|
Name |
Accession |
Description |
Interval |
E-value |
| PRK10550 |
PRK10550 |
tRNA dihydrouridine(16) synthase DusC; |
1-309 |
0e+00 |
|
tRNA dihydrouridine(16) synthase DusC;
Pssm-ID: 236713 Cd Length: 312 Bit Score: 675.37 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504697455 1 MRVLLAPMEGVLDSLVRELLTEVNDYDLCVTEFLRVVDMLLPEKSFYRLCPELHRQSRTPSGTLVRIQLLGQYPEWLAEN 80
Cdd:PRK10550 1 MRVLLAPMEGVLDSLVRELLTEVNDYDLCITEFLRVVDQLLPVKVFHRLCPELHNASRTPSGTLVRIQLLGQYPQWLAEN 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504697455 81 AARAVALGSYGVDLNCGCPSKLVNGSGGGATLLKDPELIYRGAKAMREAVPSHLPVTVKVRLGWDSGDKQFEIADAVQQA 160
Cdd:PRK10550 81 AARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAMREAVPAHLPVTVKVRLGWDSGERKFEIADAVQQA 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504697455 161 GATELVVHGRTKEDGYKAERINWQAIGEIRKRLTIPVIANGEIWDYESAQACLKETGCNAVMIGRGALNVPNLSRVVKYN 240
Cdd:PRK10550 161 GATELVVHGRTKEDGYRAEHINWQAIGEIRQRLTIPVIANGEIWDWQSAQQCMAITGCDAVMIGRGALNIPNLSRVVKYN 240
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 504697455 241 EPRMPWADVVTLLQKYSRLEKQGDTGLYHVARIKQWLSYLRKEYSEALGLFQAIRTLQTSAEIARVIHS 309
Cdd:PRK10550 241 EPRMPWPEVVALLQKYTRLEKQGDTGLYHVARIKQWLGYLRKEYDEATELFQEIRALNNSPDIARAIQA 309
|
|
| DusA |
COG0042 |
tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]; ... |
2-307 |
1.66e-115 |
|
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: 335.53 E-value: 1.66e-115
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504697455 2 RVLLAPMEGVLDSLVRELLTEVNDyDLCVTEFLRVVDMLLPEKSFYRLCPelhrqsRTPSGTLVRIQLLGQYPEWLAENA 81
Cdd:COG0042 8 PLILAPMAGVTDRPFRRLCRELGA-GLLYTEMVSARALLHGNRKTRRLLD------FDPEEHPVAVQLFGSDPEELAEAA 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504697455 82 ARAVALGSYGVDLNCGCPSKLVNGSGGGATLLKDPELIYRGAKAMREAVpsHLPVTVKVRLGWDSGDKQF-EIADAVQQA 160
Cdd:COG0042 81 RIAEELGADEIDINMGCPVKKVTKGGAGAALLRDPELVAEIVKAVVEAV--DVPVTVKIRLGWDDDDENAlEFARIAEDA 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504697455 161 GATELVVHGRTKEDGYKAErINWQAIGEIRKRLTIPVIANGEIWDYESAQACLKETGCNAVMIGRGALNVPNLSRVVKYN 240
Cdd:COG0042 159 GAAALTVHGRTREQRYKGP-ADWDAIARVKEAVSIPVIGNGDIFSPEDAKRMLEETGCDGVMIGRGALGNPWLFREIDAY 237
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 504697455 241 -----EPRMPWADVVTLLQKYSRLEKQGDTGLYHVARIKQWLSYLRKEYSEALGLFQAIRTLQTSAEIARVI 307
Cdd:COG0042 238 laggeAPPPSLEEVLELLLEHLELLLEFYGERRGLRRMRKHLLWYFKGLPGARELRRRLSKAKSLAELLELL 309
|
|
| Dus |
pfam01207 |
Dihydrouridine synthase (Dus); Members of this family catalyze the reduction of the 5,6-double ... |
4-279 |
1.57e-112 |
|
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: 328.13 E-value: 1.57e-112
