ViewGene
Locus Name:
GeneID:
Location:

GeneID:5786
TrivialName: PA14_41580
AnnotatorUID: danlee
Modification Date/Time:2006-04-06 13:01:23
LocusName:PA14_41580
PAO1 Ortholog Locus:
Sequence Length:468
Protein Length:155
Start: 3714198
Stop: 3713730
Strand: -
Type:
ChromosomeID:2
Status: INACTIVE
Frame Discrepancy: TRUE
Missense Discrepancy:TRUE
Comments:
Replaced by GID7409 (PA14_41575). Homology: gb|AAD11567.1| (AF027290) putative ECF sigma factor X [Pseudomonas aeruginosa]
Identities = 152/152 (100%), Positives = 152/152 (100%)
Sequence:
TTGAATAAGCCTCACCCCCTGTCACAGCGGTATGACCCACGCCAGCTTTCCGATGAAGAGCTGGTCGAGCGT
GCGCACTCGGAGCTGTTCCACGTGACGCGCGCCTATGAAGAATTGATGCGGCGTTACCAGCGCACGCTGTTC
AACGTCTGTGCCCGCTACCTGGGCAACGACCGCGACGCGGACGACGTGTGCCAGGAGGTGATGCTGAAAGTT
TTGTACGGGTTGAAGAACTTTGAGGGCAAGTCGAAGTTCAAAACATGGCTATATAGCATCACGTACAACGAG
TGCATCACGCAGTACCGCAAGGAGCGCCGCAAGCGCCGATTGATGGATGCGCTCAGCCTCGACCCGCTGGAG
GAGGCTTCCGAGGAGAAGTCGCCGAAGGTTGAGGAGCGGGGCGGATTGGATCGTTGGCTCGTCCATGTCAAT
CCGATAGATCGGGAGATTCTGgtctTCGCTTCGTAG
Translation:
MNKPHPLSQRYDPRQLSDEELVERAHSELFHVTRAYEELMRRYQRTLFNVCARYLGNDRDADDVCQEVMLKV
LYGLKNFEGKSKFKTWLYSITYNECITQYRKERRKRRLMDALSLDPLEEASEEKSPKVEERGGLDRWLVHVN
PIDREILVFAS*
AnnotationID:5788GeneID:5786
AnnotatorUID: danlee
Modification Date/Time: 2006-03-10 15:03:03
Gene Name:
Confidence Code:4
GeneProduct:
Cell Localization:()
Synonyms:
Cell Localization Confidence Code:5
MolecularFunction:
Functional Category:()
Alternate Gene Product Name:RNA polymerase sigma factor SigX
Functional Category Confidence Code:5
COGs:pfam04542
Secondary Functional Category(ies):transcriptional regulators
EC Number:
Status:INACTIVE
Pathway:






 
Homology:
>gb|AAD45976.1|AF115334_3 (AF115334) SigX [Pseudomonas fluorescens]
          Length = 196

 Score =  285 bits (730), Expect = 5e-77
 Identities = 138/152 (90%), Positives = 144/152 (94%)

>gb|AAN67702.1|AE016401_5 (AE016781) RNA polymerase sigma factor SigX [Pseudomonas putida
           KT2440]
          Length = 196

 Score =  284 bits (726), Expect = 1e-76
 Identities = 135/152 (88%), Positives = 144/152 (94%)

>gb|AAD34328.1|AF115335_1 (AF115335) ECF sigma factor SigX [Pseudomonas syringae pv.
           syringae]
          Length = 196

 Score =  284 bits (726), Expect = 1e-76
 Identities = 138/152 (90%), Positives = 144/152 (94%)








 
Structural Features:
pfam04542, Sigma70_r2, Sigma-70 region 2. 
CD-Length = 71 residues,  98.6% aligned
Score = 60.6 bits (147), Expect = 8e-11
Identities = 28/70 (40%), Positives = 40/70 (57%), Gaps = 2/70 (2%)






   
Genomic Context:






   
Comment:
Replaced by GID7409 (PA14_41575).


















