ViewGene
Locus Name:
GeneID:
Location:

GeneID:4645
TrivialName: PA14_65180
AnnotatorUID:
Modification Date/Time:2006-04-06 13:01:23
LocusName:PA14_65180
PAO1 Ortholog Locus:PA4935
Sequence Length:420
Protein Length:139
Start: 5809114
Stop: 5808695
Strand: -
Type:
ChromosomeID:2
Status: ACTIVE
Frame Discrepancy: FALSE
Missense Discrepancy:FALSE
Comments:
Homology: gb|AAG08320.1|AE004906_8 (AE004906) 30S ribosomal protein S6 [Pseudomonas aeruginosa PAO1]
Identities = 139/139 (100%), Positives = 139/139 (100%)
Sequence:
ATGCGTCATTACGAAATCGTGTTCCTGGTTCACCCGGACCAGAGCGAACAAGTCGGTGGCATGGTCGAGCGT
TACACCAAGGCCATCGAAGAAGACGGCGGCAAGATCCACCGTCTGGAAGACTGGGGCCGTCGTCAGCTGGCC
TACGCCATCAACAACGTGCACAAGGCCCACTACGTTCTGATGAACGTCGAGTGCAGCGCCAAGGCCCTGGCT
GAGCTGGAAGACAACTTCCGTTACAACGATGCCGTGATCCGTAACCTGGTCATGCGTCGCGACGAAGCTGTC
ACCGAGCAGTCCGAGATGCTCAAGGCTGAAGAAAGCCGCAACGAGCGTCGCGAGCGTCGTGAGCGTCCGAAC
GATAACGCTGAAGGCGCCGATGGCGACGACAACAGCGATAGCGATAACGCTGACGAGTAA
Translation:
MRHYEIVFLVHPDQSEQVGGMVERYTKAIEEDGGKIHRLEDWGRRQLAYAINNVHKAHYVLMNVECSAKALA
ELEDNFRYNDAVIRNLVMRRDEAVTEQSEMLKAEESRNERRERRERPNDNAEGADGDDNSDSDNADE*
AnnotationID:4651GeneID:4645
AnnotatorUID: diggins
Modification Date/Time: 2005-03-13 13:01:50
Gene Name:rpsF
Confidence Code:2
GeneProduct:30S ribosomal protein S6
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:COG0360,pfam01250
Secondary Functional Category(ies):
EC Number:
Status:ACTIVE
Pathway:






 
Homology:
>gb|AAN70446.1|AE016685_11 (AE016792) ribosomal protein S6 [Pseudomonas putida KT2440]
          Length = 141

 Score =  248 bits (632), Expect = 5e-66
 Identities = 121/141 (85%), Positives = 131/141 (92%), Gaps = 2/141 (1%)

>gb|AAO58361.1| (AE016873) ribosomal protein S6 [Pseudomonas syringae pv. tomato
           str. DC3000]
          Length = 141

 Score =  247 bits (630), Expect = 9e-66
 Identities = 120/141 (85%), Positives = 133/141 (94%), Gaps = 2/141 (1%)

>dbj|BAC61003.1| (AP005082) ribosomal protein S6 [Vibrio parahaemolyticus]
          Length = 129

 Score =  173 bits (439), Expect = 1e-43
 Identities = 85/129 (65%), Positives = 99/129 (76%), Gaps = 2/129 (1%)








 
Structural Features:
COG0360, RpsF, Ribosomal protein S6 [Translation, ribosomal structure and biogenesis]
CD-Length = 112 residues, 100.0% aligned
Score =  128 bits (324), Expect = 2e-31
Identities = 55/112 (49%), Positives = 78/112 (69%), Gaps = 1/112 (0%)

pfam01250, Ribosomal_S6, Ribosomal protein S6
CD-Length = 92 residues, 100.0% aligned
Score = 97.2 bits (242), Expect = 6e-22
Identities = 40/92 (43%), Positives = 59/92 (64%), Gaps = 1/92 (1%)






   
Genomic Context:






   
Comment:


















    ReferenceID:9291




  
Author/Investigator(s):
        GenNotator





  
Title:
        




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:BLASTP 







    
Data:


    		




 
URL:

















    ReferenceID:26432




  
Author/Investigator(s):
        GenNotator





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:RPSBLAST 







    
Data:


    		




 
URL:

















    ReferenceID:35129




  
Author/Investigator(s):
        





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:Misc (text/plain)







    
Data:4645_cdd.html


    		




 
URL:

















    ReferenceID:35914




  
Author/Investigator(s):
        Schnier J, Kitakawa M, Isono K.





