ViewGene
Locus Name:
GeneID:
Location:

GeneID:3940
TrivialName: PA14_17230
AnnotatorUID:
Modification Date/Time:2006-04-06 13:01:23
LocusName:PA14_17230
PAO1 Ortholog Locus:PA3642
Sequence Length:606
Protein Length:201
Start: 1476965
Stop: 1477570
Strand: +
Type:
ChromosomeID:2
Status: ACTIVE
Frame Discrepancy: FALSE
Missense Discrepancy:FALSE
Comments:
Homology: gb|AAG07030.1|AE004784_3 (AE004784) ribonuclease HII [Pseudomonas aeruginosa PAO1]
Identities = 198/201 (98%), Positives = 198/201 (98%)
Sequence:
ATGCAACTGGGCCTGGATTTCAATCTGGTGGAGGATCTGGTCGCGGGCGTCGACGAGGTCGGTCGCGGTCCG
TTGTGCGGTCCGGTGGTCACCGCCGCGGTGATTCTCGACCCGAGCCGCCCGATCCTCGGCCTGAACGACTCG
AAGAAGCTCAGCGAAGCCCGCCGCGAGGCGCTGTTCGAAGAGATCCGCGAGAAGGCCCTGGCCTGGTGCATC
GCCCGCGCCGAGGTCGAGGAGATCGACCGGCTGAACATTCTGCATGCCACCATGCTCGCCATGCAACGCGCG
GTCGAAGGCCTCAGCGTGACTCCGCGGCTGGCCCTGATCGACGGCAATCGCTGTCCGAAACTGGCGGTGCCC
AGCGCGCCGGTGGTCAAGGGCGACAGCCAGGTACCGGCGATCGCCGCGGCGTCGATCCTGGCCAAGGTCAGT
CGCGACCGGGAAATGGTCGAGCTGGACCGGGTCTATCCGGGCTATGGCATGGCCGGGCACAAGGGCTATCCG
ACCGCTGTCCATCTCGAGGCGCTTTCCCGTCTCGGCCCGACGCCGATCCATCGACGCTCGTTTGCTCCGGTT
CGCGAATTGCTGGATGTCCCTGTTCAATAA
Translation:
MQLGLDFNLVEDLVAGVDEVGRGPLCGPVVTAAVILDPSRPILGLNDSKKLSEARREALFEEIREKALAWCI
ARAEVEEIDRLNILHATMLAMQRAVEGLSVTPRLALIDGNRCPKLAVPSAPVVKGDSQVPAIAAASILAKVS
RDREMVELDRVYPGYGMAGHKGYPTAVHLEALSRLGPTPIHRRSFAPVRELLDVPVQ*
AnnotationID:3947GeneID:3940
AnnotatorUID: diggins
Modification Date/Time: 2005-04-20 21:09:33
Gene Name:rnhB
Confidence Code:2
GeneProduct:ribonuclease HII
Cell Localization:()
Synonyms:
Cell Localization Confidence Code:5
MolecularFunction:
Functional Category:(11) DNA replication, recombination, modification and repair
Alternate Gene Product Name:
Functional Category Confidence Code:5
COGs:COG0164,pfam01351
Secondary Functional Category(ies):
EC Number:3.1.26.4
Status:ACTIVE
Pathway:






 
Homology:
>gb|AAN67226.1|AE016349_7 (AE016779) ribonuclease HII [Pseudomonas putida KT2440]
          Length = 207

 Score =  336 bits (861), Expect = 6e-92
 Identities = 168/193 (87%), Positives = 182/193 (94%)

>gb|AAN41835.1|AE015054_6 (AE015054) RNAse HII, degrades RNA of DNA-RNA hybrids [Shigella
           flexneri 2a str. 301]
          Length = 198

 Score =  260 bits (664), Expect = 4e-69
 Identities = 133/184 (72%), Positives = 147/184 (79%)

>gb|AAC73294.1| (AE000127) RNAse HII, degrades RNA of DNA-RNA hybrids [Escherichia
           coli K12]
          Length = 198

 Score =  259 bits (662), Expect = 7e-69
 Identities = 133/184 (72%), Positives = 147/184 (79%)








 
Structural Features:
COG0164, RnhB, Ribonuclease HII 
[DNA replication, recombination, and repair]
CD-Length = 199 residues,  97.0% aligned
Score =  256 bits (656), Expect = 3e-69
Identities = 120/193 (62%), Positives = 136/193 (70%), Gaps = 4/193 (2%)

pfam01351, RNase_HII, Ribonuclease HII.
CD-Length = 197 residues, 100.0% aligned
Score =  184 bits (469), Expect = 1e-47
dentities = 99/198 (50%), Positives = 123/198 (62%), Gaps = 21/198 (10%)






   
Genomic Context:






   
Comment:


















    ReferenceID:7882




  
Author/Investigator(s):
        GenNotator





  
Title:
        




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:BLASTP 







    
Data:


    		




 
URL:

















    ReferenceID:25025




  
Author/Investigator(s):
        GenNotator





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:RPSBLAST 







    
Data:


    		




 
URL:

















    ReferenceID:31901




  
Author/Investigator(s):
        





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:Misc (text/plain)







    
Data:3940_cdd.html


    		




 
URL:

















    ReferenceID:34204




  
Author/Investigator(s):
        Itaya M.





