ViewGene
Locus Name:
GeneID:
Location:

GeneID:485
TrivialName: PA14_07520
AnnotatorUID:
Modification Date/Time:2006-04-06 13:01:23
LocusName:PA14_07520
PAO1 Ortholog Locus:PA0576
Sequence Length:1854
Protein Length:617
Start: 649044
Stop: 647191
Strand: -
Type:
ChromosomeID:2
Status: ACTIVE
Frame Discrepancy: FALSE
Missense Discrepancy:FALSE
Comments:
Homology: gb|AAP13091.1| (AY254392) RpoD [Pseudomonas sp. M18]
Identities = 617/617 (100%), Positives = 617/617 (100%)
Sequence:
ATGTCCGGAAAAGCGCAACAGCAATCTCGTCTGAAAGAGTTGATCGCCCGAGGCCGTGAGCAGGGATACCTG
ACTTACGCGGAGGTCAACGACCACCTGCCGGAGGATATTTCCGATCCGGAACAGGTGGAAGACATCATCCGC
ATGATCAACGACATGGGGATCAACGTATTCGAGACAGCCCCGGATGCGGATGCCCTGTTGCTGGCCGAGGCG
GATACCGACGAAGCCGCAGCGGAAGAAGCCGCAGCGGCCCTGGCCGCGGTGGAAAGCGACATCGGTCGCACC
ACCGACCCGGTGCGCATGTACATGCGTGAAATGGGTACCGTGGAACTGCTGACCCGCGAAGGCGAGATCGAA
ATCGCCAAGCGCATCGAGGAAGGCATCCGCGAAGTGATGAGCGCCATCGCCCAGTTCCCGGGCACGGTGGAC
AGCATCCTGGCCGACTACAATCGCATCGTCGCCGAAGGCGGTCGCCTCTCCGACGTCCTCAGCGGCTATATC
GATCCCGATGACGGCAGCCTGCCCGCCGAAGAGGTGGAGCCGGTCAACCTGAAGGACGATTCCGCCGACTCG
AAAGAGAAGGACGACGAGGAAGAAGAAAGCGACGACAGCAGCGACAGCGACGACGAAGGCGACGGCGGTCCG
GATCCGGAAGAAGCCCGCCTGCGTTTCACCGCGGTCTCCGAGCAGCTCGACAAGGCCAAGAAGGCCCTGAAG
AAGCACGGTCGCGGCAGCAAGCAGGCCACCGCCGAACTCACCGGCTTGGCCGAGCTGTTCATGCCGATCAAG
CTGGTGCCCAAGCAGTTCGACGCCCTGGTCGCCCGCGTGCGCTCCGCCCTGGAAGGCGTACGCGCCCAGGAA
CGCGCCATCATGCAACTCTGCGTGCGTGACGCGCGCATGCCGCGTGCCGACTTCCTGCGCCTGTTCCCGAAC
CACGAGACCGACGAGAAGTGGGTCGACAGCGTCCTGAAGAGCAAGCCGAAGTACGCCGAGGCCATCGAGCGC
CTGCGCGACGACATCCTGCGCAACCAGCAGAAGCTGGCGGCCCTGGAAAGCGAGGTCGAGCTGACCGTCGCC
GAGATCAAGGAAATCAACCGCGCGATGTCGATCGGCGAAGCCAAGGCTCGCCGGGCGAAGAAGGAAATGGTC
GAGGCCAACCTGCGCCTGGTGATTTCCATCGCCAAGAAGTACACCAACCGCGGCCTGCAATTCCTCGACCTG
ATCCAGGAAGGCAACATCGGCCTGATGAAGGCGGTGGACAAGTTCGAATACCGTCGTGGCTACAAATTCTCT
ACCTACGCCACCTGGTGGATTCGCCAGGCGATCACCCGTTCGATCGCCGACCAGGCACGCACCATCCGCATC
CCGGTGCACATGATCGAGACGATCAACAAGCTCAACCGCATCTCCCGCCAGATGCTCCAGGAAATGGGTCGC
GAGCCCACCCCGGAAGAGCTTGGCGAGCGCATGGACATGCCTGAGGACAAGATCCGCAAGGTACTGAAGATC
GCCAAAGAGCCGATCTCCATGGAAACCCCGATCGGTGACGACGAAGATTCGCACCTGGGCGATTTCATCGAG
GACTCCACCATGCAGTCGCCGATCGAGATGGCGACCAGCGAGAGCCTCAAGGAATCCACCCGCGAAGTCCTC
GCCGGCCTCACTGCCCGGGAAGCCAAGGTGCTGCGCATGCGCTTCGGCATCGACATGAACACCGACCACACC
CTCGAGGAAGTCGGCAAGCAGTTCGATGTGACCCGCGAGCGGATCCGCCAGATCGAAGCCAAGGCGTTGCGC
AAGCTGCGCCATCCGTCGCGAAGCGAGCACCTGCGCTCCTTCCTCGACGAGTGA
Translation:
MSGKAQQQSRLKELIARGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFETAPDADALLLAEA
DTDEAAAEEAAAALAAVESDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGIREVMSAIAQFPGTVD
SILADYNRIVAEGGRLSDVLSGYIDPDDGSLPAEEVEPVNLKDDSADSKEKDDEEEESDDSSDSDDEGDGGP
DPEEARLRFTAVSEQLDKAKKALKKHGRGSKQATAELTGLAELFMPIKLVPKQFDALVARVRSALEGVRAQE
RAIMQLCVRDARMPRADFLRLFPNHETDEKWVDSVLKSKPKYAEAIERLRDDILRNQQKLAALESEVELTVA
EIKEINRAMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS
TYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMDMPEDKIRKVLKI
AKEPISMETPIGDDEDSHLGDFIEDSTMQSPIEMATSESLKESTREVLAGLTAREAKVLRMRFGIDMNTDHT
LEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEHLRSFLDE*
AnnotationID:494GeneID:485
AnnotatorUID: diggins
Modification Date/Time: 2005-03-29 08:08:15
Gene Name:rpoD
Confidence Code:1
GeneProduct:sigma factor RpoD
Cell Localization:()
Synonyms:
Cell Localization Confidence Code:5
MolecularFunction:
Functional Category:(24) Transcription, RNA processing and degradation
Alternate Gene Product Name:RNA polymerase sigma-70 factor
Functional Category Confidence Code:5
COGs:COG0568,pfam04546
Secondary Functional Category(ies):transcriptional regulator
EC Number:2.7.7.6
Status:ACTIVE
Pathway:






