ViewGene
Locus Name:
GeneID:
Location:

GeneID:6913
TrivialName: PA14_69920
AnnotatorUID: danlee
Modification Date/Time:2006-04-06 13:01:23
LocusName:PA14_69920
PAO1 Ortholog Locus:
Sequence Length:1779
Protein Length:592
Start: 6238073
Stop: 6239850
Strand: +
Type:
ChromosomeID:2
Status: INACTIVE
Frame Discrepancy: TRUE
Missense Discrepancy:TRUE
Comments:
Inactivated 1/31/06. Replaced by PA14_69925 (GeneID 7374) which fuses PA14_69920 (GeneID 6913) and PA14_69930 (GeneID 6912). Homology: gb|AAG08682.1|AE004942_5 (AE004942) pyruvate dehydrogenase (cytochrome) [Pseudomonas aeruginosa PAO1]
Identities = 354/359 (98%), Positives = 358/359 (99%)
Sequence:
ATGTCGAGCAAGAAAGTCGCCGAGATCGTCGTGGAAACCCTGGAAGCCGCCGGCGTCCGCCATTGCTATGGC
ATCGTCGGCGACACCCTCAACCATGTCACCGACGCCATCCATCGCAGCCAGATCCAGTGGGTCCACGTGCGC
CACGAAGAGGCGGCGGCCTTCGCCGCGGGCGCCGAGTCCTACATCAGCGGACGCCTGACCGCCTGCGCCGGC
TCCTGCGGACCGGGCAGCCTGCACTTCATCAACGGCGTCTACGAGGCCCAGCGCAACCGCGCGCCGATGGTG
CTGATCGCCAGCCAGATCGTCACCCCGCAACTGGGCATGGAGTTTCCCCAGGAGGTCGACTTCAAGGCGGTC
TACGCCAGTTGCTCGGTGTTCTGCGAGCAGGTGCACAGCCCGGAACAGGCGCGCCGGGTGCTGGCCCTGGCC
TGCCAGGCGGCGCTCAACCGGCGCGGCGTGGCGGTGGTGATCCTGCCGGCCGACATCAGCCAGGCCACGGTG
AAGGACGACCTGCCGTTCTCGGTGCATTTCCCGCAACCGGTGCTGCGCCCCAGCGACGCCGAACTGCAGGAT
ATCGCCCGCCTGCTGGCCCACGGCAAGAAGATCGGCATCTACGCCGGCTCCGGCTGCCAGGGCGCCCACGAC
CTGCTGGTGGCCCTCGCCGACCGCCTCAAGGCGCCCATCGCGCACACGTCGCGGGCCAAGGACTTCGTCGAG
TACGACAACCCCTTCAACATGGGCATGACCGGTATGCTCGGGATCGAGTCCGGCTTCCACATGATGACCGAG
TGCGACACCCTCCTGCTGCTCGGCGCCGACTTCGCCTGGGCGCAGTTCTATCCGCAGAAGGCCACCCTGATC
CAGGTCGACCGCGACGGCAGCCACCTGGGTCGCCGCCACCCCGTCGATCTCGGCGTGGTCGGCGACGTGATC
CCCACCCTCGAGGCGCTCCTGCCGCTGCTCGAAGTCCGCGAGGAACGCAGCTTCCTCGACGAATGCCTGAAG
CACCGCGAGCGCTCGCTGCGGACGCTGGAAAAAGAGGAGCAAGCCGGCAAGGGCGAGCTGATCCACCCCcCA
