ViewGene
Locus Name:
GeneID:
Location:

GeneID:5462
TrivialName: PA14_09030
AnnotatorUID:
Modification Date/Time:2006-04-06 13:01:23
LocusName:PA14_09030
PAO1 Ortholog Locus:PA4245
Sequence Length:177
Protein Length:58
Start: 767752
Stop: 767928
Strand: +
Type:
ChromosomeID:2
Status: ACTIVE
Frame Discrepancy: FALSE
Missense Discrepancy:FALSE
Comments:
Homology: gb|AAG07633.1|AE004841_11 (AE004841) 50S ribosomal protein L30 [Pseudomonas aeruginosa PAO1]
Identities = 58/58 (100%), Positives = 58/58 (100%)
Sequence:
ATGGCAACTGTCAAAGTCACTCTGGTCAAGAGCCTGAACGGCCGTCTGGCCAACCACAAGGCTTGCGTCAAG
GGTCTCGGCCTGCGTCGCATCAATCATACCGTCGAAGTTCAGGACACTCCTGAGAACCGCGGCATGATCAAC
AAGGCCTACTACCTGCTGCGTGTGGAGGGTTAA
Translation:
MATVKVTLVKSLNGRLANHKACVKGLGLRRINHTVEVQDTPENRGMINKAYYLLRVEG*
AnnotationID:5467GeneID:5462
AnnotatorUID: diggins
Modification Date/Time: 2005-04-01 18:06:19
Gene Name:rpmD
Confidence Code:2
GeneProduct:50S ribosomal protein L30
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:COG1841,pfam00327
Secondary Functional Category(ies):translation, ribosomal structure and biogenesis
EC Number:
Status:ACTIVE
Pathway:






 
Homology:
>gb|AAN66102.1|AE016238_20 (AE016775) ribosomal protein L30 [Pseudomonas putida KT2440]
          Length = 58

 Score =  107 bits (266), Expect = 2e-23
 Identities = 50/58 (86%), Positives = 55/58 (94%)

>gb|AAO54186.1| (AE016858) ribosomal protein L30 [Pseudomonas syringae pv. tomato
          str. DC3000]
          Length = 58

 Score =  103 bits (256), Expect = 3e-22
 Identities = 47/58 (81%), Positives = 53/58 (91%)

>gb|AAO09251.1|AE016799_149 (AE016799) Ribosomal protein L30/L7E [Vibrio vulnificus CMCP6]
          Length = 58

 Score = 82.0 bits (201), Expect = 7e-16
 Identities = 39/57 (68%), Positives = 47/57 (82%)






 
Structural Features:
COG1841, RpmD, Ribosomal protein L30/L7E 
[Translation, ribosomal structure and biogenesis]
CD-Length = 55 residues,  98.2% aligned
Score = 64.7 bits (158), Expect = 2e-12
Identities = 27/54 (50%), Positives = 38/54 (70%)

pfam00327, Ribosomal_L30, Ribosomal protein L30p/L7e. 
CD-Length = 53 residues,  90.6% aligned
Score = 45.2 bits (107), Expect = 2e-06
Identities = 16/48 (33%), Positives = 25/48 (52%)







   
Genomic Context:






   
Comment:


















    ReferenceID:10921




  
Author/Investigator(s):
        GenNotator





  
Title:
        




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:BLASTP 







    
Data:


    		




 
URL:

















    ReferenceID:28067




  
Author/Investigator(s):
        GenNotator





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:RPSBLAST 







    
Data:


    		




 
URL:

















    ReferenceID:36531




  
Author/Investigator(s):
        





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:Misc (text/plain)







    
Data:5462_cdd.html


    		




 
URL:

















    ReferenceID:36719




  
Author/Investigator(s):
        Cerretti DP, Dean D, Davis GR, Bedwell DM, Nomura M.





  
Title:
        The spc ribosomal protein operon of Escherichia coli: sequence and cotranscription of the ribosomal protein genes and a protein export gene.




  
PubMed:
        6222285


MedLine:
        




    
Source:
Nucleic Acids Res. 1983 May 11;11(9):2599-616.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=6222285

















    ReferenceID:36720




  
Author/Investigator(s):
        Ritter E, Wittmann-Liebold B.





  
Title:
        The primary structure of protein L30 from Escherichia coli ribosomes.




  
PubMed:
        776670


MedLine:
        




    
Source:
FEBS Lett. 1975 Dec 1;60(1):153-5.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=76210773&dopt=Abstract









           
Homologs By Global Alignment 

           

       



     
Gene ID:5462
           
Identity:

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

                           

     
HomologID
                           Accession
                           Description
                           Length
                           PctIdentity
                           PctSimilarity
                           Gaps
                           Score
     

     
     
7862
                           PA4245_tr
                           translation of PA4245
                           58
                           99.99
                           99.99
                           0
                           296.0
     

     
     
196734
                           gb|AAG07633.1|AE004841_11
                           (AE004841) 50S ribosomal protein L30 [Pseudomonas aeruginosa PAO1]
                           58
                           99.99
                           99.99
                           0
                           296.0
     

     
     
196735
                           gb|AAN66102.1|AE016238_20
                           (AE016775) ribosomal protein L30 [Pseudomonas putida KT2440]
                           58
                           86.20
                           94.82
                           0
                           266.0
     

     
     
196736
                           gb|AAO54186.1|
                           (AE016858) ribosomal protein L30 [Pseudomonas syringae pv. tomato str. DC3000]
                           58
                           81.03
                           91.37
                           0
                           256.0
     

     






      

          
GC ORFID: 48464How Found: BLASTX

          
GC_TrimmedSeqID: 69Blast Result ID

          
Subject Sequence Name: t_PA4245Glimmer Score: 

          
Start: 4186187Stop: 4186011

          
Length: 177


          
Start Codon: ATGTruncated Start:

          
Stop Codon: TAATruncated Stop: 

          
Homolog: t_PA4245 translation of PA4245Homolog Bit Score 118.0

          
Other Homologs:  psyr_15may02_Scaffold4_revised_gene5205 (ORF: BLASTX 103.0)

          
GC ORF Sequence

           
ATGGCAACTGTCAAAGTCACTCTGGTCAAGAGCCTGAACGGCCGTCTGGCCAACCACAAGGCTTGCGTCAAG 
GGTCTCGGCCTGCGTCGCATCAATCATACCGTCGAAGTTCAGGACACTCCTGAGAACCGCGGCATGATCAAC 
AAGGCCTACTACCTGCTGCGTGTGGAGGGTTAA