 
Homology:
>emb|CAA07705.1| (AJ007830) sigma-70 factor [Pseudomonas tolaasii]
          Length = 616

 Score = 1002 bits (2591), Expect = 0.0
 Identities = 519/619 (83%), Positives = 558/619 (90%), Gaps = 5/619 (0%)

>gb|AAN54351.1|AE015572_6 (AE015572) RNA polymerase sigma-70 factor [Shewanella oneidensis
           MR-1]
          Length = 616

 Score =  824 bits (2129), Expect = 0.0
 Identities = 419/611 (68%), Positives = 499/611 (81%), Gaps = 1/611 (0%)

>gb|AAM87085.1|AE013956_10 (AE013956) RNA polymerase, sigma(70) factor [Yersinia pestis KIM]
          Length = 632

 Score =  813 bits (2099), Expect = 0.0
 Identities = 417/612 (68%), Positives = 499/612 (81%), Gaps = 7/612 (1%)






 
Structural Features:
COG0568, RpoD, DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) 
[Transcription]
CD-Length = 342 residues, 100.0% aligned
Score =  356 bits (914), Expect = 5e-99
Identities = 183/359 (50%), Positives = 233/359 (64%), Gaps = 19/359 (5%)

pfam04546, Sigma70_ner, Sigma-70, non-essential region. 
CD-Length = 218 residues, 100.0% aligned
Score =  269 bits (688), Expect = 8e-73
Identities = 128/218 (58%), Positives = 160/218 (73%), Gaps = 4/218 (1%)