GCACCTGGTCAGCCTGCTCGACCAGCACGCCAGCGAGGACGCCCTGTTCACCGCCGACGGCGGCTCGGCGAT
GGTCTGGCTGTTGCGTCACATCCACAGCAACGGCAAGCGCCGCACCCTCACCAGCCTGGTCCACGGCACCAT
GGCCAACGCCATGCCCCAGGCGCTGGGACTGAAGAAGGCCTACCCCGAGCGCCAGGTGATCTCGATCTCCGG
CGACGGCGGCCTGGCCATGCTGCTCGGCGACCTGCTGACGGCCATCCAGGAAAAACTGCCGATCAAGGTAGT
GGTGCTGAACAATGCCTCGCTGAACTTCGTCGAGCTGGAACAGAAGGTCGAGGGCCTGCTGGACAACTACAC
CGACCTGCTCAACCCGGACTTCGCCCGGCTCGCCGAGGTGATCGGCTTCCACGGACGCAAGGTGACGCGCTC
CGAGGATCTCGAGGCGGCGGTGCAGGAGTTCCTCGCCCAGCCCGGTCCGGCGCTGCTGGACGTGCATACCAA
CCCTGCGGAGCTGGTGATGCCGCCGAAGATCGAGTTCGGCCAGGTCGCCGACACCGCCCTCTACGCCGCCAA
GGCCGTGCTCAGCGGGCGCTTCAAGGACGTCGAGACGCTACTGGTGAACAACCTGCTGAAATGAGCCGGCAG
CGGCGCGGCCCGCCTGCCACGGGGCCGCGCCGGGCAGGCGCGGATTCCTGA
Translation:
MSSKKVAEIVVETLEAAGVRHCYGIVGDTLNHVTDAIHRSQIQWVHVRHEEAAAFAAGAESYISGRLTACAG
SCGPGSLHFINGVYEAQRNRAPMVLIASQIVTPQLGMEFPQEVDFKAVYASCSVFCEQVHSPEQARRVLALA
CQAALNRRGVAVVILPADISQATVKDDLPFSVHFPQPVLRPSDAELQDIARLLAHGKKIGIYAGSGCQGAHD
LLVALADRLKAPIAHTSRAKDFVEYDNPFNMGMTGMLGIESGFHMMTECDTLLLLGADFAWAQFYPQKATLI
QVDRDGSHLGRRHPVDLGVVGDVIPTLEALLPLLEVREERSFLDECLKHRERSLRTLEKEEQAGKGELIHPP
APGQPARPARQRGRPVHRRRRLGDGLAVASHPQQRQAPHPHQPGPRHHGQRHAPGAGTEEGLPRAPGDLDLR
RRRPGHAARRPADGHPGKTADQGSGAEQCLAELRRAGTEGRGPAGQLHRPAQPGLRPARRGDRLPRTQGDAL
RGSRGGGAGVPRPARSGAAGRAYQPCGAGDAAEDRVRPGRRHRPLRRQGRAQRALQGRRDATGEQPAEMSRQ
RRGPPATGPRRAGADS*
AnnotationID:6914GeneID:6913
AnnotatorUID: danlee
Modification Date/Time: 2006-01-31 18:06:54
Gene Name:
Confidence Code:4
GeneProduct:
Cell Localization:()
Synonyms:
Cell Localization Confidence Code:5
MolecularFunction:
Functional Category:()
Alternate Gene Product Name:
Functional Category Confidence Code:5
COGs:pfam02776,pfam00205
Secondary Functional Category(ies):central intermediary metabolism
EC Number:1.2.2.2
Status:INACTIVE
Pathway:






 
Homology:
>gb|AAO56017.1| (AE016864) pyruvate dehydrogenase [Pseudomonas syringae pv. tomato
           str. DC3000]
          Length = 572

 Score =  343 bits (881), Expect = 1e-93
 Identities = 171/367 (46%), Positives = 243/367 (66%), Gaps = 9/367 (2%)

>gb|AAM39525.1| (AE012116) pyruvate dehydrogenase [Xanthomonas campestris pv.
           campestris str. ATCC 33913]
          Length = 575

 Score =  339 bits (870), Expect = 3e-92
 Identities = 173/361 (47%), Positives = 242/361 (67%), Gaps = 7/361 (1%)

>gb|AAM35116.1| (AE011647) pyruvate dehydrogenase [Xanthomonas axonopodis pv. citri
           str. 306]
          Length = 575

 Score =  339 bits (869), Expect = 3e-92
 Identities = 170/369 (46%), Positives = 245/369 (66%), Gaps = 14/369 (3%)








 
Structural Features:
pfam02776, TPP_enzyme_N, Thiamine pyrophosphate enzyme, N-terminal TPP binding domain.
CD-Length = 171 residues,  97.1% aligned
Score =  133 bits (336), Expect = 6e-32
Identities = 49/166 (29%), Positives = 84/166 (50%), Gaps = 2/166 (1%)

pfam00205, TPP_enzyme_M, Thiamine pyrophosphate enzyme, central domain.
CD-Length = 154 residues,  98.7% aligned
Score =  107 bits (268), Expect = 4e-24
Identities = 51/153 (33%), Positives = 76/153 (49%), Gaps = 9/153 (5%)






   
Genomic Context:






   
Comment:
possible frameshift with gene #6912


















    ReferenceID:13522




  
Author/Investigator(s):
        GenNotator





  
Title:
        




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:BLASTP 







    
Data:


    		




 
URL:

















    ReferenceID:30905




  
Author/Investigator(s):
        GenNotator





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:RPSBLAST 







    
Data:


    		




 
URL:

















    ReferenceID:34799




  
Author/Investigator(s):
        





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:Misc (text/plain)







    
Data:6913_cdd.html


    		




 
URL:









           
Homologs By Global Alignment 

           

       



     
Gene ID:6913
           
Identity:

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

                           

     
HomologID
                           Accession
                           Description
                           Length
                           PctIdentity
                           PctSimilarity
                           Gaps
                           Score
     

     
     
8052
                           PA5297_tr
                           translation of PA5297
                           657
                           59.36
                           63.62
                           150
                           1808.0
     

     
     
203009
                           gb|AAG08682.1|AE004942_5
                           (AE004942) pyruvate dehydrogenase (cytochrome) [Pseudomonas aeruginosa PAO1]
                           657
                           59.36
                           63.62
                           150
                           1808.0
     

     
     
203012
                           gb|AAM39525.1|
                           (AE012116) pyruvate dehydrogenase [Xanthomonas campestris pv. campestris str. ATCC 33913]
                           680
                           32.64
                           44.70
                           193
                           880.0
     

     
     
203013
                           gb|AAM35116.1|
                           (AE011647) pyruvate dehydrogenase [Xanthomonas axonopodis pv. citri str. 306]
                           676
                           32.24
                           45.26
                           185
                           888.0
     

     
     
203036
                           emb|CAA22389.1|
                           (AL939126) pyruvate dehydrogenase [Streptomyces coelicolor A3(2)]
                           671
                           30.99
                           43.66
                           170
                           800.0
     

     






      

          
GC ORFID: 49915How Found: Glimmer

          
GC_TrimmedSeqID: 69Blast Result ID

          
Subject Sequence Name: Glimmer Score: 

          
Start: 5501761Stop: 5503539

          
Length: 1779


          
Start Codon: ATGTruncated Start:

          
Stop Codon: TGATruncated Stop: 

          
Homolog: t_PA5297 translation of PA5297Homolog Bit Score 715.0

          
Other Homologs:  t_PA5297 translation of PA5297 (BLASTP 715), psyr_15may02_Scaffold1_revised_gene1280 related to: gi|16121638|ref|NP_404951.1| (NC_003143) pyruvate dehydrogenase [cytochrome] [Yersinia pestis] emb|CAC90187.1| (AJ414147) pyruvate dehydrogenase [cytochrome] [Yersinia pestis] (BLASTP 342)

