRVVKYNE 241
PRK11815 PRK11815
tRNA dihydrouridine(20/20a) synthase DusA;
41-236 6.78e-22

tRNA dihydrouridine(20/20a) synthase DusA;


Pssm-ID: 236991 [Multi-domain]  Cd Length: 333  Bit Score: 94.43  E-value: 6.78e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489336524  41 EMVSDKAILYNNARTMgmLYIDEREKPLSLQIFGGKKETLVEAAKFVdQNTTADIIDINMGCPVPKITKCDAGAKWLLDP 120
Cdd:PRK11815  42 EMVTTGAIIHGDRERL--LAFDPEEHPVALQLGGSDPADLAEAAKLA-EDWGYDEINLNVGCPSDRVQNGRFGACLMAEP 118

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489336524 121 DKIYEMVSAVVDAVNKPVTVKMRMGWDE-DHIFAVKN-AQAVERAGGKAVALHGRtrvqmyegTA--------------- 183
Cdd:PRK11815 119 ELVADCVKAMKDAVSIPVTVKHRIGIDDqDSYEFLCDfVDTVAEAGCDTFIVHAR--------KAwlkglspkenreipp 190

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 489336524 184 -NWDIIKEVKQSV-SIPVIGNGDVKTPQDAKRMLDEtgVDGVMIGRAALGNPWMI 236
Cdd:PRK11815 191 lDYDRVYRLKRDFpHLTIEINGGIKTLEEAKEHLQH--VDGVMIGRAAYHNPYLL 243
arch_FMN cd02911
Archeal FMN-binding domain. This family of archaeal proteins are part of the NAD(P)H-dependent ...
 12-230 1.01e-13

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: 69.67  E-value: 1.01e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489336524  12 RVVLAPMAGVCNSAFRLTVKEfGAGLVC-----AEMVSDKAILYNNARTMGMLYIDEREKPLSLQI-------------- 72
Cdd:cd02911    1 PVALASMAGITDGDFCRKRAD-HAGLVFlggynLDERTIEAARKLVKRGRKEFLPDDPLEFIEGEIkalkdsnvlvgvnv 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489336524  73 ----FGGKKETLVEAAKFvdqnttADIIDINMGCPVPKITKCDAGAKWLLDPDKIYEMVSAvVDAVNKPVTVKMRMGWDE 148
Cdd:cd02911   80 rsssLEPLLNAAALVAKN------AAILEINAHCRQPEMVEAGAGEALLKDPERLSEFIKA-LKETGVPVSVKIRAGVDV 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489336524 149 DhifAVKNAQAVERAGGKavALHGRTrvqMYEGT-ANWDIIKEVkqSVSIPVIGNGDVKTPQDAKRMLdETGVDGVMIGR 227
Cdd:cd02911  153 D---DEELARLIEKAGAD--IIHVDA---MDPGNhADLKKIRDI--STELFIIGNNSVTTIESAKEMF-SYGADMVSVAR 221


                 ...
gi 489336524 228 AAL 230
Cdd:cd02911  222 ASL 224
OYE_like_FMN_family cd02803
Old yellow enzyme (OYE)-like FMN binding domain. OYE was the first flavin-dependent enzyme ...
 2-233 4.65e-13

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: 68.75  E-value: 4.65e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489336524   2 FKIGDIQLKNRVVLAPMA-GVCNSAFRLTVKEF---------GAGLVCAE--MVSDKAILYNNartMGMLYIDErekpls 69
Cdd:cd02803    4 IKIGGLTLKNRIVMAPMTeNMATEDGTPTDELIeyyeerakgGVGLIITEaaYVDPEGKGYPG---QLGIYDDE------ 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489336524  70 lQIFGGKKetLVEA-----AKFVDQ----NTTADIIDINMGCPVPKITKCDAGA--KWLLDPDKIYEMVSAVVDA----- 133
Cdd:cd02803   75 -QIPGLRK--LTEAvhahgAKIFAQlahaGRQAQPNLTGGPPPAPSAIPSPGGGepPREMTKEEIEQIIEDFAAAarrak 151

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489336524 134 ------------------------VNK-------------------------------PVTVKMRM------GWDEDHif 152
Cdd:cd02803  152 eagfdgveihgahgyllsqflspyTNKrtdeyggslenrarflleivaavreavgpdfPVGVRLSAddfvpgGLTLEE-- 229

