ViewGene
Locus Name:
GeneID:
Location:

GeneID:4917
TrivialName: PA14_09080
AnnotatorUID:
Modification Date/Time:2006-04-06 13:01:23
LocusName:PA14_09080
PAO1 Ortholog Locus:PA4241
Sequence Length:357
Protein Length:118
Start: 769971
Stop: 770327
Strand: +
Type:
ChromosomeID:2
Status: ACTIVE
Frame Discrepancy: FALSE
Missense Discrepancy:FALSE
Comments:
Homology: gb|AAG07629.1|AE004841_7 (AE004841) 30S ribosomal protein S13 [Pseudomonas aeruginosa PAO1]
Identities = 118/118 (100%), Positives = 118/118 (100%)
Sequence:
ATGGCCCGTATTGCAGGCGTCAACATTCCGGATAACAAGCACACTGTTATCTCGCTGACCTACATCTATGGT
GTTGGTCGCACTACTGCTCAGAGCATCTGCGCAGCCACCGGCGTAAACCCGGCTGCCAAGATCAAGGACCTG
AGCGACGAGCAGATCGATCAGCTGCGTAACGAAGTCGCGAAGATCACCACCGAAGGTGACCTGCGTCGCGAA
ATCAACATGAACATCAAGCGTCTGATGGACCTCGGTTGCTACCGCGGTCTGCGTCATCGTCGCGGTCTGCCG
GTTCGCGGTCAGCGTACCAAGACCAACGCGCGTACCCGCAAGGGCCCGCGTAAGCCGATCCGCAAGTAA
Translation:
MARIAGVNIPDNKHTVISLTYIYGVGRTTAQSICAATGVNPAAKIKDLSDEQIDQLRNEVAKITTEGDLRRE
INMNIKRLMDLGCYRGLRHRRGLPVRGQRTKTNARTRKGPRKPIRK*
AnnotationID:4922GeneID:4917
AnnotatorUID: diggins
Modification Date/Time: 2005-04-01 13:01:00
Gene Name:rpsM
Confidence Code:2
GeneProduct:30S ribosomal protein S13
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:COG0099,pfam00416
Secondary Functional Category(ies):
EC Number:
Status:ACTIVE
Pathway:






 
Homology:
>gb|AAO54190.1| (AE016858) ribosomal protein S13 [Pseudomonas syringae pv. tomato
           str. DC3000]
          Length = 118

 Score =  225 bits (574), Expect = 3e-59
 Identities = 111/118 (94%), Positives = 112/118 (94%)

>gb|AAN66106.1|AE016239_1 (AE016775) ribosomal protein S13 [Pseudomonas putida KT2440]
          Length = 118

 Score =  219 bits (559), Expect = 2e-57
 Identities = 108/118 (91%), Positives = 111/118 (94%)

>gb|AAN53338.1|AE015474_1 (AE015474) ribosomal protein S13 [Shewanella oneidensis MR-1]
          Length = 118

 Score =  190 bits (483), Expect = 1e-48
 Identities = 92/118 (77%), Positives = 104/118 (88%)






 
Structural Features:
COG0099, RpsM, Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
CD-Length = 121 residues,  98.3% aligned
Score =  166 bits (423), Expect = 5e-43
Identities = 76/119 (63%), Positives = 97/119 (81%), Gaps = 1/119 (0%)

pfam00416, Ribosomal_S13, Ribosomal protein S13/S18. 
CD-Length = 107 residues, 100.0% aligned
Score =  126 bits (317), Expect = 9e-31
Identities = 55/107 (51%), Positives = 74/107 (69%), Gaps = 1/107 (0%)






   
Genomic Context:






   
Comment:


















    ReferenceID:9834




  
Author/Investigator(s):
        GenNotator





  
Title:
        




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:BLASTP 







    
Data:


    		




 
URL:

















    ReferenceID:26975




  
Author/Investigator(s):
        GenNotator





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:RPSBLAST 







    
Data:


    		




 
URL:

















    ReferenceID:36529




  
Author/Investigator(s):
        





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:Misc (text/plain)







    
Data:4917_cdd.html


    		




 
URL:

















    ReferenceID:36707




  
Author/Investigator(s):
        Meek DW, Hayward RS.





