ViewGene
Locus Name:
GeneID:
Location:

GeneID:2131
TrivialName: PA14_64180
AnnotatorUID:
Modification Date/Time:2006-04-06 13:01:23
LocusName:PA14_64180
PAO1 Ortholog Locus:PA4852
Sequence Length:999
Protein Length:332
Start: 5718313
Stop: 5719311
Strand: +
Type:
ChromosomeID:2
Status: ACTIVE
Frame Discrepancy: FALSE
Missense Discrepancy:FALSE
Comments:
Homology: gb|AAG08237.1|AE004898_8 (AE004898) conserved hypothetical protein [Pseudomonas aeruginosa PAO1]
Identities = 330/332 (99%), Positives = 332/332 (100%)
Sequence:
ATGTCGGTGGTACGCATCGGCCCATATACACTGCCCAACAGACTGATCCTCGCGCCGATGGCCGGGGTGACC
GATCGTCCGTTCCGTCAGCTTTGCCGTCGCCTTGGCGCCGGGATGGTGGTATCGGAGATGGTGACCAGCGAC
GTCCGCCTGTGGAACAGCCGCAAGTCGCGCCTGCGCCTGATCCACGATGGCGAGGACGAGCCGCGCTCGGTG
CAGATCGCCGGCGGCGATCCGGCCATGCTGGCCGAGGCCGCTCAGCGCAATGTGGAACTCGGTGCGCAGATC
ATCGACATCAACATGGGCTGCCCGGCGAAGAAGGTATGCAACAAGGCAGCGGGGTCCGCCCTGCTGCGGGAC
GAGGCGCTGGTCGCCGAGATCCTCGATGCCGTGGTCAGGGCGGTCGACGTACCGGTCACCCTGAAGATCCGG
ACCGGCTGGGACCGGGACAACCGTAACGGCGTCAGCGTCGCGAGGCTCGCCGAACAGGCGGGGATCCAGGCT
CTTGCGGTACATGGCCGGACCCGCGCCGACCTGTACACCGGGGAGGCGGAGTACGAGACCATCGCGGCGATC
AAGCAGGCCGTGTCGATACCGGTGTTCGCCAATGGCGACATCGATTCGCCGGAGAAGGCCAGGAAAGTCATC
GAGCAGACCGGGGTGGATGCCCTGCTGATCGGTCGGGCCGCCCAGGGAAGACCGTGGATTTTCCGCGAGATC
GACCATTACCTGCGGACCGGCGAGCACCTGCCGGCGGCGCCGCTTCCCGAAGTGCAGAGCATCCTGCTCGAA
CACCTCGCGGAGCTGCACCTTTTTTATGGGGAAGAAATGGGTGTGCGGATCGCCCGCAAGCATGTGGGGTGG
TATCTCGCGACTCTGCCGGGCGCAAGGGAATTCCGCGCCCAGTTCAATCGTTTGCAGGACACGGATGCGCAG
TGCGCCAGCGTCAGGCAGTTCTTCGCCGAGCGCCAGAACAACGGAACAGGGGTGGCCGCATGA
Translation:
MSVVRIGPYTLPNRLILAPMAGVTDRPFRQLCRRLGAGMVVSEMVTSDVRLWNSRKSRLRLIHDGEDEPRSV
QIAGGDPAMLAEAAQRNVELGAQIIDINMGCPAKKVCNKAAGSALLRDEALVAEILDAVVRAVDVPVTLKIR
TGWDRDNRNGVSVARLAEQAGIQALAVHGRTRADLYTGEAEYETIAAIKQAVSIPVFANGDIDSPEKARKVI
EQTGVDALLIGRAAQGRPWIFREIDHYLRTGEHLPAAPLPEVQSILLEHLAELHLFYGEEMGVRIARKHVGW
YLATLPGAREFRAQFNRLQDTDAQCASVRQFFAERQNNGTGVAA*
AnnotationID:2139GeneID:2131
AnnotatorUID: diggins
Modification Date/Time: 2005-03-11 09:09:07
Gene Name:
Confidence Code:3
GeneProduct:putative tRNA-dihydrouridine synthase
Cell Localization:()
Synonyms:yhdG
Cell Localization Confidence Code:5
MolecularFunction:
Functional Category:(26) Translation, post-translational modification, degradation
Alternate Gene Product Name:putative TIM-barrel protein
Functional Category Confidence Code:5
COGs:pfam01207,COG0042
Secondary Functional Category(ies):translation, ribosomal structure and biogenesis
EC Number:
Status:ACTIVE
Pathway:






 
Homology:
>gb|AAO58293.1| (AE016873) TIM-barrel protein, putative, NifR3 family [Pseudomonas
           syringae pv. tomato str. DC3000]
          Length = 337

 Score =  532 bits (1371), Expect = e-150
 Identities = 264/322 (81%), Positives = 294/322 (91%)

>gb|AAN70389.1|AE016680_9 (AE016792) TIM-barrel protein, putative, NifR3 family [Pseudomonas
           putida KT2440]
          Length = 337

 Score =  532 bits (1371), Expect = e-150
 Identities = 270/337 (80%), Positives = 296/337 (87%), Gaps = 5/337 (1%)

>emb|CAD84785.1| (BX321859) Predicted TIM-barrel enzymes, possibly dehydrogenases,
           nifR3 family [Nitrosomonas europaea ATCC 19718]
          Length = 337

 Score =  423 bits (1088), Expect = e-118
 Identities = 205/324 (63%), Positives = 255/324 (78%)