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489336524 153 AVKNAQAVERAGgkAVALH---GRT-------RVQMYEGTANWDIIKEVKQSVSIPVIGNGDVKTPQDAKRMLDETGVDG 222
Cdd:cd02803  230 AIEIAKALEEAG--VDALHvsgGSYespppiiPPPYVPEGYFLELAEKIKKAVKIPVIAVGGIRDPEVAEEILAEGKADL 307

                        330
                 ....*....|.
gi 489336524 223 VMIGRAALGNP 233
Cdd:cd02803  308 VALGRALLADP 318
DHOD_1B_like cd04740
Dihydroorotate dehydrogenase (DHOD) class 1B FMN-binding domain. DHOD catalyzes the oxidation ...
 60-233 2.60e-12

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: 66.42  E-value: 2.60e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489336524  60 YIDEREKPLSLQIFGGKKETLVEAAKFVdQNTTADIIDINMGCPVPKitkcDAGAKWLLDPDKIYEMVSAVVDAVNKPVT 139
Cdd:cd04740   84 WLREFGTPVIASIAGSTVEEFVEVAEKL-ADAGADAIELNISCPNVK----GGGMAFGTDPEAVAEIVKAVKKATDVPVI 158

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489336524 140 VKMRmGWDEDhIfaVKNAQAVERAG-----------GKAVALHGRTRVQMY-----EGTAnwdiIK--------EVKQSV 195
Cdd:cd04740  159 VKLT-PNVTD-I--VEIARAAEEAGadgltlintlkGMAIDIETRKPILGNvtgglSGPA----IKpialrmvyQVYKAV 230

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 489336524 196 SIPVIGNGDVKTPQDAKRMLdETGVDGVMIGRAALGNP 233
Cdd:cd04740  231 EIPIIGVGGIASGEDALEFL-MAGASAVQVGTANFVDP 267
DHOD_DHPD_FMN cd02810
Dihydroorotate dehydrogenase (DHOD) and Dihydropyrimidine dehydrogenase (DHPD) FMN-binding ...
 65-238 6.75e-12

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: 65.07  E-value: 6.75e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489336524  65 EKPLSLQIFGGKKETLVEAAKFVDQnTTADIIDINMGCP-VPKitkcdaGAKWLLDPDKIYEMVSAVVDAVNKPVTVKMr 143
Cdd:cd02810   98 GQPLIASVGGSSKEDYVELARKIER-AGAKALELNLSCPnVGG------GRQLGQDPEAVANLLKAVKAAVDIPLLVKL- 169

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489336524 144 mGWDEDHIFAVKNAQAVERAGGKAVALHGR---------TRVQMYEGTANW-----------DIIKEVKQSVS--IPVIG 201
Cdd:cd02810  170 -SPYFDLEDIVELAKAAERAGADGLTAINTisgrvvdlkTVGPGPKRGTGGlsgapirplalRWVARLAARLQldIPIIG 248

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 489336524 202 NGDVKTPQDAKRMLDeTGVDGVMIGRAALGNPWMIYR 238
Cdd:cd02810  249 VGGIDSGEDVLEMLM-AGASAVQVATALMWDGPDVIR 284
FadH COG1902
2,4-dienoyl-CoA reductase or related NADH-dependent reductase, Old Yellow Enzyme (OYE) family ...
 125-238 4.16e-11

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: 63.26  E-value: 4.16e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489336524 125 EMVSAVVDAV--NKPVTVK------MRMGWDEDHIFAVknAQAVERAGgkAVALH-------GRTRVQMYEGTANW-DII 188
Cdd:COG1902  204 EVVEAVRAAVgpDFPVGVRlsptdfVEGGLTLEESVEL--AKALEEAG--VDYLHvssggyePDAMIPTIVPEGYQlPFA 279

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 489336524 189 KEVKQSVSIPVIGNGDVKTPQDAKRMLDETGVDGVMIGRAALGNPWMIYR 238
Cdd:COG1902  280 ARIRKAVGIPVIAVGGITTPEQAEAALASGDADLVALGRPLLADPDLPNK 329
PRK07259 PRK07259
dihydroorotate dehydrogenase;
3-233 2.53e-09

dihydroorotate dehydrogenase;