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504697455 4 LLAPMEGVLDSLVRELLTEVNDYDLCVTEFLRVVDMLLPEKSFYRLCPELHRQsrtpsgTLVRIQLLGQYPEWLAENAAR 83
Cdd:pfam01207 1 LLAPMAGVTDLPFRRLVREYGAGDLVYTEMVTAKAQLRPEKVRIRMLSELEEP------TPLAVQLGGSDPALLAEAAKL 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504697455 84 AVALGSYGVDLNCGCPSKLVNGSGGGATLLKDPELIYRGAKAMREAVPshLPVTVKVRLGWDSG-DKQFEIADAVQQAGA 162
Cdd:pfam01207 75 VEDRGADGIDINMGCPSKKVTRGGGGAALLRNPDLVAQIVKAVVKAVG--IPVTVKIRIGWDDShENAVEIAKIVEDAGA 152
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504697455 163 TELVVHGRTKEDGYKAeRINWQAIGEIRKRLTIPVIANGEIWDYESAQACLKETGCNAVMIGRGALNVPNLSRVVKY--- 239
Cdd:pfam01207 153 QALTVHGRTRAQNYEG-TADWDAIKQVKQAVSIPVIANGDITDPEDAQRCLAYTGADGVMIGRGALGNPWLFAEQHTvkt 231
|
250 260 270 280
....*....|....*....|....*....|....*....|....*
gi 504697455 240 --NEPRMPWADVVT-LLQKYSRLEKQG--DTGLYHVARIKQWLSY 279
Cdd:pfam01207 232 geFGPSPPLAEEAEkVLRHLPYLEEFLgeDKGLRHARKHLAWYLK 276
|
|
| DUS_like_FMN |
cd02801 |
Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze ... |
2-241 |
1.08e-91 |
|
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: 272.06 E-value: 1.08e-91
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504697455 2 RVLLAPMEGVLDSLVRELLTEVNdYDLCVTEFLRVVDMLLPEKSFYRLCpelhrqSRTPSGTLVRIQLLGQYPEWLAENA 81
Cdd:cd02801 1 KLILAPMVGVTDLPFRLLCRRYG-ADLVYTEMISAKALLRGNRKRLRLL------TRNPEERPLIVQLGGSDPETLAEAA 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504697455 82 ARAVALGSYGVDLNCGCPSKLVNGSGGGATLLKDPELIYRGAKAMREAVPshLPVTVKVRLGWDSGDKQFEIADAVQQAG 161
Cdd:cd02801 74 KIVEELGADGIDLNMGCPSPKVTKGGAGAALLKDPELVAEIVRAVREAVP--IPVTVKIRLGWDDEEETLELAKALEDAG 151
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504697455 162 ATELVVHGRTKEDGYKaERINWQAIGEIRKRLTIPVIANGEIWDYESAQACLKETGCNAVMIGRGALNVPNLSRVVKYNE 241
Cdd:cd02801 152 ASALTVHGRTREQRYS-GPADWDYIAEIKEAVSIPVIANGDIFSLEDALRCLEQTGVDGVMIGRGALGNPWLFREIKELL 230
|
|
| nifR3_yhdG |
TIGR00737 |
putative TIM-barrel protein, nifR3 family; This model represents one branch of COG0042 ... |
2-231 |
9.72e-59 |
|
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: 191.04 E-value: 9.72e-59
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504697455 2 RVLLAPMEGVLDSLVRELLTEVNDyDLCVTEFLRVVDML-LPEKSfyrlcpeLHRQSRTPSGTLVRIQLLGQYPEWLAEN 80
Cdd:TIGR00737 9 RVVLAPMAGVTDSPFRRLVAEYGA-GLTVCEMVSSEAIVyDSQRT-------MRLLDIAEDETPISVQLFGSDPDTMAEA 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504697455 81 AARAVALGSYGVDLNCGCPSKLVNGSGGGATLLKDPELIYRGAKAMREAVpsHLPVTVKVRLGWDSGDKQF-EIADAVQQ 159
Cdd:TIGR00737 81 AKINEELGADIIDINMGCPVPKITKKGAGSALLRDPDLIGKIVKAVVDAV--DIPVTVKIRIGWDDAHINAvEAARIAED 158
