ViewGene
Locus Name:
GeneID:
Location:

GeneID:612
TrivialName: PA14_23330
AnnotatorUID:
Modification Date/Time:2006-04-06 13:01:23
LocusName:PA14_23330
PAO1 Ortholog Locus:PA3162
Sequence Length:1680
Protein Length:559
Start: 2024157
Stop: 2025836
Strand: +
Type:
ChromosomeID:2
Status: ACTIVE
Frame Discrepancy: FALSE
Missense Discrepancy:FALSE
Comments:
Homology: gb|AAG06550.1|AE004740_3 (AE004740) 30S ribosomal protein S1 [Pseudomonas aeruginosa PAO1]
Identities = 559/559 (100%), Positives = 559/559 (100%)
Sequence:
ATGAGCGAAAGCTTCGCAGAACTCTTTGAAGAAAGTCTGAAATCCCTCGACATGCAGCCGGGTGCCATCATC
ACCGGCATCGTGGTCGACATCGATGGTGACTGGGTCACCGTCCATGCCGGTCTGAAATCCGAGGGCGTCATC
CCGGTCGAGCAGTTCTACAACGAACAGGGCGAACTGACCATCAAGGTGGGTGACGAAGTCCACGTCGCACTG
GACGCGGTAGAAGACGGCTTTGGCGAGACCAAGCTGTCCCGCGAGAAAGCCAAGCGCGCCGAGAGCTGGATT
GTTCTGGAAGCGGCTTTCGCTGCCGACGAAGTGGTCAAGGGCGTCATCAACGGCAAGGTCAAGGGCGGTTTC
ACCGTCGACGTCAACGGCATCCGCGCGTTCCTGCCGGGTTCGCTGGTCGACGTGCGTCCGGTTCGCGACACC
ACCCACCTGGAAGGCAAAGAGCTCGAGTTCAAGGTCATCAAGCTCGACCAGAAGCGCAACAACGTTGTCGTT
TCCCGCCGCAGCGTCCTGGAAGCCGAgaACAGCGCCGAGCGTGAAGCTCTGCTGGAATCGCTGCAGGAAGGC
cAGCAGGTCAAGGGCATCGTCAaGAACCTCACCGACTACGgCGCATTCGTGGACCtggGCGGCGTAgacggC
CTGCTGCACATCACCGACATGGCCTgGAAGCGCATCAAGCATCCGTCCGAGATCGTCAACGTTGGCGACGAG
ATCGACGTCAAGGTCCTGAAGTTCGACCGCGAGCGCAACCGTGTATCCCTGGGCCTGAAGCAACTGGGCGAA
GACCCGTGGGTTGCCATCAAGGCGCGTTACCCGGAAGGCACCCGCGTCATGGCCCGCGTCACCAACCTCACC
GACTACGGCTGCTTCGCCGAGCTGGAAGAGGGCGTGGAAGGCCTGGTACACGTCTCCGAAATGGACTGGACC
AACAAGAACATCCATCCGTCGAAAGTCGTCCAGGTTGGCGACGAAGTGGAAGTTCAGGTTCTGGACATCGAC
GAAGAGCGTCGTCGTATCTCCCTGGGTATCAAGCAGTGCAAATCCAACCCGTGGGAAGACTTCTCCAGCCAG
TTCAACAAGGGTGACCGTATCTCCGGTACCATCAAGTCGATCACCGACTTCGGTATCTTCATCGGTCTGGAC
GGCGGCATCGACGGCCTGGTCCACCTGTCCGACATCTCCTGGAACGAAGTCGGCGAAGAAGCCGTACGTCGC
TTCAAGAAGGGCGACGAGCTGGAAACCGTCATCCTGTCGGTCGACCCGGAGCGCGAGCGCATCTCCCTGGGC
ATCAAGCAGCTGGAAGACGATCCGTTCTCCAACTACGCGTCCCTGCACGAGAAAGGCAGCATCGTCCGCGGT
ACCGTGAAGGAAGTCGACGCCAAAGGCGCTGTCATCAGCCTGGGCGACGACATCGAAGGTATCCTGAAGGCT
TCCGAAATCAGCCGTGACCGCGTCGAAGACGCGCGCAACGTCCTGAAGGAAGGCGAGGAAGTCGAAGCCAAG
ATCATCAGCATCGACCGCAAGAGCCGCGTCATCAGCCTCTCCGTCAAGTCCAAGGACGTCGATGACGAGAAG
GACGCAATGAAAGAACTGCGTAAGCAGGAAGTAGAAAGCGCTGGTCCGACCACCATCGGTGATCTGATCCGT
GCTCAGATGGAGAATCAGGGCTAA
Translation:
MSESFAELFEESLKSLDMQPGAIITGIVVDIDGDWVTVHAGLKSEGVIPVEQFYNEQGELTIKVGDEVHVAL
DAVEDGFGETKLSREKAKRAESWIVLEAAFAADEVVKGVINGKVKGGFTVDVNGIRAFLPGSLVDVRPVRDT
THLEGKELEFKVIKLDQKRNNVVVSRRSVLEAENSAEREALLESLQEGQQVKGIVKNLTDYGAFVDLGGVDG
LLHITDMAWKRIKHPSEIVNVGDEIDVKVLKFDRERNRVSLGLKQLGEDPWVAIKARYPEGTRVMARVTNLT
DYGCFAELEEGVEGLVHVSEMDWTNKNIHPSKVVQVGDEVEVQVLDIDEERRRISLGIKQCKSNPWEDFSSQ
FNKGDRISGTIKSITDFGIFIGLDGGIDGLVHLSDISWNEVGEEAVRRFKKGDELETVILSVDPERERISLG
IKQLEDDPFSNYASLHEKGSIVRGTVKEVDAKGAVISLGDDIEGILKASEISRDRVEDARNVLKEGEEVEAK
IISIDRKSRVISLSVKSKDVDDEKDAMKELRKQEVESAGPTTIGDLIRAQMENQG*
AnnotationID:621GeneID:612
AnnotatorUID: diggins
Modification Date/Time: 2005-04-13 11:11:57
Gene Name:rpsA
Confidence Code:2
GeneProduct: 30S ribosomal protein S1
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:COG0539
Secondary Functional Category(ies):
EC Number:
Status:ACTIVE
Pathway:






 
Homology:
>gb|AAO55270.1| (AE016862) ribosomal protein S1 [Pseudomonas syringae pv. tomato
           str. DC3000]
          Length = 563

 Score =  995 bits (2572), Expect = 0.0
 Identities = 508/562 (90%), Positives = 537/562 (95%), Gaps = 4/562 (0%)

>gb|AAL19915.1| (AE008742) 30S ribosomal subunit protein S1 [Salmonella typhimurium
           LT2]
          Length = 557

 Score =  830 bits (2143), Expect = 0.0
 Identities = 415/553 (75%), Positives = 469/553 (84%)

>gb|AAN79519.1|AE016758_123 (AE016758) 30S ribosomal protein S1 [Escherichia coli CFT073]
          Length = 557

 Score =  829 bits (2141), Expect = 0.0






 
Structural Features:
COG0539, RpsA, Ribosomal protein S1 
[Translation, ribosomal structure and biogenesis]
CD-Length = 541 residues,  99.3% aligned
Score =  604 bits (1558), Expect = 1e-173
Identities = 322/546 (58%), Positives = 412/546 (75%), Gaps = 10/546 (1%)






   
Genomic Context:






   
Comment:


















    ReferenceID:1227




  
Author/Investigator(s):
        GenNotator





  
Title:
        




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:BLASTP 







    
Data:


    		




 
URL:

















    ReferenceID:18369




  
Author/Investigator(s):
        GenNotator





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:RPSBLAST 







    
Data:


    		




 
URL:

















    ReferenceID:32380




  
Author/Investigator(s):
        





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:Misc (text/plain)







    
Data:612_cdd.html


    		




 
URL:

















    ReferenceID:33934




  
Author/Investigator(s):
        Xie G, Brettin TS, Bonner CA, Jensen RA.





  
Title:
        Mixed-function supraoperons that exhibit overall conservation, albeit shuffled gene organization, across wide intergenomic distances within eubacteria.