          
GC ORF Sequence

           
ATGTCGAGCAAGAAAGTCGCCGAGATCGTCGTGGAAACCCTGGAAGCCGCCGGCGTCCGCCATTGCTATGGC 
ATCGTCGGCGACACCCTCAACCATGTCACCGACGCCATCCATCGCAGCCAGATCCAGTGGGTCCACGTGCGC 
CACGAAGAGGCGGCGGCCTTCGCCGCGGGCGCCGAGTCCTACATCAGCGGACGCCTGACCGCCTGCGCCGGC 
TCCTGCGGACCGGGCAGCCTGCACTTCATCAACGGCGTCTACGAGGCCCAGCGCAACCGCGCGCCGATGGTG 
CTGATCGCCAGCCAGATCGTCACCCCGCAACTGGGCATGGAGTTTCCCCAGGAGGTCGACTTCAAGGCGGTC 
TACGCCAGTTGCTCGGTGTTCTGCGAGCAGGTGCACAGCCCGGAACAGGCGCGCCGGGTGCTGGCCCTGGCC 
TGCCAGGCGGCGCTCAACCGGCGCGGCGTGGCGGTGGTGATCCTGCCGGCCGACATCAGCCAGGCCACGGTG 
AAGGACGACCTGCCGTTCTCGGTGCATTTCCCGCAACCGGTGCTGCGCCCCAGCGACGCCGAACTGCAGGAT 
ATCGCCCGCCTGCTGGCCCACGGCAAGAAGATCGGCATCTACGCCGGCTCCGGCTGCCAGGGCGCCCACGAC 
CTGCTGGTGGCCCTCGCCGACCGCCTCAAGGCGCCCATCGCGCACACGTCGCGGGCCAAGGACTTCGTCGAG 
TACGACAACCCCTTCAACATGGGCATGACCGGTATGCTCGGGATCGAGTCCGGCTTCCACATGATGACCGAG 
TGCGACACCCTCCTGCTGCTCGGCGCCGACTTCGCCTGGGCGCAGTTCTATCCGCAGAAGGCCACCCTGATC 
CAGGTCGACCGCGACGGCAGCCACCTGGGTCGCCGCCACCCCGTCGATCTCGGCGTGGTCGGCGACGTGATC 
CCCACCCTCGAGGCGCTCCTGCCGCTGCTCGAAGTCCGCGAGGAACGCAGCTTCCTCGACGAATGCCTGAAG 
CACCGCGAGCGCTCGCTGCGGACGCTGGAAAAAGAGGAGCAAGCCGGCAAGGGCGAGCTGATCCACCCCcCA 
GCACCTGGTCAGCCTGCTCGACCAGCACGCCAGCGAGGACGCCCTGTTCACCGCCGACGGCGGCTCGGCGAT 
GGTCTGGCTGTTGCGTCACATCCACAGCAACGGCAAGCGCCGCACCCTCACCAGCCTGGTCCACGGCACCAT 
GGCCAACGCCATGCCCCAGGCGCTGGGACTGAAGAAGGCCTACCCCGAGCGCCAGGTGATCTCGATCTCCGG 
CGACGGCGGCCTGGCCATGCTGCTCGGCGACCTGCTGACGGCCATCCAGGAAAAACTGCCGATCAAGGTAGT 
GGTGCTGAACAATGCCTCGCTGAACTTCGTCGAGCTGGAACAGAAGGTCGAGGGCCTGCTGGACAACTACAC 
CGACCTGCTCAACCCGGACTTCGCCCGGCTCGCCGAGGTGATCGGCTTCCACGGACGCAAGGTGACGCGCTC 
CGAGGATCTCGAGGCGGCGGTGCAGGAGTTCCTCGCCCAGCCCGGTCCGGCGCTGCTGGACGTGCATACCAA 
CCCTGCGGAGCTGGTGATGCCGCCGAAGATCGAGTTCGGCCAGGTCGCCGACACCGCCCTCTACGCCGCCAA 
GGCCGTGCTCAGCGGGCGCTTCAAGGACGTCGAGACGCTACTGGTGAACAACCTGCTGAAATGAGCCGGCAG 
CGGCGCGGCCCGCCTGCCACGGGGCCGCGCCGGGCAGGCGCGGATTCCTGA