ViewGene
Locus Name:
GeneID:
Location:

GeneID:4137
TrivialName: PA14_15980
AnnotatorUID:
Modification Date/Time:2006-04-06 13:01:23
LocusName:PA14_15980
PAO1 Ortholog Locus:PA3744
Sequence Length:528
Protein Length:175
Start: 1361312
Stop: 1361839
Strand: +
Type:
ChromosomeID:2
Status: ACTIVE
Frame Discrepancy: FALSE
Missense Discrepancy:FALSE
Comments:
Homology: gb|AAG07131.1|AE004793_8 (AE004793) 16S rRNA processing protein [Pseudomonas aeruginosa PAO1]
Identities = 174/175 (99%), Positives = 174/175 (99%)
Sequence:
ATGCCGACACCCGCCGACGACCTGGTCGTGATCGGCAAGATCGTTTCGGTGTACGGCATCCGCGGTGAGGTG
AAGGTGTATTCCTTTACCGACCCGTTGGACAACCTGCTGGACTATCGCCGCTGGACGCTCCGGCGCGACGGC
GAGATTCGGCAGGCCGAGCTGGTCAGGGGGCGCCTGCATGGCAAGGTCCTGGCCGCCAAGCTCAAGGGGCTC
GACGATCGCGAAGAGGCCCGCACCTTCACCGGTTACGAGATCTGCATCCCGCGTAGCGAGTTGCCCTCTCTC
GAGGAAGGTGAGTACTACTGGCACCAGCTGGAAGGCCTGAAGGTGATCGACCAGGGCGGGCAGTTGCTCGGC
GTGATCGACCATCTGCTGGAAACCGGTGCCAACGATGTCATGGTGGTCAAGCCCTGCGCGGGCAGCCTGGAC
GACCGCGAGCGCCTGTTGCCCTACACCGGGCAATGCGTGCTGTCGATCGACCTGGCCGCTGGCGAGATGCGG
GTGGACTGGGACGCGGACTTCTGA
Translation:
MPTPADDLVVIGKIVSVYGIRGEVKVYSFTDPLDNLLDYRRWTLRRDGEIRQAELVRGRLHGKVLAAKLKGL
DDREEARTFTGYEICIPRSELPSLEEGEYYWHQLEGLKVIDQGGQLLGVIDHLLETGANDVMVVKPCAGSLD
DRERLLPYTGQCVLSIDLAAGEMRVDWDADF*
AnnotationID:4144GeneID:4137
AnnotatorUID: diggins
Modification Date/Time: 2005-04-22 09:09:37
Gene Name:rimM
Confidence Code:2
GeneProduct:16S rRNA processing protein RimM
Cell Localization:()
Synonyms:
Cell Localization Confidence Code:5
MolecularFunction:
Functional Category:(24) Transcription, RNA processing and degradation
Alternate Gene Product Name:
Functional Category Confidence Code:5
COGs:COG0806,pfam01782
Secondary Functional Category(ies):
EC Number:
Status:ACTIVE
Pathway:






 
Homology:
>gb|AAO54995.1| (AE016861) 16S rRNA processing protein RimM [Pseudomonas syringae
           pv. tomato str. DC3000]
          Length = 179

 Score =  282 bits (721), Expect = 7e-76
 Identities = 134/175 (76%), Positives = 153/175 (87%), Gaps = 1/175 (0%)

>gb|AAN81579.1|AE016764_261 (AE016764) 16S rRNA processing protein rimM [Escherichia coli
           CFT073]
          Length = 185

 Score =  138 bits (347), Expect = 2e-32
 Identities = 68/171 (39%), Positives = 108/171 (63%), Gaps = 2/171 (1%)






 
Structural Features:
COG0806, RimM, RimM protein, required for 16S rRNA processing 
[Translation, ribosomal structure and biogenesis]
CD-Length = 174 residues,  98.9% aligned
Score =  188 bits (480), Expect = 5e-49
Identities = 81/176 (46%), Positives = 111/176 (63%), Gaps = 5/176 (2%)

pfam01782, RimM, RimM N-terminal domain. 
The RimM protein is essential for efficient processing of 16S rRNA.
CD-Length = 84 residues, 100.0% aligned
Score = 94.1 bits (234), Expect = 2e-20
Identities = 36/84 (42%), Positives = 50/84 (59%), Gaps = 1/84 (1%)






