ViewGene
Locus Name:
GeneID:
Location:

GeneID:109
TrivialName: PA14_65200
AnnotatorUID:
Modification Date/Time:2006-04-06 13:01:23
LocusName:PA14_65200
PAO1 Ortholog Locus:PA4937
Sequence Length:2724
Protein Length:907
Start: 5812799
Stop: 5810076
Strand: -
Type:
ChromosomeID:2
Status: ACTIVE
Frame Discrepancy: FALSE
Missense Discrepancy:FALSE
Comments:
Homology: gb|AAG08322.1|AE004906_10 (AE004906) exoribonuclease RNase R [Pseudomonas aeruginosa PAO1]
Identities = 903/907 (99%), Positives = 903/907 (99%), Gaps = 3/907 (0%)
Sequence:
ATGGCCGATTGGCAAAACCTCGATCCCGAGGCCGCTCGCGAAGCGGAAAAGTACGAAAACCCCATCCCCAGC
CGGGAACTGATCCTGGCTCACCTATCCGAGCGAGGCGCTCCTGCGACTCGCTCCCAGTTGCTCGACGAGTTC
GGGCTCGCCGGCGAGGAGCCGGAAGAGGCCTTGCGTCGTCGCCTGCGCGCCATGGAGCGCGACGGACAGCTT
ATCTATACGCGTCGTGGCGCCTACGCGCCGGTGGACAAGCTGGACCTGATCCGCGGCCGCATCAGCGGGCAC
CGCGATGGCTTCGGCTTCCTGATCCCCGACGATGGCAGCGACGACCTGTTCCTCAGCCCCACCCAGATGCGC
CTGGTGTTCGACGGCGACCGCGCCCTGGCCCGGGTGTCCGGCCATGACCGGCGCGGACGCCGCGAAGGCCAA
CTGGTCGAGGTGATCGAGCGGGCCCACGAGATCGTGGTCGGCCGCTACTTCGAGGAAAGCGGCATCGGCGTG
GTGGTCGCGGACAACCCGAAGATCCAGCAGGAAGTCCTGATCCCGCCGGGCAAGGCCGGCAAGGCCAGGCAC
AACCAGTTCGTCCAGGTGCGCATCGAGCAATGGCCGAGCATCCACCGCCAGGCCCAGGGCGAGATCGTCGAG
GTGCTCGGCGACTACATGGCGCCAGGGATGGAGATCGAAGTCGCCCTGCGCAGCTACGATATCCCCCACGTC
TGGCCGGCCGCGGTGGAGAAGGAAGCGGCCAAGCTCAAGCCGGAAGTGGCGGAGAAGGACAAGGAAAAGCGT
GTCGACCTGCGCCAGGTGCCCTTCGTCACCATCGACGGCGAGGATGCCCGCGACTTCGACGACGCGGTGTAC
GCCGAGGCCAAGCGCGGCGGCGGCTGGCGCCTGTTCGTGGCGATCGCCGATGTCTCGCACTACGTGAAGGTC
GGTTCGGCGCTGGACGAAGAGGCGGCCAGGCGCGGCAACTCGGTGTATTTCCCCGAGCGGGTGATCCCGATG
CTGCCGGAGGTGCTGTCCAATGGTCTCTGCTCGCTGAATCCGCTGGTCGACCGGCTGGCCATGGTCTGCGAG
ATGACCCTGTCCAAGGCCGGCAAGCTGACCGGCTATCAGTTCTACGAAGCGGTGATCCACTCCCATGCGCGC
CTGACCTACACCAAGGTCAGCCAGTTGCTCGAGCATCCCGACAGCGTCGAGGCCGAGAACCTGCGCCAGCAG
TTGCCCGGCGTGGTGCCGCACCTGCAGCAGCTGTATGCGCTGTATAAAGCGCTGCTGGCCGGCCGCCATGTC
CGCGGCGCGATCGATTTCGAGACCCAGGAAACCCGCATCGTCTTCGGCGCCGACCGGAAGATCTCGGAAATC
CGCCCGACCCAGCGCAACGATGCGCACCGCCTGATCGAAGAGTGCATGCTCTGCGCCAACGTGGCGACCGCA
CGCTTCCTGCAGAAGCACGCCATCCCGGCGTTGTACCGGGTGCATGACGGCCCGCCGCAGGAAAAGCTCAAC
AACCTGCGCCAGTTCCTCGGCGAGCTGGGGTTGAGCCTCGGCCGCGGCAAGGCCGCGCCGACCCCGGGCGAC
TACCAGGAGTTGCTGGAGAAGATCCACGACCGCGCCGACTTCCGCCTGATCCAGACGGTCATGCTGCGTTCG
CTCAGCCAGGCGGTGTACAGCCCGGACAACAATGGCCACTTCGGCCTCAACTACGACGCCTACACCCACTTC
ACCTCGCCGATCCGGCGCTACCCGGACCTGCTGGTGCATCGTGCGATCCGCAGTGTGATCCGCTCCAAGGCG
