ViewGene
Locus Name:
GeneID:
Location:

GeneID:4839
TrivialName: PA14_62740
AnnotatorUID:
Modification Date/Time:2006-04-06 13:01:23
LocusName:PA14_62740
PAO1 Ortholog Locus:PA4743
Sequence Length:390
Protein Length:129
Start: 5599253
Stop: 5598864
Strand: -
Type:
ChromosomeID:2
Status: ACTIVE
Frame Discrepancy: FALSE
Missense Discrepancy:FALSE
Comments:
Homology: gb|AAG08129.1|AE004888_4 (AE004888) ribosome-binding factor A [Pseudomonas aeruginosa PAO1]
Identities = 129/129 (100%), Positives = 129/129 (100%)
Sequence:
ATGGCAAAAGACTACAGCCGTACCCAGCGTATCGGCGATCAGATGCAACGCGAACTGGCTCAACTGATCCAG
CGCGAGATCAAggACCCGCGCCTGGGCCTGGTCACCATCACCGGTGTCGAGGTCAGCCGCGACGTGGCGCAC
GCCAAGGTGTTCATCACCGTCATGGGCCagGACGATGCCGGCAAGATCGCCCTGAACATGGAAATCCTCAAC
GACGCCGCCGGCTACCTGCGCATGTTGCTGGGCAAGTCGATGAAGCTGCGCAGCGTGCCGCAACTGCATTTC
CACTACGACGAAAGCATCCGCCGCGGCGCCGAGCTGTCCGCGCTGATCGAACGTGCGGTGGCCGAAGACGGC
CGCCGCCACGGCGACGAGACCGAGGACTGA
Translation:
MAKDYSRTQRIGDQMQRELAQLIQREIKDPRLGLVTITGVEVSRDVAHAKVFITVMGQDDAGKIALNMEILN
DAAGYLRMLLGKSMKLRSVPQLHFHYDESIRRGAELSALIERAVAEDGRRHGDETED*
AnnotationID:4844GeneID:4839
AnnotatorUID: diggins
Modification Date/Time: 2005-03-09 08:08:49
Gene Name:rbfA
Confidence Code:2
GeneProduct:ribosome-binding factor A
Cell Localization:()
Synonyms:
Cell Localization Confidence Code:5
MolecularFunction:
Functional Category:(26) Translation, post-translational modification, degradation
Alternate Gene Product Name:
Functional Category Confidence Code:5
COGs:COG0858,pfam02033
Secondary Functional Category(ies):translation, ribosomal structure and biogenesis
EC Number:
Status:ACTIVE
Pathway:






 
Homology:
>gb|AAO57937.1| (AE016872) ribosome-binding factor A [Pseudomonas syringae pv.
           tomato str. DC3000]
          Length = 138

 Score =  186 bits (472), Expect = 2e-47
 Identities = 93/121 (76%), Positives = 108/121 (89%)

>gb|AAN70283.1|AE016669_1 (AE016791) ribosome-binding factor A [Pseudomonas putida KT2440]
          Length = 132

 Score =  177 bits (448), Expect = 1e-44
 Identities = 89/128 (69%), Positives = 108/128 (84%), Gaps = 1/128 (0%)

>gb|AAN82364.1|AE016767_124 (AE016767) Ribosome-binding factor A [Escherichia coli CFT073]
          Length = 139

 Score =  122 bits (305), Expect = 5e-28
 Identities = 60/133 (45%), Positives = 91/133 (68%), Gaps = 4/133 (3%)








 
Structural Features:
COG0858, RbfA, Ribosome-binding factor A 
[Translation, ribosomal structure and biogenesis]
CD-Length = 118 residues,  99.2% aligned
Score =  129 bits (326), Expect = 9e-32
Identities = 60/119 (50%), Positives = 86/119 (72%), Gaps = 2/119 (1%)

pfam02033, RBFA, Ribosome-binding factor A.
CD-Length = 105 residues, 100.0% aligned
Score =  108 bits (271), Expect = 2e-25
Identities = 53/107 (49%), Positives = 73/107 (68%), Gaps = 3/107 (2%)







