ViewGene
Locus Name:
GeneID:
Location:

GeneID:4593
TrivialName: PA14_57590
AnnotatorUID:
Modification Date/Time:2006-04-06 13:01:23
LocusName:PA14_57590
PAO1 Ortholog Locus:PA4433
Sequence Length:429
Protein Length:142
Start: 5129502
Stop: 5129074
Strand: -
Type:
ChromosomeID:2
Status: ACTIVE
Frame Discrepancy: FALSE
Missense Discrepancy:FALSE
Comments:
Homology: gb|AAG07821.1|AE004857_12 (AE004857) 50S ribosomal protein L13 [Pseudomonas aeruginosa PAO1]
Identities = 142/142 (100%), Positives = 142/142 (100%)
Sequence:
ATGAAAACCTATACCGCGAAACCGGAAACTGTACAGCGCGACTGGTTCGTCGTCGACGCTGCCGGCCAGACC
CTGGGTCGTCTGGCGACCGAAATTGCCCGCCGCCTGCGTGGCAAGCACAAGCCTGAGTACACTCCGCACGTT
GACACCGGCGACTACATCGTCGTCATCAACGCCGAGCAGGTGCGTGTGACCGGTGCCAAGACCACCGACAAG
ATGTACTACCACCACTCCGGCTTCCCGGGCGGCATCAAGTCGATCAACTTCGAGAAGCTGATCGCCAAGGCC
CCTGAGCGCGTCATCGAGACCGCTGTAAAAGGCATGCTGCCGAAGAACCCTCTGGGTCGCGATATGTATCGC
AAGCTGAAGGTGTACAAGGGTGCCAGCCACCCGCACACCGCTCAGCAGCCCCAAGAACTGAAGATTTAA
Translation:
MKTYTAKPETVQRDWFVVDAAGQTLGRLATEIARRLRGKHKPEYTPHVDTGDYIVVINAEQVRVTGAKTTDK
MYYHHSGFPGGIKSINFEKLIAKAPERVIETAVKGMLPKNPLGRDMYRKLKVYKGASHPHTAQQPQELKI*
AnnotationID:4599GeneID:4593
AnnotatorUID: diggins
Modification Date/Time: 2005-05-02 20:08:28
Gene Name:rplM
Confidence Code:2
GeneProduct:ribosomal protein L13
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:COG0102,pfam00572,KOG3203
Secondary Functional Category(ies):
EC Number:
Status:ACTIVE
Pathway:






 
Homology:
>gb|AAN66939.1|AE016322_6 (AE016778) ribosomal protein L13 [Pseudomonas putida KT2440]
          Length = 142

 Score =  273 bits (699), Expect = 1e-73
 Identities = 132/142 (92%), Positives = 138/142 (97%)


>gb|AAO57875.1| (AE016871) ribosomal protein L13 [Pseudomonas syringae pv. tomato
           str. DC3000]
          Length = 142

 Score =  272 bits (696), Expect = 3e-73
 Identities = 132/141 (93%), Positives = 136/141 (96%)








 
Structural Features:
COG0102, RplM, Ribosomal protein L13 
[Translation, ribosomal structure and biogenesis]
CD-Length = 148 residues,  96.6% aligned
Score =  209 bits (533), Expect = 2e-55
Identities = 89/143 (62%), Positives = 115/143 (80%), Gaps = 1/143 (0%)

pfam00572, Ribosomal_L13, Ribosomal protein L13.
CD-Length = 128 residues, 100.0% aligned
Score =  181 bits (460), Expect = 6e-47
Identities = 75/128 (58%), Positives = 98/128 (76%)

KOG3203, Mitochondrial/chloroplast ribosomal protein L13 
[Translation, ribosomal structure and biogenesis]
CD-Length = 165 residues,  83.0% aligned
Score =  143 bits (362), Expect = 1e-35
Identities = 59/137 (43%), Positives = 81/137 (59%), Gaps = 6/137 (4%)







   
Genomic Context:






   
Comment:


















    ReferenceID:9187




  
Author/Investigator(s):
        GenNotator





  
Title:
        




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:BLASTP 







    
Data:


    		




 
URL:

















    ReferenceID:26328




  
Author/Investigator(s):
        GenNotator





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:RPSBLAST 







    
Data:


    		




 
URL:

















    ReferenceID:31472




  
Author/Investigator(s):
        





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:Misc (text/plain)







    
Data:4593_cdd.html


    		




 
URL:

















    ReferenceID:32818




  
Author/Investigator(s):
        Isono S, Thamm S, Kitakawa M, Isono K.