  
PubMed:
        10518299


MedLine:
        




    
Source:
Microb Comp Genomics. 1999;4(1):5-28.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10518299

















    ReferenceID:33935




  
Author/Investigator(s):
        Xie G, Bonner CA, Jensen RA.





  
Title:
        A probable mixed-function supraoperon in Pseudomonas exhibits gene organization features of both intergenomic conservation and gene shuffling.




  
PubMed:
        10368439


MedLine:
        




    
Source:
J Mol Evol. 1999 Jul;49(1):108-21.
Erratum in:
    * J Mol Evol 2000 Feb;50(2):202.







    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10368439

















    ReferenceID:33936




  
Author/Investigator(s):
        Sorokin A, Serror P, Pujic P, Azevedo V, Ehrlich SD.





  
Title:
        The Bacillus subtilis chromosome region encoding homologues of the Escherichia coli mssA and rpsA gene products.




  
PubMed:
        7704259


MedLine:
        




    
Source:
Microbiology. 1995 Feb;141 ( Pt 2):311-9.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=7704259

















    ReferenceID:33937




  
Author/Investigator(s):
        Pedersen S, Skouv J, Kajitani M, Ishihama A.





  
Title:
        Transcriptional organization of the rpsA operon of Escherichia coli.




  
PubMed:
        6384724


MedLine:
        




    
Source:
Mol Gen Genet. 1984;196(1):135-40.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=6384724

















    ReferenceID:33938




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





  
Title:
        The DNA sequence of the gene rpsA of Escherichia coli coding for ribosomal protein S1.




  
PubMed:
        6281725


MedLine:
        




    
Source:
Nucleic Acids Res. 1982 Mar 25;10(6):1857-65.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=6281725

















    ReferenceID:33939




  
Author/Investigator(s):
        Schnier J, Kimura M, Foulaki K, Subramanian AR, Isono K, Wittmann-Liebold B.





  
Title:
        Primary structure of Escherichia coli ribosomal protein S1 and of its gene rpsA.




  
PubMed:
        7041110


MedLine:
        




    
Source:
Proc Natl Acad Sci U S A. 1982 Feb;79(4):1008-11.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=7041110

















    ReferenceID:33940




  
Author/Investigator(s):
        Christiansen L, Pedersen S.





  
Title:
        Cloning, restriction endonuclease mapping and post-transcriptional regulation of rpsA, the structural gene for ribosomal protein S1.




  
PubMed:
        6267426


MedLine:
        




    
Source:
Mol Gen Genet. 1981;181(4):548-51.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=6267426









           
Homologs By Global Alignment 

           

       



     
Gene ID:612
           
Identity:

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

                           

     
HomologID
                           Accession
                           Description
                           Length
                           PctIdentity
                           PctSimilarity
                           Gaps
                           Score
     

     
     
1042
                           PA3162_tr
                           translation of PA3162
                           559
                           99.99
                           99.99
                           0
                           2821.0
     

     
     
40530
                           gb|AAG06550.1|AE004740_3
                           (AE004740) 30S ribosomal protein S1 [Pseudomonas aeruginosa PAO1]
                           559
                           99.99
                           99.99
                           0
                           2821.0
     

     
     
40531
                           gb|AAO55270.1|
                           (AE016862) ribosomal protein S1 [Pseudomonas syringae pv. tomato str. DC3000]
                           563
                           90.23
                           95.38
                           4
                           2578.0
     

     
     
40532
                           gb|AAN67392.1|AE016365_7
                           (AE016780) ribosomal protein S1 [Pseudomonas putida KT2440]
                           577
                           86.30
                           92.02
                           19
                           2555.0
     

     
     
40543
                           emb|CAE13915.1|
                           (BX571864) 30S ribosomal protein S1 [Photorhabdus luminescens subsp. laumondii TTO1]
                           559
                           74.41
                           84.07
                           2
                           2133.0
     

     






      

          
GC ORFID: 43614How Found: BLASTX

          
GC_TrimmedSeqID: 69Blast Result ID

          
Subject Sequence Name: t_PA3162Glimmer Score: 

          
Start: 2929774Stop: 2928095

          
Length: 1680


          
Start Codon: ATGTruncated Start:

          
Stop Codon: TAATruncated Stop: 