   
Genomic Context:






   
Comment:


















    ReferenceID:973




  
Author/Investigator(s):
        GenNotator





  
Title:
        




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:BLASTP 







    
Data:


    		




 
URL:

















    ReferenceID:18115




  
Author/Investigator(s):
        GenNotator





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:RPSBLAST 







    
Data:


    		




 
URL:

















    ReferenceID:33868




  
Author/Investigator(s):
        





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:Misc (text/plain)







    
Data:485_cdd.html


    		




 
URL:

















    ReferenceID:35282




  
Author/Investigator(s):
        Tanaka K, Takahashi H.





  
Title:
        Cloning and analysis of the gene (rpoDA) for the principal sigma factor of Pseudomonas aeruginosa.




  
PubMed:
        1902749


MedLine:
        




    
Source:
Biochim Biophys Acta. 1991 May 2;1089(1):113-9.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=1902749

















    ReferenceID:35283




  
Author/Investigator(s):
        Tseng YS, Yu CT, Tseng YH, Yang MT.





  
Title:
        Cloning, sequencing, and expression of the rpoD gene encoding the primary sigma factor of Xanthomonas campestris.




  
PubMed:
        9126341


MedLine:
        




    
Source:
Biochem Biophys Res Commun. 1997 Mar 27;232(3):712-8.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=9126341









           
Homologs By Global Alignment 

           

       



     
Gene ID:485
           
Identity:

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

                           

     
HomologID
                           Accession
                           Description
                           Length
                           PctIdentity
                           PctSimilarity
                           Gaps
                           Score
     

     
     
849
                           PA0576_tr
                           translation of PA0576
                           617
                           99.99
                           99.99
                           0
                           3084.0
     

     
     
34722
                           gb|AAP13091.1|
                           (AY254392) RpoD [Pseudomonas sp. M18]
                           617
                           99.99
                           99.99
                           0
                           3084.0
     

     
     
34723
                           gb|AAG03965.1|AE004494_1
                           (AE004494) sigma factor RpoD [Pseudomonas aeruginosa PAO1]
                           617
                           99.99
                           99.99
                           0
                           3084.0
     

     
     
34724
                           dbj|BAA14146.1|
                           (D90118) principal sigma factor [Pseudomonas aeruginosa]
                           617
                           99.99
                           99.99
                           0
                           3084.0
     

     
     
34728
                           gb|AAO54079.1|
                           (AE016857) RNA polymerase sigma-70 factor [Pseudomonas syringae pv. tomato str. DC3000]
                           618
                           84.46
                           89.64
                           3
                           2588.0
     

     






      

          
GC ORFID: 43487How Found: BLASTX

          
GC_TrimmedSeqID: 69Blast Result ID

          
Subject Sequence Name: t_PA0576Glimmer Score: 

          
Start: 6450387Stop: 6448534

          
Length: 1854


          
Start Codon: ATGTruncated Start:

          
Stop Codon: TGATruncated Stop: 

          
Homolog: t_PA0576 translation of PA0576Homolog Bit Score 1192.0

          
Other Homologs:  psyr_15may02_Scaffold6_revised_gene6771 (ORF: BLASTX 996.0), t_PA3622 (ORF: BLASTX 211.0), psyr_15may02_Scaffold3_revised_gene4653 (ORF: BLASTX 209.0), t_PA0576 (ORF: GLIMMER)