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 504697455 160 AGATELVVHGRTKEDGYKAERiNWQAIGEIRKRLTIPVIANGEIWDYESAQACLKETGCNAVMIGRGALNVP 231
Cdd:TIGR00737 159 AGAQAVTLHGRTRAQGYSGEA-NWDIIARVKQAVRIPVIGNGDIFSPEDAKAMLETTGCDGVMIGRGALGNP 229
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| PRK10550 |
PRK10550 |
tRNA dihydrouridine(16) synthase DusC; |
1-309 |
0e+00 |
|
tRNA dihydrouridine(16) synthase DusC;
Pssm-ID: 236713 Cd Length: 312 Bit Score: 675.37 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504697455 1 MRVLLAPMEGVLDSLVRELLTEVNDYDLCVTEFLRVVDMLLPEKSFYRLCPELHRQSRTPSGTLVRIQLLGQYPEWLAEN 80
Cdd:PRK10550 1 MRVLLAPMEGVLDSLVRELLTEVNDYDLCITEFLRVVDQLLPVKVFHRLCPELHNASRTPSGTLVRIQLLGQYPQWLAEN 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504697455 81 AARAVALGSYGVDLNCGCPSKLVNGSGGGATLLKDPELIYRGAKAMREAVPSHLPVTVKVRLGWDSGDKQFEIADAVQQA 160
Cdd:PRK10550 81 AARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAMREAVPAHLPVTVKVRLGWDSGERKFEIADAVQQA 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504697455 161 GATELVVHGRTKEDGYKAERINWQAIGEIRKRLTIPVIANGEIWDYESAQACLKETGCNAVMIGRGALNVPNLSRVVKYN 240
Cdd:PRK10550 161 GATELVVHGRTKEDGYRAEHINWQAIGEIRQRLTIPVIANGEIWDWQSAQQCMAITGCDAVMIGRGALNIPNLSRVVKYN 240
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 504697455 241 EPRMPWADVVTLLQKYSRLEKQGDTGLYHVARIKQWLSYLRKEYSEALGLFQAIRTLQTSAEIARVIHS 309
Cdd:PRK10550 241 EPRMPWPEVVALLQKYTRLEKQGDTGLYHVARIKQWLGYLRKEYDEATELFQEIRALNNSPDIARAIQA 309
|
|
| DusA |
COG0042 |
tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]; ... |
2-307 |
1.66e-115 |
|
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: 335.53 E-value: 1.66e-115
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504697455 2 RVLLAPMEGVLDSLVRELLTEVNDyDLCVTEFLRVVDMLLPEKSFYRLCPelhrqsRTPSGTLVRIQLLGQYPEWLAENA 81
Cdd:COG0042 8 PLILAPMAGVTDRPFRRLCRELGA-GLLYTEMVSARALLHGNRKTRRLLD------FDPEEHPVAVQLFGSDPEELAEAA 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504697455 82 ARAVALGSYGVDLNCGCPSKLVNGSGGGATLLKDPELIYRGAKAMREAVpsHLPVTVKVRLGWDSGDKQF-EIADAVQQA 160
Cdd:COG0042 81 RIAEELGADEIDINMGCPVKKVTKGGAGAALLRDPELVAEIVKAVVEAV--DVPVTVKIRLGWDDDDENAlEFARIAEDA 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504697455 161 GATELVVHGRTKEDGYKAErINWQAIGEIRKRLTIPVIANGEIWDYESAQACLKETGCNAVMIGRGALNVPNLSRVVKYN 240
Cdd:COG0042 159 GAAALTVHGRTREQRYKGP-ADWDAIARVKEAVSIPVIGNGDIFSPEDAKRMLEETGCDGVMIGRGALGNPWLFREIDAY 237
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 504697455 241 -----EPRMPWADVVTLLQKYSRLEKQGDTGLYHVARIKQWLSYLRKEYSEALGLFQAIRTLQTSAEIARVI 307
Cdd:COG0042 238 laggeAPPPSLEEVLELLLEHLELLLEFYGERRGLRRMRKHLLWYFKGLPGARELRRRLSKAKSLAELLELL 309