  
Title:
        Nucleotide sequence of the rpoA-rplQ DNA of Escherichia coli: a second regulatory binding site for protein S4?




  
PubMed:
        6379605


MedLine:
        




    
Source:
Nucleic Acids Res. 1984 Jul 25;12(14):5813-21.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=6379605

















    ReferenceID:36709




  
Author/Investigator(s):
        Koivula T, Hemila H.





  
Title:
        Nucleotide sequence of a Lactococcus lactis gene cluster encoding adenylate kinase, initiation factor 1 and ribosomal proteins.




  
PubMed:
        1783905


MedLine:
        




    
Source:
J Gen Microbiol. 1991 Nov;137 ( Pt 11):2595-600.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=1783905

















    ReferenceID:36756




  
Author/Investigator(s):
        Bedwell D, Davis G, Gosink M, Post L, Nomura M, Kestler H, Zengel JM, Lindahl L.





  
Title:
        Nucleotide sequence of the alpha ribosomal protein operon of Escherichia coli.




  
PubMed:
        2989779


MedLine:
        




    
Source:
Nucleic Acids Res. 1985 Jun 11;13(11):3891-903.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=2989779









           
Homologs By Global Alignment 

           

       



     
Gene ID:4917
           
Identity:

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

                           

     
HomologID
                           Accession
                           Description
                           Length
                           PctIdentity
                           PctSimilarity
                           Gaps
                           Score
     

     
     
7319
                           PA4241_tr
                           translation of PA4241
                           118
                           99.99
                           99.99
                           0
                           606.0
     

     
     
190416
                           gb|AAG07629.1|AE004841_7
                           (AE004841) 30S ribosomal protein S13 [Pseudomonas aeruginosa PAO1]
                           118
                           99.99
                           99.99
                           0
                           606.0
     

     
     
190417
                           gb|AAO54190.1|
                           (AE016858) ribosomal protein S13 [Pseudomonas syringae pv. tomato str. DC3000]
                           118
                           94.06
                           94.91
                           0
                           574.0
     

     
     
190418
                           gb|AAN66106.1|AE016239_1
                           (AE016775) ribosomal protein S13 [Pseudomonas putida KT2440]
                           118
                           91.52
                           94.06
                           0
                           559.0
     

     
     
190420
                           gb|AAN53338.1|AE015474_1
                           (AE015474) ribosomal protein S13 [Shewanella oneidensis MR-1]
                           118
                           77.96
                           88.13
                           0
                           483.0
     

     






      

          
GC ORFID: 47919How Found: BLASTX

          
GC_TrimmedSeqID: 69Blast Result ID

          
Subject Sequence Name: t_PA4241Glimmer Score: 

          
Start: 4183968Stop: 4183612

          
Length: 357


          
Start Codon: ATGTruncated Start:

          
Stop Codon: TAATruncated Stop: 

          
Homolog: t_PA4241 translation of PA4241Homolog Bit Score 238.0

          
Other Homologs:  psyr_15may02_Scaffold4_revised_gene5209 (ORF: BLASTX 225.0), t_PA4241 (ORF: GLIMMER)

          
GC ORF Sequence

           
ATGGCCCGTATTGCAGGCGTCAACATTCCGGATAACAAGCACACTGTTATCTCGCTGACCTACATCTATGGT 
GTTGGTCGCACTACTGCTCAGAGCATCTGCGCAGCCACCGGCGTAAACCCGGCTGCCAAGATCAAGGACCTG 
AGCGACGAGCAGATCGATCAGCTGCGTAACGAAGTCGCGAAGATCACCACCGAAGGTGACCTGCGTCGCGAA 
ATCAACATGAACATCAAGCGTCTGATGGACCTCGGTTGCTACCGCGGTCTGCGTCATCGTCGCGGTCTGCCG 
GTTCGCGGTCAGCGTACCAAGACCAACGCGCGTACCCGCAAGGGCCCGCGTAAGCCGATCCGCAAGTAA