  
Title:
        Isolation and characterization of a second RNase H (RNase HII) of Escherichia coli K-12 encoded by the rnhB gene.




  
PubMed:
        2172991


MedLine:
        




    
Source:
Proc Natl Acad Sci U S A. 1990 Nov;87(21):8587-91.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=2172991

















    ReferenceID:34205




  
Author/Investigator(s):
        Zhang YB, Ayalew S, Lacks SA.





  
Title:
        The rnhB gene encoding RNase HII of Streptococcus pneumoniae and evidence of conserved motifs in eucaryotic genes.




  
PubMed:
        9190796


MedLine:
        




    
Source:
J Bacteriol. 1997 Jun;179(12):3828-36.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=9190796









           
Homologs By Global Alignment 

           

       



     
Gene ID:3940
           
Identity:

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

                           

     
HomologID
                           Accession
                           Description
                           Length
                           PctIdentity
                           PctSimilarity
                           Gaps
                           Score
     

     
     
6176
                           PA3642_tr
                           translation of PA3642
                           201
                           98.50
                           98.50
                           0
                           994.0
     

     
     
171371
                           gb|AAG07030.1|AE004784_3
                           (AE004784) ribonuclease HII [Pseudomonas aeruginosa PAO1]
                           201
                           98.50
                           98.50
                           0
                           994.0
     

     
     
171372
                           gb|AAN67226.1|AE016349_7
                           (AE016779) ribonuclease HII [Pseudomonas putida KT2440]
                           207
                           81.15
                           88.40
                           6
                           853.0
     

     
     
171373
                           gb|AAO55068.1|
                           (AE016861) ribonuclease HII [Pseudomonas syringae pv. tomato str. DC3000]
                           217
                           76.03
                           83.87
                           16
                           845.0
     

     
     
171378
                           gb|AAN78712.1|AE016755_212
                           (AE016755) Ribonuclease HII [Escherichia coli CFT073]
                           207
                           65.21
                           72.46
                           15
                           656.0
     

     






      

          
GC ORFID: 46942How Found: BLASTX

          
GC_TrimmedSeqID: 69Blast Result ID

          
Subject Sequence Name: t_PA3642Glimmer Score: 

          
Start: 3476972Stop: 3476367

          
Length: 606


          
Start Codon: ATGTruncated Start:

          
Stop Codon: TAATruncated Stop: 

          
Homolog: t_PA3642 translation of PA3642Homolog Bit Score 387.0

          
Other Homologs:  psyr_15may02_Scaffold3_revised_gene4633 (ORF: BLASTX 335.0), t_PA3642 (ORF: GLIMMER)

          
GC ORF Sequence

           
ATGCAACTGGGCCTGGATTTCAATCTGGTGGAGGATCTGGTCGCGGGCGTCGACGAGGTCGGTCGCGGTCCG 
TTGTGCGGTCCGGTGGTCACCGCCGCGGTGATTCTCGACCCGAGCCGCCCGATCCTCGGCCTGAACGACTCG 
AAGAAGCTCAGCGAAGCCCGCCGCGAGGCGCTGTTCGAAGAGATCCGCGAGAAGGCCCTGGCCTGGTGCATC 
GCCCGCGCCGAGGTCGAGGAGATCGACCGGCTGAACATTCTGCATGCCACCATGCTCGCCATGCAACGCGCG 
GTCGAAGGCCTCAGCGTGACTCCGCGGCTGGCCCTGATCGACGGCAATCGCTGTCCGAAACTGGCGGTGCCC 
AGCGCGCCGGTGGTCAAGGGCGACAGCCAGGTACCGGCGATCGCCGCGGCGTCGATCCTGGCCAAGGTCAGT 
CGCGACCGGGAAATGGTCGAGCTGGACCGGGTCTATCCGGGCTATGGCATGGCCGGGCACAAGGGCTATCCG 
ACCGCTGTCCATCTCGAGGCGCTTTCCCGTCTCGGCCCGACGCCGATCCATCGACGCTCGTTTGCTCCGGTT 
CGCGAATTGCTGGATGTCCCTGTTCAATAA