|
|
| Dus |
pfam01207 |
Dihydrouridine synthase (Dus); Members of this family catalyze the reduction of the 5,6-double ... |
4-279 |
1.57e-112 |
|
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: 328.13 E-value: 1.57e-112
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504697455 4 LLAPMEGVLDSLVRELLTEVNDYDLCVTEFLRVVDMLLPEKSFYRLCPELHRQsrtpsgTLVRIQLLGQYPEWLAENAAR 83
Cdd:pfam01207 1 LLAPMAGVTDLPFRRLVREYGAGDLVYTEMVTAKAQLRPEKVRIRMLSELEEP------TPLAVQLGGSDPALLAEAAKL 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504697455 84 AVALGSYGVDLNCGCPSKLVNGSGGGATLLKDPELIYRGAKAMREAVPshLPVTVKVRLGWDSG-DKQFEIADAVQQAGA 162
Cdd:pfam01207 75 VEDRGADGIDINMGCPSKKVTRGGGGAALLRNPDLVAQIVKAVVKAVG--IPVTVKIRIGWDDShENAVEIAKIVEDAGA 152
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504697455 163 TELVVHGRTKEDGYKAeRINWQAIGEIRKRLTIPVIANGEIWDYESAQACLKETGCNAVMIGRGALNVPNLSRVVKY--- 239
Cdd:pfam01207 153 QALTVHGRTRAQNYEG-TADWDAIKQVKQAVSIPVIANGDITDPEDAQRCLAYTGADGVMIGRGALGNPWLFAEQHTvkt 231
|
250 260 270 280
....*....|....*....|....*....|....*....|....*
gi 504697455 240 --NEPRMPWADVVT-LLQKYSRLEKQG--DTGLYHVARIKQWLSY 279
Cdd:pfam01207 232 geFGPSPPLAEEAEkVLRHLPYLEEFLgeDKGLRHARKHLAWYLK 276
|
|
| DUS_like_FMN |
cd02801 |
Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze ... |
2-241 |
1.08e-91 |
|
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: 272.06 E-value: 1.08e-91
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504697455 2 RVLLAPMEGVLDSLVRELLTEVNdYDLCVTEFLRVVDMLLPEKSFYRLCpelhrqSRTPSGTLVRIQLLGQYPEWLAENA 81
Cdd:cd02801 1 KLILAPMVGVTDLPFRLLCRRYG-ADLVYTEMISAKALLRGNRKRLRLL------TRNPEERPLIVQLGGSDPETLAEAA 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504697455 82 ARAVALGSYGVDLNCGCPSKLVNGSGGGATLLKDPELIYRGAKAMREAVPshLPVTVKVRLGWDSGDKQFEIADAVQQAG 161
Cdd:cd02801 74 KIVEELGADGIDLNMGCPSPKVTKGGAGAALLKDPELVAEIVRAVREAVP--IPVTVKIRLGWDDEEETLELAKALEDAG 151
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504697455 162 ATELVVHGRTKEDGYKaERINWQAIGEIRKRLTIPVIANGEIWDYESAQACLKETGCNAVMIGRGALNVPNLSRVVKYNE 241
Cdd:cd02801 152 ASALTVHGRTREQRYS-GPADWDYIAEIKEAVSIPVIANGDIFSLEDALRCLEQTGVDGVMIGRGALGNPWLFREIKELL 230
|
|
| nifR3_yhdG |
TIGR00737 |
putative TIM-barrel protein, nifR3 family; This model represents one branch of COG0042 ... |
2-231 |
9.72e-59 |
|
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: 191.04 E-value: 9.72e-59
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504697455 2 RVLLAPMEGVLDSLVRELLTEVNDyDLCVTEFLRVVDML-LPEKSfyrlcpeLHRQSRTPSGTLVRIQLLGQYPEWLAEN 80