Pssm-ID: 235982  Cd Length: 301  Bit Score: 57.47  E-value: 2.53e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489336524   3 KIGDIQLKNRVVLApmAGVCnsAFRLTVKEF----GAGLVCAEMVSDKAIL-YNNAR----TMGML------------YI 61
Cdd:PRK07259   5 ELPGLKLKNPVMPA--SGTF--GFGGEYARFydlnGLGAIVTKSTTLEPREgNPTPRiaetPGGMLnaiglqnpgvdaFI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489336524  62 DEREKPLSLQ-------IFGGKKETLVEAAKFVDQNTTADIIDINMGCPVPKitkcDAGAKWLLDPDKIYEMVSAVVDAV 134
Cdd:PRK07259  81 EEELPWLEEFdtpiianVAGSTEEEYAEVAEKLSKAPNVDAIELNISCPNVK----HGGMAFGTDPELAYEVVKAVKEVV 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489336524 135 NKPVTVKmrMGWDEDHIfaVKNAQAVERAGGKAVAL------------HGR----TRVQMYEGTAnwdiIK--------E 190
Cdd:PRK07259 157 KVPVIVK--LTPNVTDI--VEIAKAAEEAGADGLSLintlkgmaidikTRKpilaNVTGGLSGPA----IKpialrmvyQ 228

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|...
gi 489336524 191 VKQSVSIPVIGNGDVKTPQDAKRMLdETGVDGVMIGRAALGNP 233
Cdd:PRK07259 229 VYQAVDIPIIGMGGISSAEDAIEFI-MAGASAVQVGTANFYDP 270
PyrD COG0167
Dihydroorotate dehydrogenase [Nucleotide transport and metabolism]; Dihydroorotate ...
 3-244 1.79e-08

Dihydroorotate dehydrogenase [Nucleotide transport and metabolism]; Dihydroorotate dehydrogenase is part of the Pathway/BioSystem: Pyrimidine biosynthesis


Pssm-ID: 439937 [Multi-domain]  Cd Length: 296  Bit Score: 54.69  E-value: 1.79e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489336524   3 KIGDIQLKNRVVLApmAGVC--NSAFRLTVKEFGAGLVC-----------------AEMVSDKAILynNArtMG------ 57
Cdd:COG0167    5 ELAGLKFPNPVGLA--SGFFdkNAEYIDALDLLGFGAVEvktvtpepqpgnprprlFRLPEDSGLI--NR--MGlnnpgv 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489336524  58 ------MLYIDEREKPLSLQIFGGKKETLVEAAKFVDqNTTADIIDINMGCP-VPKitkcdAGAKWLLDPDKIYEMVSAV 130
Cdd:COG0167   79 daflerLLPAKRYDVPVIVNIGGNTVEDYVELARRLA-DAGADYLELNISCPnTPG-----GGRALGQDPEALAELLAAV 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489336524 131 VDAVNKPVTVKmrMGWDEDHIFAVknAQAVERAGGKAVALhGRTRVQMYEGTANWD---------------------IIK 189
Cdd:COG0167  153 KAATDKPVLVK--LAPDLTDIVEI--ARAAEEAGADGVIA-INTTLGRAIDLETRRpvlaneagglsgpalkpialrMVR 227

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 489336524 190 EVKQSV--SIPVIGNGDVKTPQDAKRMLdETGVDGVMIGRAALGN-PWMIYRTVQYLE 244
Cdd:COG0167  228 EVAQAVggDIPIIGVGGISTAEDALEFI-LAGASAVQVGTALFYEgPGLVRRIIRGLE 284
His_biosynth pfam00977
Histidine biosynthesis protein; Proteins involved in steps 4 and 6 of the histidine ...
 119-228 8.68e-07

Histidine biosynthesis protein; Proteins involved in steps 4 and 6 of the histidine biosynthesis pathway are contained in this family. Histidine is formed by several complex and distinct biochemical reactions catalyzed by eight enzymes. The enzymes in this Pfam entry are called His6 and His7 in eukaryotes and HisA and HisF in prokaryotes. The structure of HisA is known to be a TIM barrel fold. In some archaeal HisA proteins the TIM barrel is composed of two tandem repeats of a half barrel. This family belong to the common phosphate binding site TIM barrel family.


Pssm-ID: 425971  Cd Length: 228  Bit Score: 49.01  E-value: 8.68e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489336524  119 DPDKIYEMVSAV--------VDAVNKPVTVKmrmGWDED-HIFAVKNAQAVERAGGKAVALHGRTRVQMYEGtANWDIIK 189
Cdd:pfam00977 108 NPELIKEAAEKFgsqcivvaIDARRGKVAIN---GWREDtGIDAVEWAKELEELGAGEILLTDIDRDGTLSG-PDLELTR 183