          
GC ORF Sequence

           
ATGTCCGGAAAAGCGCAACAGCAATCTCGTCTGAAAGAGTTGATCGCCCGAGGCCGTGAGCAGGGATACCTG 
ACTTACGCGGAGGTCAACGACCACCTGCCGGAGGATATTTCCGATCCGGAACAGGTGGAAGACATCATCCGC 
ATGATCAACGACATGGGGATCAACGTATTCGAGACAGCCCCGGATGCGGATGCCCTGTTGCTGGCCGAGGCG 
GATACCGACGAAGCCGCAGCGGAAGAAGCCGCAGCGGCCCTGGCCGCGGTGGAAAGCGACATCGGTCGCACC 
ACCGACCCGGTGCGCATGTACATGCGTGAAATGGGTACCGTGGAACTGCTGACCCGCGAAGGCGAGATCGAA 
ATCGCCAAGCGCATCGAGGAAGGCATCCGCGAAGTGATGAGCGCCATCGCCCAGTTCCCGGGCACGGTGGAC 
AGCATCCTGGCCGACTACAATCGCATCGTCGCCGAAGGCGGTCGCCTCTCCGACGTCCTCAGCGGCTATATC 
GATCCCGATGACGGCAGCCTGCCCGCCGAAGAGGTGGAGCCGGTCAACCTGAAGGACGATTCCGCCGACTCG 
AAAGAGAAGGACGACGAGGAAGAAGAAAGCGACGACAGCAGCGACAGCGACGACGAAGGCGACGGCGGTCCG 
GATCCGGAAGAAGCCCGCCTGCGTTTCACCGCGGTCTCCGAGCAGCTCGACAAGGCCAAGAAGGCCCTGAAG 
AAGCACGGTCGCGGCAGCAAGCAGGCCACCGCCGAACTCACCGGCTTGGCCGAGCTGTTCATGCCGATCAAG 
CTGGTGCCCAAGCAGTTCGACGCCCTGGTCGCCCGCGTGCGCTCCGCCCTGGAAGGCGTACGCGCCCAGGAA 
CGCGCCATCATGCAACTCTGCGTGCGTGACGCGCGCATGCCGCGTGCCGACTTCCTGCGCCTGTTCCCGAAC 
CACGAGACCGACGAGAAGTGGGTCGACAGCGTCCTGAAGAGCAAGCCGAAGTACGCCGAGGCCATCGAGCGC 
CTGCGCGACGACATCCTGCGCAACCAGCAGAAGCTGGCGGCCCTGGAAAGCGAGGTCGAGCTGACCGTCGCC 
GAGATCAAGGAAATCAACCGCGCGATGTCGATCGGCGAAGCCAAGGCTCGCCGGGCGAAGAAGGAAATGGTC 
GAGGCCAACCTGCGCCTGGTGATTTCCATCGCCAAGAAGTACACCAACCGCGGCCTGCAATTCCTCGACCTG 
ATCCAGGAAGGCAACATCGGCCTGATGAAGGCGGTGGACAAGTTCGAATACCGTCGTGGCTACAAATTCTCT 
ACCTACGCCACCTGGTGGATTCGCCAGGCGATCACCCGTTCGATCGCCGACCAGGCACGCACCATCCGCATC 
CCGGTGCACATGATCGAGACGATCAACAAGCTCAACCGCATCTCCCGCCAGATGCTCCAGGAAATGGGTCGC 
GAGCCCACCCCGGAAGAGCTTGGCGAGCGCATGGACATGCCTGAGGACAAGATCCGCAAGGTACTGAAGATC 
GCCAAAGAGCCGATCTCCATGGAAACCCCGATCGGTGACGACGAAGATTCGCACCTGGGCGATTTCATCGAG 
GACTCCACCATGCAGTCGCCGATCGAGATGGCGACCAGCGAGAGCCTCAAGGAATCCACCCGCGAAGTCCTC 
GCCGGCCTCACTGCCCGGGAAGCCAAGGTGCTGCGCATGCGCTTCGGCATCGACATGAACACCGACCACACC 
CTCGAGGAAGTCGGCAAGCAGTTCGATGTGACCCGCGAGCGGATCCGCCAGATCGAAGCCAAGGCGTTGCGC 
AAGCTGCGCCATCCGTCGCGAAGCGAGCACCTGCGCTCCTTCCTCGACGAGTGA