Cdd:TIGR00737 9 RVVLAPMAGVTDSPFRRLVAEYGA-GLTVCEMVSSEAIVyDSQRT-------MRLLDIAEDETPISVQLFGSDPDTMAEA 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504697455 81 AARAVALGSYGVDLNCGCPSKLVNGSGGGATLLKDPELIYRGAKAMREAVpsHLPVTVKVRLGWDSGDKQF-EIADAVQQ 159
Cdd:TIGR00737 81 AKINEELGADIIDINMGCPVPKITKKGAGSALLRDPDLIGKIVKAVVDAV--DIPVTVKIRIGWDDAHINAvEAARIAED 158
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 504697455 160 AGATELVVHGRTKEDGYKAERiNWQAIGEIRKRLTIPVIANGEIWDYESAQACLKETGCNAVMIGRGALNVP 231
Cdd:TIGR00737 159 AGAQAVTLHGRTRAQGYSGEA-NWDIIARVKQAVRIPVIGNGDIFSPEDAKAMLETTGCDGVMIGRGALGNP 229
|
|
| PRK10415 |
PRK10415 |
tRNA-dihydrouridine synthase B; Provisional |
2-258 |
1.92e-34 |
|
tRNA-dihydrouridine synthase B; Provisional
Pssm-ID: 182440 Cd Length: 321 Bit Score: 127.78 E-value: 1.92e-34
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504697455 2 RVLLAPMEGVLDSLVRELLTEVNdydlcvtEFLRVVDMLLPEKSFYRLCPELHRQSRTPSGTLVRIQLLGQYPEWLAENA 81
Cdd:PRK10415 11 RLIAAPMAGITDRPFRTLCYEMG-------AGLTVSEMMSSNPQVWESDKSRLRMVHIDEPGIRTVQIAGSDPKEMADAA 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504697455 82 ARAVALGSYGVDLNCGCPSKLVNGSGGGATLLKDPELIYRGAKAMREAVpsHLPVTVKVRLGWDSGDKQ-FEIADAVQQA 160
Cdd:PRK10415 84 RINVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDLVKSILTEVVNAV--DVPVTLKIRTGWAPEHRNcVEIAQLAEDC 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504697455 161 GATELVVHGRTKEDGYKAErINWQAIGEIRKRLTIPVIANGEIWDYESAQACLKETGCNAVMIGRGALNVPNLSRVVKY- 239
Cdd:PRK10415 162 GIQALTIHGRTRACLFNGE-AEYDSIRAVKQKVSIPVIANGDITDPLKARAVLDYTGADALMIGRAAQGRPWIFREIQHy 240
|
250 260
....*....|....*....|....
gi 504697455 240 ---NE--PRMPWADVVTLLQKYSR 258
Cdd:PRK10415 241 ldtGEllPPLPLAEVKRLLCAHVR 264
|
|
| PRK11815 |
PRK11815 |
tRNA dihydrouridine(20/20a) synthase DusA; |
65-294 |
2.51e-22 |
|
tRNA dihydrouridine(20/20a) synthase DusA;
Pssm-ID: 236991 [Multi-domain] Cd Length: 333 Bit Score: 94.82 E-value: 2.51e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504697455 65 VRIQLLGQYPEWLAENAARAVALGSYGVDLNCGCPSKLVNgSGG-GATLLKDPELIYRGAKAMREAVPshLPVTVKVRLG 143
Cdd:PRK11815 67 VALQLGGSDPADLAEAAKLAEDWGYDEINLNVGCPSDRVQ-NGRfGACLMAEPELVADCVKAMKDAVS--IPVTVKHRIG 143
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504697455 144 WDSGD-----KQFeiADAVQQAGATELVVHGR--------TKEDgykaeRinwqaigEI--------------RKRLTIp 196
Cdd:PRK11815 144 IDDQDsyeflCDF--VDTVAEAGCDTFIVHARkawlkglsPKEN-----R-------EIppldydrvyrlkrdFPHLTI- 208
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504697455 197 VIaNGEIWDYESAQACLKEtgCNAVMIGRGALNVPNL-----SRVvkYNEPRMP--WADVVTLLQKYsrLEKQGDTG--L 267
Cdd:PRK11815 209 EI-NGGIKTLEEAKEHLQH--VDGVMIGRAAYHNPYLlaevdREL--FGEPAPPlsRSEVLEAMLPY--IERHLAQGgrL 281
|
250 260
....*....|....*....|....*..