          
Homolog: t_PA3162 translation of PA3162Homolog Bit Score 1091.0

          
Other Homologs:  psyr_15may02_Scaffold8_revised_gene7734 (ORF: BLASTX 962.0), t_PA3162 (ORF: GLIMMER)

          
GC ORF Sequence

           
ATGAGCGAAAGCTTCGCAGAACTCTTTGAAGAAAGTCTGAAATCCCTCGACATGCAGCCGGGTGCCATCATC 
ACCGGCATCGTGGTCGACATCGATGGTGACTGGGTCACCGTCCATGCCGGTCTGAAATCCGAGGGCGTCATC 
CCGGTCGAGCAGTTCTACAACGAACAGGGCGAACTGACCATCAAGGTGGGTGACGAAGTCCACGTCGCACTG 
GACGCGGTAGAAGACGGCTTTGGCGAGACCAAGCTGTCCCGCGAGAAAGCCAAGCGCGCCGAGAGCTGGATT 
GTTCTGGAAGCGGCTTTCGCTGCCGACGAAGTGGTCAAGGGCGTCATCAACGGCAAGGTCAAGGGCGGTTTC 
ACCGTCGACGTCAACGGCATCCGCGCGTTCCTGCCGGGTTCGCTGGTCGACGTGCGTCCGGTTCGCGACACC 
ACCCACCTGGAAGGCAAAGAGCTCGAGTTCAAGGTCATCAAGCTCGACCAGAAGCGCAACAACGTTGTCGTT 
TCCCGCCGCAGCGTCCTGGAAGCCGAgaACAGCGCCGAGCGTGAAGCTCTGCTGGAATCGCTGCAGGAAGGC 
cAGCAGGTCAAGGGCATCGTCAaGAACCTCACCGACTACGgCGCATTCGTGGACCtggGCGGCGTAgacggC 
CTGCTGCACATCACCGACATGGCCTgGAAGCGCATCAAGCATCCGTCCGAGATCGTCAACGTTGGCGACGAG 
ATCGACGTCAAGGTCCTGAAGTTCGACCGCGAGCGCAACCGTGTATCCCTGGGCCTGAAGCAACTGGGCGAA 
GACCCGTGGGTTGCCATCAAGGCGCGTTACCCGGAAGGCACCCGCGTCATGGCCCGCGTCACCAACCTCACC 
GACTACGGCTGCTTCGCCGAGCTGGAAGAGGGCGTGGAAGGCCTGGTACACGTCTCCGAAATGGACTGGACC 
AACAAGAACATCCATCCGTCGAAAGTCGTCCAGGTTGGCGACGAAGTGGAAGTTCAGGTTCTGGACATCGAC 
GAAGAGCGTCGTCGTATCTCCCTGGGTATCAAGCAGTGCAAATCCAACCCGTGGGAAGACTTCTCCAGCCAG 
TTCAACAAGGGTGACCGTATCTCCGGTACCATCAAGTCGATCACCGACTTCGGTATCTTCATCGGTCTGGAC 
GGCGGCATCGACGGCCTGGTCCACCTGTCCGACATCTCCTGGAACGAAGTCGGCGAAGAAGCCGTACGTCGC 
TTCAAGAAGGGCGACGAGCTGGAAACCGTCATCCTGTCGGTCGACCCGGAGCGCGAGCGCATCTCCCTGGGC 
ATCAAGCAGCTGGAAGACGATCCGTTCTCCAACTACGCGTCCCTGCACGAGAAAGGCAGCATCGTCCGCGGT 
ACCGTGAAGGAAGTCGACGCCAAAGGCGCTGTCATCAGCCTGGGCGACGACATCGAAGGTATCCTGAAGGCT 
TCCGAAATCAGCCGTGACCGCGTCGAAGACGCGCGCAACGTCCTGAAGGAAGGCGAGGAAGTCGAAGCCAAG 
ATCATCAGCATCGACCGCAAGAGCCGCGTCATCAGCCTCTCCGTCAAGTCCAAGGACGTCGATGACGAGAAG 
GACGCAATGAAAGAACTGCGTAAGCAGGAAGTAGAAAGCGCTGGTCCGACCACCATCGGTGATCTGATCCGT 
GCTCAGATGGAGAATCAGGGCTAA