 
Structural Features:
pfam01207, Dus, Dihydrouridine synthase (Dus).
CD-Length = 309 residues, 100.0% aligned
Score =  348 bits (893), Expect = 8e-97
Identities = 160/310 (51%), Positives = 206/310 (66%), Gaps = 1/310 (0%)

COG0042, COG0042, tRNA-dihydrouridine synthase 
[Translation, ribosomal structure and biogenesis]
CD-Length = 323 residues,  98.5% aligned
Score =  345 bits (886), Expect = 5e-96
Identities = 162/321 (50%), Positives = 212/321 (66%), Gaps = 6/321 (1%)






   
Genomic Context:






   
Comment:


















    ReferenceID:4265




  
Author/Investigator(s):
        GenNotator





  
Title:
        




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:BLASTP 







    
Data:


    		




 
URL:

















    ReferenceID:21411




  
Author/Investigator(s):
        GenNotator





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:RPSBLAST 







    
Data:


    		




 
URL:

















    ReferenceID:35200




  
Author/Investigator(s):
        





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:Misc (text/plain)







    
Data:2131_cdd.html


    		




 
URL:









           
Homologs By Global Alignment 

           

       



     
Gene ID:2131
           
Identity:

                               
                                   0%
                               
                                   10%
                               
                                   20%
                               
                                   30%
                               
                                   40%
                               
                                   50%
                               
                                   60%
                               
                                   70%
                               
                                   80%
                               
                                   90%
                               
                                   100%
                               
                             

                           

     
HomologID
                           Accession
                           Description
                           Length
                           PctIdentity
                           PctSimilarity
                           Gaps
                           Score
     

     
     
3641
                           PA4852_tr
                           translation of PA4852
                           332
                           99.39
                           99.99
                           0
                           1685.0
     

     
     
112033
                           gb|AAG08237.1|AE004898_8
                           (AE004898) conserved hypothetical protein [Pseudomonas aeruginosa PAO1]
                           332
                           99.39
                           99.99
                           0
                           1685.0
     

     
     
112035
                           gb|AAN70389.1|AE016680_9
                           (AE016792) TIM-barrel protein, putative, NifR3 family [Pseudomonas putida KT2440]
                           337
                           80.11
                           87.83
                           5
                           1375.0
     

     
     
112034
                           gb|AAO58293.1|
                           (AE016873) TIM-barrel protein, putative, NifR3 family [Pseudomonas syringae pv. tomato str. DC3000]
                           337
                           79.52
                           88.42
                           5
                           1371.0
     

     
     
112042
                           gb|AAM40078.1|
                           (AE012176) conserved hypothetical protein [Xanthomonas campestris pv. campestris str. ATCC 33913]
                           342
                           60.52
                           71.34
                           20
                           1038.0
     

     






      

          
GC ORFID: 45133How Found: BLASTX

          
GC_TrimmedSeqID: 69Blast Result ID

          
Subject Sequence Name: t_PA4852Glimmer Score: 

          
Start: 4981993Stop: 4982991

          
Length: 999


          
Start Codon: ATGTruncated Start:

          
Stop Codon: TGATruncated Stop: 

          
Homolog: t_PA4852 translation of PA4852Homolog Bit Score 653.0

          
Other Homologs:  psyr_15may02_Scaffold4_revised_gene5774 (ORF: BLASTX 538.0), t_PA4852 (ORF: GLIMMER)

          
GC ORF Sequence

           
ATGTCGGTGGTACGCATCGGCCCATATACACTGCCCAACAGACTGATCCTCGCGCCGATGGCCGGGGTGACC 
GATCGTCCGTTCCGTCAGCTTTGCCGTCGCCTTGGCGCCGGGATGGTGGTATCGGAGATGGTGACCAGCGAC 
GTCCGCCTGTGGAACAGCCGCAAGTCGCGCCTGCGCCTGATCCACGATGGCGAGGACGAGCCGCGCTCGGTG 
CAGATCGCCGGCGGCGATCCGGCCATGCTGGCCGAGGCCGCTCAGCGCAATGTGGAACTCGGTGCGCAGATC 
ATCGACATCAACATGGGCTGCCCGGCGAAGAAGGTATGCAACAAGGCAGCGGGGTCCGCCCTGCTGCGGGAC 
GAGGCGCTGGTCGCCGAGATCCTCGATGCCGTGGTCAGGGCGGTCGACGTACCGGTCACCCTGAAGATCCGG 
ACCGGCTGGGACCGGGACAACCGTAACGGCGTCAGCGTCGCGAGGCTCGCCGAACAGGCGGGGATCCAGGCT 
CTTGCGGTACATGGCCGGACCCGCGCCGACCTGTACACCGGGGAGGCGGAGTACGAGACCATCGCGGCGATC 
AAGCAGGCCGTGTCGATACCGGTGTTCGCCAATGGCGACATCGATTCGCCGGAGAAGGCCAGGAAAGTCATC 
GAGCAGACCGGGGTGGATGCCCTGCTGATCGGTCGGGCCGCCCAGGGAAGACCGTGGATTTTCCGCGAGATC 
GACCATTACCTGCGGACCGGCGAGCACCTGCCGGCGGCGCCGCTTCCCGAAGTGCAGAGCATCCTGCTCGAA 
CACCTCGCGGAGCTGCACCTTTTTTATGGGGAAGAAATGGGTGTGCGGATCGCCCGCAAGCATGTGGGGTGG 
TATCTCGCGACTCTGCCGGGCGCAAGGGAATTCCGCGCCCAGTTCAATCGTTTGCAGGACACGGATGCGCAG 
TGCGCCAGCGTCAGGCAGTTCTTCGCCGAGCGCCAGAACAACGGAACAGGGGTGGCCGCATGA