gi 504697455 268 YHVARikqwlsylrkeysEALGLFQAI 294
Cdd:PRK11815 282 NHITR-------------HMLGLFQGL 295
|
|
| OYE_like_FMN_family |
cd02803 |
Old yellow enzyme (OYE)-like FMN binding domain. OYE was the first flavin-dependent enzyme ... |
124-233 |
7.32e-12 |
|
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: 64.90 E-value: 7.32e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504697455 124 KAMREAVPSHLPVTVkvRL-GWDSGDKQFEIADAVQ------QAGATELVV-------HGRTKEDGYKAERINWQAIGEI 189
Cdd:cd02803 199 AAVREAVGPDFPVGV--RLsADDFVPGGLTLEEAIEiakaleEAGVDALHVsggsyesPPPIIPPPYVPEGYFLELAEKI 276
|
90 100 110 120
....*....|....*....|....*....|....*....|....
gi 504697455 190 RKRLTIPVIANGEIWDYESAQACLKETGCNAVMIGRGALNVPNL 233
Cdd:cd02803 277 KKAVKIPVIAVGGIRDPEVAEEILAEGKADLVALGRALLADPDL 320
|
|
| FadH |
COG1902 |
2,4-dienoyl-CoA reductase or related NADH-dependent reductase, Old Yellow Enzyme (OYE) family ... |
124-228 |
1.04e-09 |
|
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: 58.64 E-value: 1.04e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504697455 124 KAMREAVPSHLPVTVK------VRLGWDSGDkQFEIADAVQQAGATEL-VVHGRTKEDG--YKAERINWQA--IGEIRKR 192
Cdd:COG1902 207 EAVRAAVGPDFPVGVRlsptdfVEGGLTLEE-SVELAKALEEAGVDYLhVSSGGYEPDAmiPTIVPEGYQLpfAARIRKA 285
|
90 100 110
....*....|....*....|....*....|....*.
gi 504697455 193 LTIPVIANGEIWDYESAQACLKETGCNAVMIGRGAL 228
Cdd:COG1902 286 VGIPVIAVGGITTPEQAEAALASGDADLVALGRPLL 321
|
|
| OYE_YqiM_FMN |
cd02932 |
Old yellow enzyme (OYE) YqjM-like FMN binding domain. YqjM is involved in the oxidative stress ... |
123-233 |
2.45e-09 |
|
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: 57.50 E-value: 2.45e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504697455 123 AKAMREAVPSHLPVTVkvRLG---WDSGDKQFE----IADAVQQAGAtELV------VHGRTK---EDGYK---AERInw 183
Cdd:cd02932 211 VDAVRAVWPEDKPLFV--RISatdWVEGGWDLEdsveLAKALKELGV-DLIdvssggNSPAQKipvGPGYQvpfAERI-- 285
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|
gi 504697455 184 qaigeiRKRLTIPVIANGEIWDYESAQACLKETGCNAVMIGRGALNVPNL 233
Cdd:cd02932 286 ------RQEAGIPVIAVGLITDPEQAEAILESGRADLVALGRELLRNPYW 329
|
|
| arch_FMN |
cd02911 |
Archeal FMN-binding domain. This family of archaeal proteins are part of the NAD(P)H-dependent ... |
78-238 |
1.38e-07 |
|
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: 51.56 E-value: 1.38e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504697455 78 AENAARAVALGSYGVDLNCGCPSKLVNGSGGGATLLKDPELIYRGAKAMREAvpsHLPVTVKVRLGWDSGDKqfEIADAV 157
Cdd:cd02911 87 LLNAAALVAKNAAILEINAHCRQPEMVEAGAGEALLKDPERLSEFIKALKET---GVPVSVKIRAGVDVDDE--ELARLI 161
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504697455 158 QQAGAteLVVHGRTKEDGYKAErinWQAIGEIRKRLTIpvIANGEIWDYESAQACLKeTGCNAVMIGRGALNvPNLSRVV 237
Cdd:cd02911 162 EKAGA--DIIHVDAMDPGNHAD---LKKIRDISTELFI--IGNNSVTTIESAKEMFS-YGADMVSVARASLP-ENIEWLV 232
|
.