   
Genomic Context:






   
Comment:


















    ReferenceID:8276




  
Author/Investigator(s):
        GenNotator





  
Title:
        




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:BLASTP 







    
Data:


    		




 
URL:

















    ReferenceID:25419




  
Author/Investigator(s):
        GenNotator





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:RPSBLAST 







    
Data:


    		




 
URL:

















    ReferenceID:31814




  
Author/Investigator(s):
        





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:Misc (text/plain)







    
Data:4137_cdd.html


    		




 
URL:

















    ReferenceID:34265




  
Author/Investigator(s):
        Bylund GO, Wipemo LC, Lundberg LA, Wikstrom PM.





  
Title:
        RimM and RbfA are essential for efficient processing of 16S rRNA in Escherichia coli.




  
PubMed:
        9422595


MedLine:
        




    
Source:
J Bacteriol. 1998 Jan;180(1):73-82.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=9422595









           
Homologs By Global Alignment 

           

       



     
Gene ID:4137
           
Identity:

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

                           

     
HomologID
                           Accession
                           Description
                           Length
                           PctIdentity
                           PctSimilarity
                           Gaps
                           Score
     

     
     
6392
                           PA3744_tr
                           translation of PA3744
                           175
                           99.42
                           99.42
                           0
                           910.0
     

     
     
175258
                           gb|AAG07131.1|AE004793_8
                           (AE004793) 16S rRNA processing protein [Pseudomonas aeruginosa PAO1]
                           175
                           99.42
                           99.42
                           0
                           910.0
     

     
     
175259
                           gb|AAO54995.1|
                           (AE016861) 16S rRNA processing protein RimM [Pseudomonas syringae pv. tomato str. DC3000]
                           179
                           74.86
                           85.47
                           4
                           722.0
     

     
     
175260
                           gb|AAN67085.1|AE016337_8
                           (AE016779) 16S rRNA processing protein RimM [Pseudomonas putida KT2440]
                           178
                           72.47
                           82.58
                           3
                           685.0
     

     
     
175261
                           gb|AAQ61336.1|
                           (AE016923) 16S rRNA processing protein [Chromobacterium violaceum ATCC 12472]
                           175
                           45.14
                           62.28
                           6
                           384.0
     

     






      

          
GC ORFID: 47139How Found: BLASTX

          
GC_TrimmedSeqID: 69Blast Result ID

          
Subject Sequence Name: t_PA3744Glimmer Score: 

          
Start: 3592625Stop: 3592098

          
Length: 528


          
Start Codon: ATGTruncated Start:

          
Stop Codon: TGATruncated Stop: 

          
Homolog: t_PA3744 translation of PA3744Homolog Bit Score 355.0

          
Other Homologs:  psyr_15may02_Scaffold3_revised_gene4559 (ORF: BLASTX 285.0), t_PA3744 (ORF: GLIMMER)

          
GC ORF Sequence

           
ATGCCGACACCCGCCGACGACCTGGTCGTGATCGGCAAGATCGTTTCGGTGTACGGCATCCGCGGTGAGGTG 
AAGGTGTATTCCTTTACCGACCCGTTGGACAACCTGCTGGACTATCGCCGCTGGACGCTCCGGCGCGACGGC 
GAGATTCGGCAGGCCGAGCTGGTCAGGGGGCGCCTGCATGGCAAGGTCCTGGCCGCCAAGCTCAAGGGGCTC 
GACGATCGCGAAGAGGCCCGCACCTTCACCGGTTACGAGATCTGCATCCCGCGTAGCGAGTTGCCCTCTCTC 
GAGGAAGGTGAGTACTACTGGCACCAGCTGGAAGGCCTGAAGGTGATCGACCAGGGCGGGCAGTTGCTCGGC 
GTGATCGACCATCTGCTGGAAACCGGTGCCAACGATGTCATGGTGGTCAAGCCCTGCGCGGGCAGCCTGGAC 
GACCGCGAGCGCCTGTTGCCCTACACCGGGCAATGCGTGCTGTCGATCGACCTGGCCGCTGGCGAGATGCGG 
GTGGACTGGGACGCGGACTTCTGA