    ReferenceID:15670




  
Author/Investigator(s):
        GenNotator





  
Title:
        




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:BLASTP 







    
Data:


    		




 
URL:

















    ReferenceID:28703




  
Author/Investigator(s):
        GenNotator





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:RPSBLAST 







    
Data:


    		




 
URL:

















    ReferenceID:37147




  
Author/Investigator(s):
        





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:Misc (text/plain)







    
Data:5786_cdd.html


    		




 
URL:









           
Homologs By Global Alignment 

           

       



     
Gene ID:5786
           
Identity:

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

                           

     
HomologID
                           Accession
                           Description
                           Length
                           PctIdentity
                           PctSimilarity
                           Gaps
                           Score
     

     
     
197541
                           gb|AAD11567.1|
                           (AF027290) putative ECF sigma factor X [Pseudomonas aeruginosa]
                           196
                           77.04
                           77.55
                           41
                           797.0
     

     
     
197542
                           gb|AAD45976.1|AF115334_3
                           (AF115334) SigX [Pseudomonas fluorescens]
                           196
                           69.89
                           73.46
                           41
                           724.0
     

     
     
197544
                           gb|AAD34328.1|AF115335_1
                           (AF115335) ECF sigma factor SigX [Pseudomonas syringae pv. syringae]
                           196
                           69.89
                           73.46
                           41
                           720.0
     

     
     
197545
                           gb|AAD34329.1|AF115338_1
                           (AF115338) ECF sigma factor SigX [Pseudomonas fluorescens]
                           196
                           68.87
                           72.95
                           41
                           707.0
     

     
     
197543
                           gb|AAN67702.1|AE016401_5
                           (AE016781) RNA polymerase sigma factor SigX [Pseudomonas putida KT2440]
                           196
                           68.36
                           73.46
                           41
                           720.0
     

     






      

          
GC ORFID: 48788How Found: Glimmer

          
GC_TrimmedSeqID: 69Blast Result ID

          
Subject Sequence Name: Glimmer Score: 

          
Start: 1239711Stop: 1240178

          
Length: 468


          
Start Codon: TTGTruncated Start:

          
Stop Codon: TAGTruncated Stop: 

          
Homolog: psyr_15may02_Scaffold1_revised_gene1072 related to: gi|4959390|gb|AAD34328.1|AF115335_1 (AF115335) ECF sigma factor SigX [Pseudomonas syringae pv. syringae]Homolog Bit Score 290.0

          
Other Homologs:  psyr_15may02_Scaffold1_revised_gene1072 related to: gi|4959390|gb|AAD34328.1|AF115335_1 (AF115335) ECF sigma factor SigX [Pseudomonas syringae pv. syringae] (BLASTP 290), t_PA1776 translation of PA1776 (BLASTP 249)

          
GC ORF Sequence

           
TTGAATAAGCCTCACCCCCTGTCACAGCGGTATGACCCACGCCAGCTTTCCGATGAAGAGCTGGTCGAGCGT 
GCGCACTCGGAGCTGTTCCACGTGACGCGCGCCTATGAAGAATTGATGCGGCGTTACCAGCGCACGCTGTTC 
AACGTCTGTGCCCGCTACCTGGGCAACGACCGCGACGCGGACGACGTGTGCCAGGAGGTGATGCTGAAAGTT 
TTGTACGGGTTGAAGAACTTTGAGGGCAAGTCGAAGTTCAAAACATGGCTATATAGCATCACGTACAACGAG 
TGCATCACGCAGTACCGCAAGGAGCGCCGCAAGCGCCGATTGATGGATGCGCTCAGCCTCGACCCGCTGGAG 
GAGGCTTCCGAGGAGAAGTCGCCGAAGGTTGAGGAGCGGGGCGGATTGGATCGTTGGCTCGTCCATGTCAAT 
CCGATAGATCGGGAGATTCTGgtctTCGCTTCGTAG