ViewGene
Locus Name:
GeneID:
Location:

GeneID:3802
TrivialName: PA14_09100
AnnotatorUID:
Modification Date/Time:2006-04-06 13:01:23
LocusName:PA14_09100
PAO1 Ortholog Locus:PA4239
Sequence Length:621
Protein Length:206
Start: 770752
Stop: 771372
Strand: +
Type:
ChromosomeID:2
Status: ACTIVE
Frame Discrepancy: FALSE
Missense Discrepancy:FALSE
Comments:
Homology: gb|AAG07627.1|AE004841_5 (AE004841) 30S ribosomal protein S4 [Pseudomonas aeruginosa PAO1]
Identities = 206/206 (100%), Positives = 206/206 (100%)
Sequence:
ATGGCTCGTTACAtTGGTCCCAAGTGCAAACTGTCTCGCCGTGAAGGCACCGACCTGTTCCTGAAGAGCGGC
GCCCGCGCCCTCGACTCGAAGTGCAAGGCTGAAAACGTTCCTGGCCAGCATGGCCAGCGTCGTGGCCGTCTG
TCCGACTACGGTCTGCAGCTGCGTGAAAAGCAGAAAGTACGTCGCATCTACGGCGTGCTGGAGCGTCAGTTC
CGCGGTTACTACCAGGAAGCTTCCCGTCGCAAGGGTTCTACCGGTGAGAACCTGCTGCAACTGCTCGAGTGC
CGCCTGGACAACGTCGTATACCGCATGGGCTTCGGTTCCACTCGTTCGGAATCCCGCCAGCTGGTATCCCAC
AAGGCCATCACCGTCAACGGTCAGACCGTCAACATCCCTTCCTACCAAGTGAAGGCCGGTGACGTCGTAGCT
GTTCGCGAAAAATCGAAGAACCAGCTGCGTATCGCTCAGGCTCTGGAACTCTGTGGCCAGCGCGGTCGCGTC
GAGTGGGTCGAAGTCGACCTCGACAAGAAGGCTGGTACCTTCAAGAGTGCTCCGGCTCGCAGCGACCTGTCC
GCTGATATCAACGAAAACCTGATTGTCGAGCTCTACTCCAAGTAA
Translation:
MARYIGPKCKLSRREGTDLFLKSGARALDSKCKAENVPGQHGQRRGRLSDYGLQLREKQKVRRIYGVLERQF
RGYYQEASRRKGSTGENLLQLLECRLDNVVYRMGFGSTRSESRQLVSHKAITVNGQTVNIPSYQVKAGDVVA
VREKSKNQLRIAQALELCGQRGRVEWVEVDLDKKAGTFKSAPARSDLSADINENLIVELYSK*
AnnotationID:3809GeneID:3802
AnnotatorUID: diggins
Modification Date/Time: 2005-04-01 13:01:32
Gene Name:rpsD
Confidence Code:2
GeneProduct:30S ribosomal protein S4
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:COG0522
Secondary Functional Category(ies):translation, ribosomal structure and biogenesis
EC Number:
Status:ACTIVE
Pathway:






 
Homology:
>gb|AAN66108.1|AE016239_3 (AE016775) ribosomal protein S4 [Pseudomonas putida KT2440]
          Length = 206

 Score =  353 bits (907), Expect = 3e-97
 Identities = 177/206 (85%), Positives = 187/206 (90%)

>gb|AAO54192.1| (AE016858) ribosomal protein S4 [Pseudomonas syringae pv. tomato
           str. DC3000]
          Length = 206

 Score =  352 bits (902), Expect = 1e-96
 Identities = 170/206 (82%), Positives = 191/206 (92%)

>emb|CAB83419.1| (AL162752) 30S ribosomal protein S4 [Neisseria meningitidis Z2491]
          Length = 206

 Score =  310 bits (793), Expect = 5e-84
 Identities = 155/206 (75%), Positives = 174/206 (84%)








 
Structural Features:
COG0522, RpsD, Ribosomal protein S4 and related proteins 
[Translation, ribosomal structure and biogenesis]
CD-Length = 205 residues, 100.0% aligned
Score =  230 bits (589), Expect = 6e-62
Identities = 128/208 (61%), Positives = 146/208 (70%), Gaps = 5/208 (2%)






   
Genomic Context:






   
Comment:


















    ReferenceID:7607




  
Author/Investigator(s):
        GenNotator





  
Title:
        




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:BLASTP 







    
Data:


    		




 
URL:

















    ReferenceID:24749




  
Author/Investigator(s):
        GenNotator





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:RPSBLAST 







    
Data:


    		




 
URL:

















    ReferenceID:36626




  
Author/Investigator(s):
        





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:Misc (text/plain)







    
Data:3802_cdd.html


    		




 
URL:

















    ReferenceID:36705




  
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.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=6379605

















    ReferenceID:36708




  
Author/Investigator(s):
        Grundy FJ, Henkin TM.