GAGACTCCGCACGTGCAGCGGGCCGGCGCGGCGAGCATGCCCAAGGCGCGCATCTATCCGTACGACGAATTG
CGCCTGGACCAGTTGGGCGAGCAGTGCTCGATGACCGAGCGGCGTGCCGACGAGGCCACCCGCGACGTGACC
AACTGGCTGAAGTGCGAATACATGCGCGAGCGGGTCGGCGAGACCTTCCCTGGCGTAATCACCGCGGTCACC
GGTTTCGGTCTGTTCGTCGAGCTGACCGACATCTTCGTCGAAGGCCTGGTGCATGTGACCGCGCTGCCCGGC
GATTACTATCATTTCGACGCCGTGCACCATCGCCTCAGCGGCGAGCGCACCGGGCGCAGCTTCCGTCTCGGC
GACACCACGGAAGTGGTAGTGGCGCGGGTCGACCTGGACGAGCGGAAGATCGATTTCGAGCTGGCCGGAAAC
GTGCTGAGCGCGCCGATCGGACGCAAGAAGCGCAACGGCGACAAGTCGGCGAACGCCGGCAAGGCGCCGAAG
GGGCGCAAGGGCGCATCCGTGCCCGAGGTCGACCTGGAGCCGGCGCTGGCCAGTCCCGACGCCGCGGTGGTG
CCGCGGCGCAAGGCCGGCAAGGTGCAGGCGCTGCCGCCGGTCGCGCCGGAGCTGCTGGCGCAGGCCGCGGAG
ATGCTCGGCAACACCGACGTGCGCAAGAGTCGCGAGGTGAAGCAGGCGCTGCTCGCCGAGGCGCGTGTCGGC
GGCAAGGACAAGGGCGGGAAGAAGGGCAAGGTCGTTCCTGCGGGCAAGAGCGCGAAGGGCAAGGCCAAGGAC
GGCAAGCCCGCCGCTGCCGCCAAGCCGGGCAAGCCGGGCAAGCCGACCAAGCATCGCAAGGGGCCTTCCAAG
CCGAAGGCCGACAACGCTCCGGCCGTCACCGGGGCGCGCAAACGTAAGGCCAAGTCATGA
Translation:
MADWQNLDPEAAREAEKYENPIPSRELILAHLSERGAPATRSQLLDEFGLAGEEPEEALRRRLRAMERDGQL
IYTRRGAYAPVDKLDLIRGRISGHRDGFGFLIPDDGSDDLFLSPTQMRLVFDGDRALARVSGHDRRGRREGQ
LVEVIERAHEIVVGRYFEESGIGVVVADNPKIQQEVLIPPGKAGKARHNQFVQVRIEQWPSIHRQAQGEIVE
VLGDYMAPGMEIEVALRSYDIPHVWPAAVEKEAAKLKPEVAEKDKEKRVDLRQVPFVTIDGEDARDFDDAVY
AEAKRGGGWRLFVAIADVSHYVKVGSALDEEAARRGNSVYFPERVIPMLPEVLSNGLCSLNPLVDRLAMVCE
MTLSKAGKLTGYQFYEAVIHSHARLTYTKVSQLLEHPDSVEAENLRQQLPGVVPHLQQLYALYKALLAGRHV
RGAIDFETQETRIVFGADRKISEIRPTQRNDAHRLIEECMLCANVATARFLQKHAIPALYRVHDGPPQEKLN
NLRQFLGELGLSLGRGKAAPTPGDYQELLEKIHDRADFRLIQTVMLRSLSQAVYSPDNNGHFGLNYDAYTHF
TSPIRRYPDLLVHRAIRSVIRSKAETPHVQRAGAASMPKARIYPYDELRLDQLGEQCSMTERRADEATRDVT
NWLKCEYMRERVGETFPGVITAVTGFGLFVELTDIFVEGLVHVTALPGDYYHFDAVHHRLSGERTGRSFRLG
DTTEVVVARVDLDERKIDFELAGNVLSAPIGRKKRNGDKSANAGKAPKGRKGASVPEVDLEPALASPDAAVV
PRRKAGKVQALPPVAPELLAQAAEMLGNTDVRKSREVKQALLAEARVGGKDKGGKKGKVVPAGKSAKGKAKD
GKPAAAAKPGKPGKPTKHRKGPSKPKADNAPAVTGARKRKAKS*
AnnotationID:119GeneID:109
AnnotatorUID: diggins
Modification Date/Time: 2005-04-26 07:07:08
Gene Name:rnr
Confidence Code:2
GeneProduct:exoribonuclease RNase R
Cell Localization:()
Synonyms:vacB
Cell Localization Confidence Code:5
MolecularFunction:
Functional Category:(24) Transcription, RNA processing and degradation
Alternate Gene Product Name:
Functional Category Confidence Code:5
COGs:COG0557,pfam00773
Secondary Functional Category(ies):
EC Number:3.1.-.-
Status:ACTIVE
Pathway:






 
Homology:
>gb|AAO58363.1| (AE016873) ribonuclease R [Pseudomonas syringae pv. tomato str.
           DC3000]
          Length = 877

 Score = 1259 bits (3258), Expect = 0.0
 Identities = 642/916 (70%), Positives = 734/916 (80%), Gaps = 48/916 (5%)

>gb|AAN70448.1|AE016686_2 (AE016792) ribonuclease R [Pseudomonas putida KT2440]
          Length = 857

 Score = 1213 bits (3139), Expect = 0.0
 Identities = 628/896 (70%), Positives = 705/896 (78%), Gaps = 52/896 (5%)

>gb|AAM84225.1|AE013666_5 (AE013666) ribonuclease R [Yersinia pestis KIM]
          Length = 844

 Score =  818 bits (2113), Expect = 0.0
 Identities = 422/763 (55%), Positives = 537/763 (70%), Gaps = 23/763 (3%)








 
Structural Features:
COG0557, VacB, Exoribonuclease R [Transcription]
CD-Length = 706 residues, 100.0% aligned
Score =  763 bits (1970), Expect = 0.0
Identities = 357/729 (48%), Positives = 454/729 (62%), Gaps = 26/729 (3%)

pfam00773, RNB, RNB-like protein.
CD-Length = 370 residues,  99.2% aligned
Score =  338 bits (869), Expect = 1e-93
Identities = 165/373 (44%), Positives = 219/373 (58%), Gaps = 7/373 (1%)






   
Genomic Context:






   
Comment:


















    ReferenceID:221




  
Author/Investigator(s):
        GenNotator





  
Title:
        




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:BLASTP 







    
Data:


    		




 
URL:

















    ReferenceID:17363




  
Author/Investigator(s):
        GenNotator





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:RPSBLAST 







    
Data:


    		




 
URL:

















    ReferenceID:35106




  
Author/Investigator(s):
        





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:Misc (text/plain)







    
Data:109_cdd.html


    		




 
URL:

















    ReferenceID:35911




  
Author/Investigator(s):
        Riera J, Robb FT, Weiss R, Fontecave M.





  
Title:
        Ribonucleotide reductase in the archaeon Pyrococcus furiosus: a critical enzyme in the evolution of DNA genomes?




  
PubMed:
        9012808


MedLine:
        




    
Source:
Proc Natl Acad Sci U S A. 1997 Jan 21;94(2):475-8.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=9012808

















    ReferenceID:35912




  
Author/Investigator(s):
        Cheng ZF, Deutscher MP.





  
Title:
        Purification and characterization of the Escherichia coli exoribonuclease RNase R. Comparison with RNase II.




  
PubMed:
        11948193


MedLine:
        




    
Source:
J Biol Chem. 2002 Jun 14;277(24):21624-9. Epub 2002 Apr 10.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11948193

















    ReferenceID:35913




  
Author/Investigator(s):
        Tobe T, Sasakawa C, Okada N, Honma Y, Yoshikawa M.