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 489336524  190 EVKQSVSIPVIGNGDVKTPQDAKRmLDETGVDGVMIGRA 228
Cdd:pfam00977 184 ELAEAVNIPVIASGGVGSLEDLKE-LFTEGVDGVIAGSA 221
OYE_YqiM_FMN cd02932
Old yellow enzyme (OYE) YqjM-like FMN binding domain. YqjM is involved in the oxidative stress ...
 130-233 1.48e-06

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: 49.03  E-value: 1.48e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489336524 130 VVDAV------NKPVTVKMRM------GWDEDHifAVKNAQAVERAGGKAV-----ALHGRTRVQMYEGtANWDIIKEVK 192
Cdd:cd02932  210 VVDAVravwpeDKPLFVRISAtdwvegGWDLED--SVELAKALKELGVDLIdvssgGNSPAQKIPVGPG-YQVPFAERIR 286

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 489336524 193 QSVSIPVIGNGDVKTPQDAKRMLDETGVDGVMIGRAALGNP 233
Cdd:cd02932  287 QEAGIPVIAVGLITDPEQAEAILESGRADLVALGRELLRNP 327
OYE_like_4_FMN cd04735
Old yellow enzyme (OYE)-related FMN binding domain, group 4. Each monomer of OYE contains FMN ...
 167-247 5.34e-06

Old yellow enzyme (OYE)-related FMN binding domain, group 4. 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. Other members of OYE family include trimethylamine dehydrogenase, 2,4-dienoyl-CoA reductase, enoate reductase, pentaerythriol tetranitrate reductase, xenobiotic reductase, and morphinone reductase.


Pssm-ID: 240086 [Multi-domain]  Cd Length: 353  Bit Score: 47.59  E-value: 5.34e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489336524 167 AVALHGRTRVQMYEGTANWDIIKEVKQSVS--IPVIGNGDVKTPQDAKRMLdETGVDGVMIGRAALGNP-WmiyrtVQYL 243
Cdd:cd04735  253 HISLWDFDRKSRRGRDDNQTIMELVKERIAgrLPLIAVGSINTPDDALEAL-ETGADLVAIGRGLLVDPdW-----VEKI 326


                 ....
gi 489336524 244 ETGK 247
Cdd:cd04735  327 KEGR 330
HisA cd04732
HisA. Phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide (ProFAR) isomerase ...
 180-228 1.06e-05

HisA. Phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide (ProFAR) isomerase catalyzes the fourth step in histidine biosynthesis, an isomerisation of the aminoaldose moiety of ProFAR to the aminoketose of PRFAR (N-(5'-phospho-D-1'-ribulosylformimino)-5-amino-1-(5''-phospho-ribosyl)-4-imidazolecarboxamide). In bacteria and archaea, ProFAR isomerase is encoded by the HisA gene.


Pssm-ID: 240083  Cd Length: 234  Bit Score: 45.93  E-value: 1.06e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 489336524 180 EGT---ANWDIIKEVKQSVSIPVIGNGDVKTPQDAKRmLDETGVDGVMIGRA 228
Cdd:cd04732  171 DGTlsgPNFELYKELAAATGIPVIASGGVSSLDDIKA-LKELGVAGVIVGKA 221
OYE_like_3_FMN cd04734
Old yellow enzyme (OYE)-related FMN binding domain, group 3. Each monomer of OYE contains FMN ...
 125-236 5.67e-05

Old yellow enzyme (OYE)-related FMN binding domain, group 3. 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. Other members of OYE family include trimethylamine dehydrogenase, 2,4-dienoyl-CoA reductase, enoate reductase, pentaerythriol tetranitrate reductase, xenobiotic reductase, and morphinone reductase. One member of this subgroup, the Sinorhizobium meliloti stachydrine utilization protein stcD, has been idenified as a putative N-methylproline demethylase.


Pssm-ID: 240085 [Multi-domain]  Cd Length: 343  Bit Score: 44.53  E-value: 5.67e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489336524 125 EMVSAVVDAVNKPVTVKMRMGWDEDHIF------AVKNAQAVERAG---------GKAVALHGRTRV--QMYEGTANW-D 186
Cdd:cd04734  196 EVLAAVRAAVGPDFIVGIRISGDEDTEGglspdeALEIAARLAAEGlidyvnvsaGSYYTLLGLAHVvpSMGMPPGPFlP 275

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 489336524 187 IIKEVKQSVSIPVIGNGDVKTPQDAKRMLDETGVDGVMIGRAALGNPWMI 236
Cdd:cd04734  276 LAARIKQAVDLPVFHAGRIRDPAEAEQALAAGHADMVGMTRAHIADPHLV 325
PRK00748 PRK00748
1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide ...
 120-228 6.14e-05