   
Genomic Context:






   
Comment:


















    ReferenceID:9678




  
Author/Investigator(s):
        GenNotator





  
Title:
        




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:BLASTP 







    
Data:


    		




 
URL:

















    ReferenceID:26819




  
Author/Investigator(s):
        GenNotator





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:RPSBLAST 







    
Data:


    		




 
URL:

















    ReferenceID:37649




  
Author/Investigator(s):
        





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:Misc (text/plain)







    
Data:4839_cdd.html


    		




 
URL:

















    ReferenceID:37729




  
Author/Investigator(s):
        Jones PG, Inouye M.





  
Title:
        RbfA, a 30S ribosomal binding factor, is a cold-shock protein whose absence triggers the cold-shock response.




  
PubMed:
        8898389


MedLine:
        




    
Source:
Mol Microbiol. 1996 Sep;21(6):1207-18.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=8898389









           
Homologs By Global Alignment 

           

       



     
Gene ID:4839
           
Identity:

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

                           

     
HomologID
                           Accession
                           Description
                           Length
                           PctIdentity
                           PctSimilarity
                           Gaps
                           Score
     

     
     
7217
                           PA4743_tr
                           translation of PA4743
                           129
                           99.99
                           99.99
                           0
                           644.0
     

     
     
188746
                           gb|AAG08129.1|AE004888_4
                           (AE004888) ribosome-binding factor A [Pseudomonas aeruginosa PAO1]
                           129
                           99.99
                           99.99
                           0
                           644.0
     

     
     
188747
                           gb|AAO57937.1|
                           (AE016872) ribosome-binding factor A [Pseudomonas syringae pv. tomato str. DC3000]
                           138
                           68.84
                           81.15
                           9
                           473.0
     

     
     
188748
                           gb|AAN70283.1|AE016669_1
                           (AE016791) ribosome-binding factor A [Pseudomonas putida KT2440]
                           133
                           66.91
                           81.20
                           5
                           450.0
     

     
     
188749
                           emb|CAD84673.1|
                           (BX321858) Ribosome-binding factor A [Nitrosomonas europaea ATCC 19718]
                           129
                           52.71
                           67.44
                           12
                           320.0
     

     






      

          
GC ORFID: 47841How Found: BLASTX

          
GC_TrimmedSeqID: 69Blast Result ID

          
Subject Sequence Name: t_PA4743Glimmer Score: 

          
Start: 4862933Stop: 4862544

          
Length: 390


          
Start Codon: ATGTruncated Start:

          
Stop Codon: TGATruncated Stop: 

          
Homolog: t_PA4743 translation of PA4743Homolog Bit Score 252.0

          
Other Homologs:  psyr_15may02_Scaffold4_revised_gene5494 (ORF: BLASTX 191.0), t_PA4743 (ORF: GLIMMER)

          
GC ORF Sequence

           
ATGGCAAAAGACTACAGCCGTACCCAGCGTATCGGCGATCAGATGCAACGCGAACTGGCTCAACTGATCCAG 
CGCGAGATCAAggACCCGCGCCTGGGCCTGGTCACCATCACCGGTGTCGAGGTCAGCCGCGACGTGGCGCAC 
GCCAAGGTGTTCATCACCGTCATGGGCCagGACGATGCCGGCAAGATCGCCCTGAACATGGAAATCCTCAAC 
GACGCCGCCGGCTACCTGCGCATGTTGCTGGGCAAGTCGATGAAGCTGCGCAGCGTGCCGCAACTGCATTTC 
CACTACGACGAAAGCATCCGCCGCGGCGCCGAGCTGTCCGCGCTGATCGAACGTGCGGTGGCCGAAGACGGC 
CGCCGCCACGGCGACGAGACCGAGGACTGA