gi 504697455 238 K 238
Cdd:cd02911 233 E 233
|
|
| DHOD_DHPD_FMN |
cd02810 |
Dihydroorotate dehydrogenase (DHOD) and Dihydropyrimidine dehydrogenase (DHPD) FMN-binding ... |
39-229 |
5.84e-07 |
|
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: 50.05 E-value: 5.84e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504697455 39 MLLPEKSFYRLCPE-LHRQSRTPSGTLVrIQLLGQYPEWLAENAARAVALGSYGVDLNCGCPsklvNGsGGGATLLKDPE 117
Cdd:cd02810 75 FGLPNLGLDVWLQDiAKAKKEFPGQPLI-ASVGGSSKEDYVELARKIERAGAKALELNLSCP----NV-GGGRQLGQDPE 148
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504697455 118 LIYRGAKAMREAVPshLPVTVKVRLGWDSGDKQfEIADAVQQAGATELVVHGRT------KED-------------GYKA 178
Cdd:cd02810 149 AVANLLKAVKAAVD--IPLLVKLSPYFDLEDIV-ELAKAAERAGADGLTAINTIsgrvvdLKTvgpgpkrgtgglsGAPI 225
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....*
gi 504697455 179 ERINWQAIGEIRKRL--TIPVIANGEIwdyESAQACLK--ETGCNAVMIGRGALN 229
Cdd:cd02810 226 RPLALRWVARLAARLqlDIPIIGVGGI---DSGEDVLEmlMAGASAVQVATALMW 277
|
|
| PyrD |
COG0167 |
Dihydroorotate dehydrogenase [Nucleotide transport and metabolism]; Dihydroorotate ... |
75-263 |
2.12e-06 |
|
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: 48.15 E-value: 2.12e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504697455 75 EWLAenAARAVAlgSYGVD---LNCGCPsklvNGSGGGATLLKDPELIYRGAKAMREAVpsHLPVTVKvrLGWDSGDKQf 151
Cdd:COG0167 106 DYVE--LARRLA--DAGADyleLNISCP----NTPGGGRALGQDPEALAELLAAVKAAT--DKPVLVK--LAPDLTDIV- 172
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504697455 152 EIADAVQQAGATELVVHGRTKE-----DGYKAERINWQA--------------IGEIRKRL--TIPVIANGEIWDYESAQ 210
Cdd:COG0167 173 EIARAAEEAGADGVIAINTTLGraidlETRRPVLANEAGglsgpalkpialrmVREVAQAVggDIPIIGVGGISTAEDAL 252
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|...