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


Pssm-ID: 179108  Cd Length: 233  Bit Score: 43.52  E-value: 6.14e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489336524 120 PDKIyemvsAV-VDAVNKPVTVKmrmGWDED-HIFAVKNAQAVERAGGKAV---------ALHGrtrvqmyegtANWDII 188
Cdd:PRK00748 121 PGKI-----VVgLDARDGKVATD---GWLETsGVTAEDLAKRFEDAGVKAIiytdisrdgTLSG----------PNVEAT 182

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 489336524 189 KEVKQSVSIPVIGNGDVKTPQDAKRMLDETGVDGVMIGRA 228
Cdd:PRK00748 183 RELAAAVPIPVIASGGVSSLDDIKALKGLGAVEGVIVGRA 222
PRK01130 PRK01130
putative N-acetylmannosamine-6-phosphate 2-epimerase;
154-228 6.57e-05

putative N-acetylmannosamine-6-phosphate 2-epimerase;


Pssm-ID: 234907  Cd Length: 221  Bit Score: 43.60  E-value: 6.57e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489336524 154 VKNAQAVERAGGKAVA--LHGRTrvqmyEGTAN-----WDIIKEVKQSVSIPVIGNGDVKTPQDAKRMLdETGVDGVMIG 226
Cdd:PRK01130 129 LEEGLAAQKLGFDFIGttLSGYT-----EETKKpeepdFALLKELLKAVGCPVIAEGRINTPEQAKKAL-ELGAHAVVVG 202


                 ..
gi 489336524 227 RA 228
Cdd:PRK01130 203 GA 204
NanE cd04729
N-acetylmannosamine-6-phosphate epimerase (NanE) converts N-acetylmannosamine-6-phosphate to ...
 170-228 1.13e-04

N-acetylmannosamine-6-phosphate epimerase (NanE) converts N-acetylmannosamine-6-phosphate to N-acetylglucosamine-6-phosphate. This reaction is part of the pathway that allows the usage of sialic acid as a carbohydrate source. Sialic acids are a family of related sugars that are found as a component of glycoproteins, gangliosides, and other sialoglycoconjugates.


Pssm-ID: 240080 [Multi-domain]  Cd Length: 219  Bit Score: 42.56  E-value: 1.13e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 489336524 170 LHGRTRVQMYEGTANWDIIKEVKQSVSIPVIGNGDVKTPQDAKRMLdETGVDGVMIGRA 228
Cdd:cd04729  151 LSGYTEETAKTEDPDFELLKELRKALGIPVIAEGRINSPEQAAKAL-ELGADAVVVGSA 208
PRK13585 PRK13585
1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide ...
 188-228 1.15e-04

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


Pssm-ID: 184165  Cd Length: 241  Bit Score: 42.97  E-value: 1.15e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 489336524 188 IKEVKQSVSIPVIGNGDVKTPQDAkRMLDETGVDGVMIGRA 228
Cdd:PRK13585 185 VKELVDSVDIPVIASGGVTTLDDL-RALKEAGAAGVVVGSA 224
PRK13585 PRK13585
1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide ...
 183-236 1.81e-04

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


Pssm-ID: 184165  Cd Length: 241  Bit Score: 42.20  E-value: 1.81e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 489336524 183 ANWDIIKEVKQSVSIPVIGNGDVKTPQDAKRMLDeTGVDGVMIGRAALGNPWMI 236
Cdd:PRK13585  63 KNAEAIEKIIEAVGVPVQLGGGIRSAEDAASLLD-LGVDRVILGTAAVENPEIV 115
TIM_phosphate_binding cd04722
TIM barrel proteins share a structurally conserved phosphate binding motif and in general ...
 93-227 4.51e-04

TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate comes either from the substrate, as in the case of inosine monophosphate dehydrogenase (IMPDH), or from ribulose-5-phosphate 3-epimerase (RPE) or from cofactors, like FMN.