  
Title:
        The nucleotide sequence of an Escherichia coli chromosomal region containing the genes for ribosomal proteins S6, S18, L9 and an open reading frame.




  
PubMed:
        3528756


MedLine:
        




    
Source:
Mol Gen Genet. 1986 Jul;204(1):126-32.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=3528756

















    ReferenceID:35917




  
Author/Investigator(s):
        Ropp PA, Nicholas RA.





  
Title:
        Nucleotide sequence of a three gene cluster in Neisseria Gonorrhoeae encoding ribosomal proteins S6, S18, and L9.




  
PubMed:
        10524762


MedLine:
        




    
Source:
DNA Seq. 1998;9(5-6):341-5.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10524762









           
Homologs By Global Alignment 

           

       



     
Gene ID:4645
           
Identity:

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

                           

     
HomologID
                           Accession
                           Description
                           Length
                           PctIdentity
                           PctSimilarity
                           Gaps
                           Score
     

     
     
7013
                           PA4935_tr
                           translation of PA4935
                           139
                           99.99
                           99.99
                           0
                           725.0
     

     
     
185700
                           gb|AAG08320.1|AE004906_8
                           (AE004906) 30S ribosomal protein S6 [Pseudomonas aeruginosa PAO1]
                           139
                           99.99
                           99.99
                           0
                           725.0
     

     
     
185701
                           gb|AAN70446.1|AE016685_11
                           (AE016792) ribosomal protein S6 [Pseudomonas putida KT2440]
                           141
                           85.81
                           92.90
                           2
                           634.0
     

     
     
185702
                           gb|AAO58361.1|
                           (AE016873) ribosomal protein S6 [Pseudomonas syringae pv. tomato str. DC3000]
                           141
                           85.10
                           94.32
                           2
                           632.0
     

     
     
185714
                           gb|AAN56905.1|AE015825_4
                           (AE015825) ribosomal protein S6 [Shewanella oneidensis MR-1]
                           142
                           60.56
                           71.12
                           14
                           435.0
     

     






      

          
GC ORFID: 47647How Found: BLASTX

          
GC_TrimmedSeqID: 69Blast Result ID

          
Subject Sequence Name: t_PA4935Glimmer Score: 

          
Start: 5072795Stop: 5072376

          
Length: 420


          
Start Codon: ATGTruncated Start:

          
Stop Codon: TAATruncated Stop: 

          
Homolog: t_PA4935 translation of PA4935Homolog Bit Score 283.0

          
Other Homologs:  psyr_15may02_Scaffold2_revised_gene3439 (ORF: BLASTX 247.0), t_PA4935 (ORF: GLIMMER)

          
GC ORF Sequence

           
ATGCGTCATTACGAAATCGTGTTCCTGGTTCACCCGGACCAGAGCGAACAAGTCGGTGGCATGGTCGAGCGT 
TACACCAAGGCCATCGAAGAAGACGGCGGCAAGATCCACCGTCTGGAAGACTGGGGCCGTCGTCAGCTGGCC 
TACGCCATCAACAACGTGCACAAGGCCCACTACGTTCTGATGAACGTCGAGTGCAGCGCCAAGGCCCTGGCT 
GAGCTGGAAGACAACTTCCGTTACAACGATGCCGTGATCCGTAACCTGGTCATGCGTCGCGACGAAGCTGTC 
ACCGAGCAGTCCGAGATGCTCAAGGCTGAAGAAAGCCGCAACGAGCGTCGCGAGCGTCGTGAGCGTCCGAAC 
GATAACGCTGAAGGCGCCGATGGCGACGACAACAGCGATAGCGATAACGCTGACGAGTAA