Conserved Protein Domain Family
yjbN

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TIGR00742: yjbN 
tRNA dihydrouridine synthase A
This model represents one branch of COG0042 (Predicted TIM-barrel enzymes, possibly dehydrogenases, nifR3 family). It represents a distinct subset by a set of shared unique motifs, a conserved pattern of insertions/deletions relative to other nifR3 homologs, and by subclustering based on cross-genome bidirectional best hits. Members are found in species as diverse as the proteobacteria, a spirochete, a cyanobacterium, and Deinococcus radiodurans. NifR3 itself, a protein of unknown function associated with nitrogen regulation in Rhodobacter capsulatus, is not a member of this branch. Members of this family show a distant relationship to alpha/beta (TIM) barrel enzymes such as dihydroorotate dehydrogenase and glycolate oxidase. [Protein synthesis, tRNA and rRNA base modification]
Statistics
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PSSM-Id: 129825
View PSSM: TIGR00742
Aligned: 4 rows
Threshold Bit Score: 531.321
Threshold Setting Gi: 224533852
Created: 7-Oct-2014
Updated: 23-Jan-2015
Structure
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Aligned Rows:
PubMed ReferencesClick to see Conserved Features Help

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2829606    11 NPLSVAPMMDHTDRHFRYFLRQLTRHTLLYTEMITAQAILHGdRQRLLNFSPEEKPVALQLGGDDPQLLAECARIGQD-W 89
gi 1176344    11 GRFSVAPMLDWTTRHCRYFHRQFSKHALLYTEMVTAPAIIHA-KYDHLDFDLQENPVALQLGGSDPEQLKYCAKLAEE-R 88
gi 485666227  11 GRFSVAPMLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPAALAQCAKLAEA-R 88
gi 488741562   3 RKISIAPMVNITDEHFRYLIRLLSKKVTLYTPMISAKSIIMGdVKKIVKQNPLESPIAIQIATNSKNDALKAIQILEKhF 82
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2829606    90 GYDEINLNVGCPSDRVQSGNFGACLMAQPDLVAQCVSAMQKAVEIPVTVKHRIGIDHR------DSYEDLVHFVEIVANA 163
gi 1176344    89 GYHEINLNVGCPSDRVQNGMFGACLMAKADLVADCVEQMQSAVKIPVTVKTRIGIDEL------DSYEFLCDFIEKVQGK 162
gi 485666227  89 GYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVTVKTRIGIDDQ------DSYEFLCDFINTVSGK 162
gi 488741562  83 NFDEYNLNVGCPSLKIQNANCGACLMGNANQVGEILKTMKENTNKPISIKHRLGIRPLssdyknESYSEVKNFVKIISDF 162
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2829606   164 G-CQRFTVHARKAWLQGLSPKENRTIPPLRYEDVYQLKKDFPQLLIEINGGITQTEQIQQHLSHVDAVMVGRAAYENPYL 242
gi 1176344   163 G-CQEFIIHARKAWLSGLSPKENREIPPLDYIRVYQLKRDFPHLTIAINGGIKTIEEMKQHLQYVDGVMVGREAYQNPSL 241
gi 485666227 163 GeCEMFIIHARKAWLSGLSPKENREIPPLDYPRVYQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGI 242
gi 488741562 163 G-IKNFIVHARIAILKGFSPKNNRNIPKLRHEFVYKLKKENKNLFIEINGGINNSEQIKKHLSFVDSVMIGRSAFENPYF 241
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2829606   243 FATVDRDIYHKTNLVPSRAEIIERMLPYVEERLRHGDRLNQITRHLLSLFNGQPRAKFWRRTLSDSTLLASAGPELLQTA 322
gi 1176344   242 LGQIDQALFDPNAPIVTAHEAVESMLPYIEQQLSQGIHLNHIVRHILGAFQNCKGARQWRRYLSENAFKQGAGIEVVETA 321
gi 485666227 243 LAAVDREIFGSSDTDADPVAVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLSENAHKAGADINVLEHA 322
gi 488741562 242 IANASREFLNETDEILTRKDILMQMVEYIKEYEN-YLSINILFKHLMGIVFSKEGAKKFRQNLTAPFPKNLKKHEILLKA 320

                 ....*.
gi 2829606   323 LQAQKF 328
gi 1176344   322 LSFVES 327
gi 485666227 323 LKLVAD 328
gi 488741562 321 IETLPE 326
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