Pssm-ID: 240073 [Multi-domain]  Cd Length: 200  Bit Score: 40.65  E-value: 4.51e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489336524  93 ADIIDINMGCPVpkitkcdagaKWLLDPDKIYEMVSAVVDAvnkPVTVKMRMGWDEDHIfavknaqAVERAGGKAVALHG 172
Cdd:cd04722   85 ADGVEIHGAVGY----------LAREDLELIRELREAVPDV---KVVVKLSPTGELAAA-------AAEEAGVDEVGLGN 144

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 489336524 173 RTRVQM---YEGTANWDIIKeVKQSVSIPVIGNGDVKTPQDAKRMLdETGVDGVMIGR 227
Cdd:cd04722  145 GGGGGGgrdAVPIADLLLIL-AKRGSKVPVIAGGGINDPEDAAEAL-ALGADGVIVGS 200
TIGR00007 TIGR00007
phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase; This protein family ...
 119-230 6.29e-04

phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase; This protein family consists of HisA, phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase, the enzyme catalyzing the fourth step in histidine biosynthesis. It is closely related to the enzyme HisF for the sixth step. Examples of this enzyme in Actinobacteria have been found to be bifunctional, also possessing phosphoribosylanthranilate isomerase activity; the trusted cutoff here has now been raised to 275.0 to exclude the bifunctional group, now represented by model TIGR01919. HisA from Lactococcus lactis was reported to be inactive (MEDLINE:93322317). [Amino acid biosynthesis, Histidine family]


Pssm-ID: 272850 [Multi-domain]  Cd Length: 230  Bit Score: 40.65  E-value: 6.29e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489336524  119 DPDKIYEMVSAV--------VDAVNKPVTVKmrmGWDED-HIFAVKNAQAVERAGGKAVALHGRTRvqmyEGT---ANWD 186
Cdd:TIGR00007 107 NPDLVKELLKEYgperivvsLDARGGEVAVK---GWLEKsEVSLEELAKRLEELGLEGIIYTDISR----DGTlsgPNFE 179

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 489336524  187 IIKEVKQSVSIPVIGNGDVKTPQDAKRmLDETGVDGVMIGRAAL 230
Cdd:TIGR00007 180 LTKELVKAVNVPVIASGGVSSIDDLIA-LKKLGVYGVIVGKALY 222
RspA COG4948
L-alanine-DL-glutamate epimerase or related enzyme of enolase superfamily [Cell wall/membrane ...
 66-225 7.54e-04

L-alanine-DL-glutamate epimerase or related enzyme of enolase superfamily [Cell wall/membrane/envelope biogenesis, General function prediction only]; L-alanine-DL-glutamate epimerase or related enzyme of enolase superfamily is part of the Pathway/BioSystem: Non-phosphorylated Entner-Doudoroff pathway


Pssm-ID: 443975 [Multi-domain]  Cd Length: 359  Bit Score: 40.96  E-value: 7.54e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489336524  66 KPLSlQIFGGKKETLVEAAKFVDQNTTADIID-----INMGCPVPKItkcDAGAkwlLDPDKIYEMVSAVVDAV--NKPV 138
Cdd:COG4948  113 VPVY-QLLGGKVRDRVPVYATLGIDTPEEMAEeareaVARGFRALKL---KVGG---PDPEEDVERVRAVREAVgpDARL 185

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489336524 139 TVKMRMGWDEDHifAVKNAQAVERAGgkavalhgrtrVQMYE---GTANWDIIKEVKQSVSIPVIGNGDVKTPQDAKRML 215
Cdd:COG4948  186 RVDANGAWTLEE--AIRLLRALEDLG-----------LEWIEqplPAEDLEGLAELRRATPVPIAADESLTSRADFRRLI 252

                        170
                 ....*....|
gi 489336524 216 DETGVDGVMI 225
Cdd:COG4948  253 EAGAVDIVNI 262
OYE_like_FMN cd02933
Old yellow enzyme (OYE)-like FMN binding domain. OYE was the first flavin-dependent enzyme ...
 2-53 1.40e-03

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 12-oxophytodienoate reductase, pentaerythritol tetranitrate reductase, morphinone reductase, and related enzymes.


Pssm-ID: 239243 [Multi-domain]  Cd Length: 338  Bit Score: 40.15  E-value: 1.40e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 489336524   2 FKIGDIQLKNRVVLAPM------AGVCNSAFrltVKEF-----GAGLVCAE--MVSDKAILYNNA 53
Cdd:cd02933    6 LKLGNLTLKNRIVMAPLtrsradPDGVPTDL---MAEYyaqraSAGLIITEatQISPQGQGYPNT 67
DCR_FMN cd02930
2,4-dienoyl-CoA reductase (DCR) FMN-binding domain. DCR in E. coli is an iron-sulfur ...
 125-233 1.46e-03