  
Title:
        Cloning and nucleotide sequencing of the genes for ribosomal proteins S9 (rpsI) and L13 (rplM) of Escherichia coli.




  
PubMed:
        3884974


MedLine:
        




    
Source:
Mol Gen Genet. 1985;198(2):279-82. 	Related Articles, Links







    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=3884974

















    ReferenceID:32819




  
Author/Investigator(s):
        Dabbs ER.





  
Title:
        The gene for ribosomal protein L13, rplM, is located near argR, at about 70 minutes on the Escherichia coli chromosomal linkage map.




  
PubMed:
        7035437


MedLine:
        




    
Source:
J Bacteriol. 1982 Feb;149(2):779-82.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=7035437









           
Homologs By Global Alignment 

           

       



     
Gene ID:4593
           
Identity:

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

                           

     
HomologID
                           Accession
                           Description
                           Length
                           PctIdentity
                           PctSimilarity
                           Gaps
                           Score
     

     
     
6960
                           PA4433_tr
                           translation of PA4433
                           142
                           99.99
                           99.99
                           0
                           747.0
     

     
     
185005
                           gb|AAG07821.1|AE004857_12
                           (AE004857) 50S ribosomal protein L13 [Pseudomonas aeruginosa PAO1]
                           142
                           99.99
                           99.99
                           0
                           747.0
     

     
     
185006
                           gb|AAN66939.1|AE016322_6
                           (AE016778) ribosomal protein L13 [Pseudomonas putida KT2440]
                           142
                           92.95
                           97.18
                           0
                           699.0
     

     
     
185007
                           gb|AAO57875.1|
                           (AE016871) ribosomal protein L13 [Pseudomonas syringae pv. tomato str. DC3000]
                           142
                           92.95
                           95.77
                           0
                           696.0
     

     
     
185022
                           gb|AAN56915.1|AE015825_14
                           (AE015825) ribosomal protein L13 [Shewanella oneidensis MR-1]
                           142
                           76.76
                           82.39
                           0
                           567.0
     

     






      

          
GC ORFID: 47595How Found: BLASTX

          
GC_TrimmedSeqID: 69Blast Result ID

          
Subject Sequence Name: t_PA4433Glimmer Score: 

          
Start: 4393181Stop: 4392753

          
Length: 429


          
Start Codon: ATGTruncated Start:

          
Stop Codon: TAATruncated Stop: 

          
Homolog: t_PA4433 translation of PA4433Homolog Bit Score 292.0

          
Other Homologs:  psyr_15may02_Scaffold12_revised_gene2030 (ORF: BLASTX 275.0), t_PA4433 (ORF: GLIMMER)

          
GC ORF Sequence

           
ATGAAAACCTATACCGCGAAACCGGAAACTGTACAGCGCGACTGGTTCGTCGTCGACGCTGCCGGCCAGACC 
CTGGGTCGTCTGGCGACCGAAATTGCCCGCCGCCTGCGTGGCAAGCACAAGCCTGAGTACACTCCGCACGTT 
GACACCGGCGACTACATCGTCGTCATCAACGCCGAGCAGGTGCGTGTGACCGGTGCCAAGACCACCGACAAG 
ATGTACTACCACCACTCCGGCTTCCCGGGCGGCATCAAGTCGATCAACTTCGAGAAGCTGATCGCCAAGGCC 
CCTGAGCGCGTCATCGAGACCGCTGTAAAAGGCATGCTGCCGAAGAACCCTCTGGGTCGCGATATGTATCGC 
AAGCTGAAGGTGTACAAGGGTGCCAGCCACCCGCACACCGCTCAGCAGCCCCAAGAACTGAAGATTTAA