gi 504697455 211 ACLkETGCNAVMIGRGALnvpnlsrvvkYNEPRMPwADVVTLLQKYsrLEKQG 263
Cdd:COG0167 253 EFI-LAGASAVQVGTALF----------YEGPGLV-RRIIRGLEAY--LEEKG 291
|
|
| DHOD_1B_like |
cd04740 |
Dihydroorotate dehydrogenase (DHOD) class 1B FMN-binding domain. DHOD catalyzes the oxidation ... |
84-224 |
5.31e-05 |
|
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: 44.08 E-value: 5.31e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504697455 84 AVALGSYGVD---LNCGCPsklvNGSGGGATLLKDPELIYRGAKAMREAVPshLPVTVKvrLGWDSGDKQfEIADAVQQA 160
Cdd:cd04740 108 AEKLADAGADaieLNISCP----NVKGGGMAFGTDPEAVAEIVKAVKKATD--VPVIVK--LTPNVTDIV-EIARAAEEA 178
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504697455 161 GAtelvvhgrtkeDGY------KAERINWQ------------------------AIGEIRKRLTIPVIANGEIWDYESAQ 210
Cdd:cd04740 179 GA-----------DGLtlintlKGMAIDIEtrkpilgnvtgglsgpaikpialrMVYQVYKAVEIPIIGVGGIASGEDAL 247
|
170
....*....|....
gi 504697455 211 ACLkETGCNAVMIG 224
Cdd:cd04740 248 EFL-MAGASAVQVG 260
|
|
| His_biosynth |
pfam00977 |
Histidine biosynthesis protein; Proteins involved in steps 4 and 6 of the histidine ... |
113-225 |
6.34e-05 |
|
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: 43.24 E-value: 6.34e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504697455 113 LKDPELIyrgaKAMREAVPSHLPV--------TVKVRlGW--DSGDKQFEIADAVQQAGATELVVHGRTKeDGYKAErIN 182
Cdd:pfam00977 106 VKNPELI----KEAAEKFGSQCIVvaidarrgKVAIN-GWreDTGIDAVEWAKELEELGAGEILLTDIDR-DGTLSG-PD 178
|
90 100 110 120
....*....|....*....|....*....|....*....|...
gi 504697455 183 WQAIGEIRKRLTIPVIANGEIWDYESAQAcLKETGCNAVMIGR 225
Cdd:pfam00977 179 LELTRELAEAVNIPVIASGGVGSLEDLKE-LFTEGVDGVIAGS 220
|
|
| PRK07259 |
PRK07259 |
dihydroorotate dehydrogenase; |
91-166 |
5.93e-04 |
|
dihydroorotate dehydrogenase;
Pssm-ID: 235982 Cd Length: 301 Bit Score: 40.90 E-value: 5.93e-04
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 504697455 91 GVDLNCGCPsklvNGSGGGATLLKDPELIYRGAKAMREAVpsHLPVTVKvrLGWDSGDKQfEIADAVQQAGATELV 166
Cdd:PRK07259 121 AIELNISCP----NVKHGGMAFGTDPELAYEVVKAVKEVV--KVPVIVK--LTPNVTDIV-EIAKAAEEAGADGLS 187
|
|
| NanE |
cd04729 |
N-acetylmannosamine-6-phosphate epimerase (NanE) converts N-acetylmannosamine-6-phosphate to ... |
175-224 |
1.53e-03 |
|
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: 39.10 E-value: 1.53e-03
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*
gi 504697455 175 GYKAERIN-----WQAIGEIRKRLTIPVIANGEIWDYESAQACLkETGCNAVMIG 224
Cdd:cd04729 153 GYTEETAKtedpdFELLKELRKALGIPVIAEGRINSPEQAAKAL-ELGADAVVVG 206
|
|
| His_biosynth |
pfam00977 |
Histidine biosynthesis protein; Proteins involved in steps 4 and 6 of the histidine ... |
152-233 |
6.61e-03 |
|
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: 37.46 E-value: 6.61e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504697455 152 EIADAVQQAGATELVV-------HGRtkedgykaeRINWQAIGEIRKRLTIPVIANGEIWDYESAQACLkETGCNAVMIG 224
Cdd:pfam00977 33 ELAKRYEEEGADELHFvdldaakEGR---------PVNLDVVEEIAEEVFIPVQVGGGIRSLEDVERLL-SAGADRVIIG 102
|
....*....
gi 504697455 225 RGALNVPNL 233
Cdd:pfam00977 103 TAAVKNPEL 111
|
|
| |