2,4-dienoyl-CoA reductase (DCR) FMN-binding domain. DCR in E. coli is an iron-sulfur flavoenzyme which contains FMN, FAD, and a 4Fe-4S cluster. It is also a monomer, unlike that of its eukaryotic counterparts which form homotetramers and lack the flavin and iron-sulfur cofactors. Metabolism of unsaturated fatty acids requires auxiliary enzymes in addition to those used in b-oxidation. After a given number of cycles through the b-oxidation pathway, those unsaturated fatty acyl-CoAs with double bonds at even-numbered carbon positions contain 2-trans, 4-cis double bonds that can not be modified by enoyl-CoA hydratase. DCR utilizes NADPH to remove the C4-C5 double bond. DCR can catalyze the reduction of both natural fatty acids with cis double bonds, as well as substrates containing trans double bonds. The reaction is initiated by hybrid transfer from NADPH to FAD, which in turn transfers electrons, one at a time, to FMN via the 4Fe-4S cluster. The fully reduced FMN provides a hydrid ion to the C5 atom of substrate, and Tyr and His are proposed to form a catalytic dyad that protonates the C4 atom of the substrate and completes the reaction.


Pssm-ID: 239240 [Multi-domain]  Cd Length: 353  Bit Score: 39.96  E-value: 1.46e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489336524 125 EMVSAVVDAV--NKPVTVKMRM--------GWDEdhifAVKNAQAVERAGGKA----VALHgRTRV---QMYEGTANW-D 186
Cdd:cd02930  192 EIVRAVRAAVgeDFIIIYRLSMldlveggsTWEE----VVALAKALEAAGADIlntgIGWH-EARVptiATSVPRGAFaW 266

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 489336524 187 IIKEVKQSVSIPVIGNGDVKTPQDAKRMLDETGVDGVMIGRAALGNP 233
Cdd:cd02930  267 ATAKLKRAVDIPVIASNRINTPEVAERLLADGDADMVSMARPFLADP 313
PRK00748 PRK00748
1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide ...
 184-233 2.02e-03

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


Pssm-ID: 179108  Cd Length: 233  Bit Score: 38.89  E-value: 2.02e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 489336524 184 NWDIIKEVKQSVSIPV-IGNGdVKTPQDAKRMLDeTGVDGVMIGRAALGNP 233
Cdd:PRK00748  62 NLELIEAIVKAVDIPVqVGGG-IRSLETVEALLD-AGVSRVIIGTAAVKNP 110
HisA cd04732
HisA. Phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide (ProFAR) isomerase ...
 184-233 2.20e-03

HisA. Phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide (ProFAR) isomerase catalyzes the fourth step in histidine biosynthesis, an isomerisation of the aminoaldose moiety of ProFAR to the aminoketose of PRFAR (N-(5'-phospho-D-1'-ribulosylformimino)-5-amino-1-(5''-phospho-ribosyl)-4-imidazolecarboxamide). In bacteria and archaea, ProFAR isomerase is encoded by the HisA gene.


Pssm-ID: 240083  Cd Length: 234  Bit Score: 39.00  E-value: 2.20e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 489336524 184 NWDIIKEVKQSVSIPV-IGNGdVKTPQDAKRMLDeTGVDGVMIGRAALGNP 233
Cdd:cd04732   61 NLELIEEIVKAVGIPVqVGGG-IRSLEDIERLLD-LGVSRVIIGTAAVKNP 109
L-Ala-DL-Glu_epimerase cd03319
L-Ala-D/L-Glu epimerase catalyzes the epimerization of L-Ala-D/L-Glu and other dipeptides. The ...
 119-225 3.36e-03

L-Ala-D/L-Glu epimerase catalyzes the epimerization of L-Ala-D/L-Glu and other dipeptides. The genomic context and the substrate specificity of characterized members of this family from E.coli and B.subtilis indicates a possible role in the metabolism of the murein peptide of peptidoglycan, of which L-Ala-D-Glu is a component. L-Ala-D/L-Glu epimerase is a member of the enolase-superfamily, which is characterized by the presence of an enolate anion intermediate which is generated by abstraction of the alpha-proton of the carboxylate substrate by an active site residue and is stabilized by coordination to the essential Mg2+ ion.