  
Title:
        vacB, a novel chromosomal gene required for expression of virulence genes on the large plasmid of Shigella flexneri.




  
PubMed:
        1400189


MedLine:
        




    
Source:
J Bacteriol. 1992 Oct;174(20):6359-67.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=1400189









           
Homologs By Global Alignment 

           

       



     
Gene ID:109
           
Identity:

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

                           

     
HomologID
                           Accession
                           Description
                           Length
                           PctIdentity
                           PctSimilarity
                           Gaps
                           Score
     

     
     
207
                           PA4937_tr
                           translation of PA4937
                           907
                           99.55
                           99.55
                           3
                           4643.0
     

     
     
15317
                           gb|AAG08322.1|AE004906_10
                           (AE004906) exoribonuclease RNase R [Pseudomonas aeruginosa PAO1]
                           907
                           99.55
                           99.55
                           3
                           4643.0
     

     
     
15318
                           gb|AAO58363.1|
                           (AE016873) ribonuclease R [Pseudomonas syringae pv. tomato str. DC3000]
                           925
                           70.05
                           79.35
                           66
                           3297.0
     

     
     
15319
                           gb|AAN70448.1|AE016686_2
                           (AE016792) ribonuclease R [Pseudomonas putida KT2440]
                           912
                           69.40
                           77.96
                           60
                           3184.0
     

     
     
15320
                           gb|AAM84225.1|AE013666_5
                           (AE013666) ribonuclease R [Yersinia pestis KIM]
                           932
                           48.39
                           61.90
                           113
                           2160.0
     

     






      

          
GC ORFID: 43111How Found: BLASTX

          
GC_TrimmedSeqID: 69Blast Result ID

          
Subject Sequence Name: t_PA4937Glimmer Score: 

          
Start: 5076480Stop: 5073757

          
Length: 2724


          
Start Codon: ATGTruncated Start:

          
Stop Codon: TGATruncated Stop: 

          
Homolog: t_PA4937 translation of PA4937Homolog Bit Score 1791.0

          
Other Homologs:  psyr_15may02_Scaffold2_revised_gene3437 (ORF: BLASTX 1258.0), t_PA4937 (ORF: GLIMMER)