  
Title:
        Cloning and analysis of the Bacillus subtilis rpsD gene, encoding ribosomal protein S4.




  
PubMed:
        1699930


MedLine:
        




    
Source:
J Bacteriol. 1990 Nov;172(11):6372-9.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=1699930









           
Homologs By Global Alignment 

           

       



     
Gene ID:3802
           
Identity:

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

                           

     
HomologID
                           Accession
                           Description
                           Length
                           PctIdentity
                           PctSimilarity
                           Gaps
                           Score
     

     
     
6023
                           PA4239_tr
                           translation of PA4239
                           206
                           99.99
                           99.99
                           0
                           1047.0
     

     
     
167862
                           gb|AAG07627.1|AE004841_5
                           (AE004841) 30S ribosomal protein S4 [Pseudomonas aeruginosa PAO1]
                           206
                           99.99
                           99.99
                           0
                           1047.0
     

     
     
167863
                           gb|AAN66108.1|AE016239_3
                           (AE016775) ribosomal protein S4 [Pseudomonas putida KT2440]
                           206
                           85.92
                           90.77
                           0
                           907.0
     

     
     
167864
                           gb|AAO54192.1|
                           (AE016858) ribosomal protein S4 [Pseudomonas syringae pv. tomato str. DC3000]
                           206
                           82.52
                           92.71
                           0
                           902.0
     

     
     
167865
                           gb|AAQ61822.1|
                           (AE016924) 30S ribosomal protein S4 [Chromobacterium violaceum ATCC 12472]
                           206
                           78.15
                           84.95
                           0
                           822.0
     

     






      

          
GC ORFID: 46804How Found: BLASTX

          
GC_TrimmedSeqID: 69Blast Result ID

          
Subject Sequence Name: t_PA4239Glimmer Score: 

          
Start: 4183187Stop: 4182567

          
Length: 621


          
Start Codon: ATGTruncated Start:

          
Stop Codon: TAATruncated Stop: 

          
Homolog: t_PA4239 translation of PA4239Homolog Bit Score 407.0

          
Other Homologs:  psyr_15may02_Scaffold4_revised_gene5211 (ORF: BLASTX 352.0), t_PA4239 (ORF: GLIMMER)

          
GC ORF Sequence

           
ATGGCTCGTTACAtTGGTCCCAAGTGCAAACTGTCTCGCCGTGAAGGCACCGACCTGTTCCTGAAGAGCGGC 
GCCCGCGCCCTCGACTCGAAGTGCAAGGCTGAAAACGTTCCTGGCCAGCATGGCCAGCGTCGTGGCCGTCTG 
TCCGACTACGGTCTGCAGCTGCGTGAAAAGCAGAAAGTACGTCGCATCTACGGCGTGCTGGAGCGTCAGTTC 
CGCGGTTACTACCAGGAAGCTTCCCGTCGCAAGGGTTCTACCGGTGAGAACCTGCTGCAACTGCTCGAGTGC 
CGCCTGGACAACGTCGTATACCGCATGGGCTTCGGTTCCACTCGTTCGGAATCCCGCCAGCTGGTATCCCAC 
AAGGCCATCACCGTCAACGGTCAGACCGTCAACATCCCTTCCTACCAAGTGAAGGCCGGTGACGTCGTAGCT 
GTTCGCGAAAAATCGAAGAACCAGCTGCGTATCGCTCAGGCTCTGGAACTCTGTGGCCAGCGCGGTCGCGTC 
GAGTGGGTCGAAGTCGACCTCGACAAGAAGGCTGGTACCTTCAAGAGTGCTCCGGCTCGCAGCGACCTGTCC 
GCTGATATCAACGAAAACCTGATTGTCGAGCTCTACTCCAAGTAA