Pssm-ID: 239435 [Multi-domain]  Cd Length: 316  Bit Score: 38.71  E-value: 3.36e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489336524 119 DPDKIYEMVSAVVDAV-NKPVTVKMRMGWDEDHifAVKNAQAVERAGgkavalhgrtrVQMYE---GTANWDIIKEVKQS 194
Cdd:cd03319  160 DLEDDIERIRAIREAApDARLRVDANQGWTPEE--AVELLRELAELG-----------VELIEqpvPAGDDDGLAYLRDK 226

                         90       100       110
                 ....*....|....*....|....*....|.
gi 489336524 195 VSIPVIGNGDVKTPQDAKRMLDETGVDGVMI 225
Cdd:cd03319  227 SPLPIMADESCFSAADAARLAGGGAYDGINI 257
DHPD_FMN cd02940
Dihydropyrimidine dehydrogenase (DHPD) FMN-binding domain. DHPD catalyzes the first step in ...
 41-170 3.51e-03

Dihydropyrimidine dehydrogenase (DHPD) FMN-binding domain. 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 the dimer interface twice. Two of the Fe-S clusters show a hitherto unobserved coordination involving a glutamine residue.


Pssm-ID: 239244  Cd Length: 299  Bit Score: 38.80  E-value: 3.51e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489336524  41 EMVSDKAILYNnARTMGMLYIDEREKPLSLQIFGG-KKETLVEAAKFVdQNTTADIIDINMGCPvPKITKCDAGAKWLLD 119
Cdd:cd02940   76 ELISEKPLEYW-LKEIRELKKDFPDKILIASIMCEyNKEDWTELAKLV-EEAGADALELNFSCP-HGMPERGMGAAVGQD 152

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 489336524 120 PDKIYEMVSAVVDAVNKPVTVKMRMGWDEdhifAVKNAQAVERAGGKAVAL 170
Cdd:cd02940  153 PELVEEICRWVREAVKIPVIAKLTPNITD----IREIARAAKEGGADGVSA 199
PRK08255 PRK08255
bifunctional salicylyl-CoA 5-hydroxylase/oxidoreductase;
2-43 3.75e-03

bifunctional salicylyl-CoA 5-hydroxylase/oxidoreductase;


Pssm-ID: 236203 [Multi-domain]  Cd Length: 765  Bit Score: 39.15  E-value: 3.75e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 489336524   2 FKIGDIQLKNRVVLAPMA------GVCNsafrltvkEF-----------GAGLVCAEMV 43
Cdd:PRK08255 403 FRLRGLTLKNRVVVSPMAmysavdGVPG--------DFhlvhlgaralgGAGLVMTEMT 453
ER_like_FMN cd02931
Enoate reductase (ER)-like FMN-binding domain. Enoate reductase catalyzes the NADH-dependent ...
 189-250 4.19e-03

Enoate reductase (ER)-like FMN-binding domain. Enoate reductase catalyzes the NADH-dependent reduction of carbon-carbon double bonds of several molecules, including nonactivated 2-enoates, alpha,beta-unsaturated aldehydes, cyclic ketones, and methylketones. ERs are similar to 2,4-dienoyl-CoA reductase from E. coli and to the old yellow enzyme from Saccharomyces cerevisiae.


Pssm-ID: 239241 [Multi-domain]  Cd Length: 382  Bit Score: 38.64  E-value: 4.19e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 489336524 189 KEVKQSVSIPVIGNGDVKTPQDAKRMLDETGVDGVMIGRAALGNPWMiyrtVQYLETGKLKE 250
Cdd:cd02931  298 KALKEVVDVPVIMAGRMEDPELASEAINEGIADMISLGRPLLADPDV----VNKIRRGRFKN 355
HisF cd04731
The cyclase subunit of imidazoleglycerol phosphate synthase (HisF). Imidazole glycerol ...
 186-226 6.83e-03

The cyclase subunit of imidazoleglycerol phosphate synthase (HisF). Imidazole glycerol phosphate synthase (IGPS) catalyzes the fifth step of histidine biosynthesis, the formation of the imidazole ring. IGPS converts N1-(5'-phosphoribulosyl)-formimino-5-aminoimidazole-4-carboxamide ribonucleotide (PRFAR) to imidazole glycerol phosphate (ImGP) and 5'-(5-aminoimidazole-4-carboxamide) ribonucleotide (AICAR). This conversion involves two tightly coupled reactions in distinct active sites of IGPS. The two catalytic domains can be fused, like in fungi and plants, or peformed by a heterodimer (HisH-glutaminase and HisF-cyclase), like in bacteria.


Pssm-ID: 240082  Cd Length: 243  Bit Score: 37.45  E-value: 6.83e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 489336524 186 DIIKEVKQSVSIPVIGNGDVKTPQDAKRMLDETGVDGVMIG 226
Cdd:cd04731  183 ELIRAVSSAVNIPVIASGGAGKPEHFVEAFEEGGADAALAA 223
 
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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