          
GC ORF Sequence

           
ATGGCCGATTGGCAAAACCTCGATCCCGAGGCCGCTCGCGAAGCGGAAAAGTACGAAAACCCCATCCCCAGC 
CGGGAACTGATCCTGGCTCACCTATCCGAGCGAGGCGCTCCTGCGACTCGCTCCCAGTTGCTCGACGAGTTC 
GGGCTCGCCGGCGAGGAGCCGGAAGAGGCCTTGCGTCGTCGCCTGCGCGCCATGGAGCGCGACGGACAGCTT 
ATCTATACGCGTCGTGGCGCCTACGCGCCGGTGGACAAGCTGGACCTGATCCGCGGCCGCATCAGCGGGCAC 
CGCGATGGCTTCGGCTTCCTGATCCCCGACGATGGCAGCGACGACCTGTTCCTCAGCCCCACCCAGATGCGC 
CTGGTGTTCGACGGCGACCGCGCCCTGGCCCGGGTGTCCGGCCATGACCGGCGCGGACGCCGCGAAGGCCAA 
CTGGTCGAGGTGATCGAGCGGGCCCACGAGATCGTGGTCGGCCGCTACTTCGAGGAAAGCGGCATCGGCGTG 
GTGGTCGCGGACAACCCGAAGATCCAGCAGGAAGTCCTGATCCCGCCGGGCAAGGCCGGCAAGGCCAGGCAC 
AACCAGTTCGTCCAGGTGCGCATCGAGCAATGGCCGAGCATCCACCGCCAGGCCCAGGGCGAGATCGTCGAG 
GTGCTCGGCGACTACATGGCGCCAGGGATGGAGATCGAAGTCGCCCTGCGCAGCTACGATATCCCCCACGTC 
TGGCCGGCCGCGGTGGAGAAGGAAGCGGCCAAGCTCAAGCCGGAAGTGGCGGAGAAGGACAAGGAAAAGCGT 
GTCGACCTGCGCCAGGTGCCCTTCGTCACCATCGACGGCGAGGATGCCCGCGACTTCGACGACGCGGTGTAC 
GCCGAGGCCAAGCGCGGCGGCGGCTGGCGCCTGTTCGTGGCGATCGCCGATGTCTCGCACTACGTGAAGGTC 
GGTTCGGCGCTGGACGAAGAGGCGGCCAGGCGCGGCAACTCGGTGTATTTCCCCGAGCGGGTGATCCCGATG 
CTGCCGGAGGTGCTGTCCAATGGTCTCTGCTCGCTGAATCCGCTGGTCGACCGGCTGGCCATGGTCTGCGAG 
ATGACCCTGTCCAAGGCCGGCAAGCTGACCGGCTATCAGTTCTACGAAGCGGTGATCCACTCCCATGCGCGC 
CTGACCTACACCAAGGTCAGCCAGTTGCTCGAGCATCCCGACAGCGTCGAGGCCGAGAACCTGCGCCAGCAG 
TTGCCCGGCGTGGTGCCGCACCTGCAGCAGCTGTATGCGCTGTATAAAGCGCTGCTGGCCGGCCGCCATGTC 
CGCGGCGCGATCGATTTCGAGACCCAGGAAACCCGCATCGTCTTCGGCGCCGACCGGAAGATCTCGGAAATC 
CGCCCGACCCAGCGCAACGATGCGCACCGCCTGATCGAAGAGTGCATGCTCTGCGCCAACGTGGCGACCGCA 
CGCTTCCTGCAGAAGCACGCCATCCCGGCGTTGTACCGGGTGCATGACGGCCCGCCGCAGGAAAAGCTCAAC 
AACCTGCGCCAGTTCCTCGGCGAGCTGGGGTTGAGCCTCGGCCGCGGCAAGGCCGCGCCGACCCCGGGCGAC 
TACCAGGAGTTGCTGGAGAAGATCCACGACCGCGCCGACTTCCGCCTGATCCAGACGGTCATGCTGCGTTCG 
CTCAGCCAGGCGGTGTACAGCCCGGACAACAATGGCCACTTCGGCCTCAACTACGACGCCTACACCCACTTC 
ACCTCGCCGATCCGGCGCTACCCGGACCTGCTGGTGCATCGTGCGATCCGCAGTGTGATCCGCTCCAAGGCG 
GAGACTCCGCACGTGCAGCGGGCCGGCGCGGCGAGCATGCCCAAGGCGCGCATCTATCCGTACGACGAATTG 
CGCCTGGACCAGTTGGGCGAGCAGTGCTCGATGACCGAGCGGCGTGCCGACGAGGCCACCCGCGACGTGACC 
AACTGGCTGAAGTGCGAATACATGCGCGAGCGGGTCGGCGAGACCTTCCCTGGCGTAATCACCGCGGTCACC 
GGTTTCGGTCTGTTCGTCGAGCTGACCGACATCTTCGTCGAAGGCCTGGTGCATGTGACCGCGCTGCCCGGC 
GATTACTATCATTTCGACGCCGTGCACCATCGCCTCAGCGGCGAGCGCACCGGGCGCAGCTTCCGTCTCGGC 
GACACCACGGAAGTGGTAGTGGCGCGGGTCGACCTGGACGAGCGGAAGATCGATTTCGAGCTGGCCGGAAAC 
GTGCTGAGCGCGCCGATCGGACGCAAGAAGCGCAACGGCGACAAGTCGGCGAACGCCGGCAAGGCGCCGAAG 
GGGCGCAAGGGCGCATCCGTGCCCGAGGTCGACCTGGAGCCGGCGCTGGCCAGTCCCGACGCCGCGGTGGTG 
CCGCGGCGCAAGGCCGGCAAGGTGCAGGCGCTGCCGCCGGTCGCGCCGGAGCTGCTGGCGCAGGCCGCGGAG 
ATGCTCGGCAACACCGACGTGCGCAAGAGTCGCGAGGTGAAGCAGGCGCTGCTCGCCGAGGCGCGTGTCGGC 
GGCAAGGACAAGGGCGGGAAGAAGGGCAAGGTCGTTCCTGCGGGCAAGAGCGCGAAGGGCAAGGCCAAGGAC 
GGCAAGCCCGCCGCTGCCGCCAAGCCGGGCAAGCCGGGCAAGCCGACCAAGCATCGCAAGGGGCCTTCCAAG 
CCGAAGGCCGACAACGCTCCGGCCGTCACCGGGGCGCGCAAACGTAAGGCCAAGTCATGA