ViewGene
Locus Name:
GeneID:
Location:

GeneID:3407
TrivialName: PA14_70420
AnnotatorUID:
Modification Date/Time:2006-04-06 13:01:23
LocusName:PA14_70420
PAO1 Ortholog Locus:PA5334
Sequence Length:720
Protein Length:239
Start: 6277015
Stop: 6276296
Strand: -
Type:
ChromosomeID:2
Status: ACTIVE
Frame Discrepancy: FALSE
Missense Discrepancy:FALSE
Comments:
Homology: gb|AAG08719.1|AE004946_3 (AE004946) ribonuclease PH [Pseudomonas aeruginosa PAO1]
Identities = 239/239 (100%), Positives = 239/239 (100%)
Sequence:
ATGAATCGTCCCAGTGGCCGTGCCGCCGACCAGCTGCGCCCGATCCGCATCACCCGCCATTACACCAAGCAC
GCAGAAGGTTCGGTGCTGGTCGAGTTCGGCGATACCAAGGTGATCTGCACCGTCAGCGCCGAGTCCGGGGTG
CCGCGCTTCCTCAAGGGCCAGGGGCAGGGTTGGCTGACCGCCGAGTACGGCATGCTGCCGCGCTCCACCGGC
GAGCGTAACCAGCGCGAGGCCAGCCGCGGCAAGCAGGGCGGTCGTACCCTGGAGATCCAGCGCCTGATCGGC
CGTTCCCTGCGAGCGGCGCTGGACCTCAGCAAGCTCGGCGAGAACACCCTGTACATCGACTGCGACGTGATC
CAGGCCGACGGCGGCACCCGCACCGCCTCGATCACCGGCGCCACCGTGGCGCTGATCGACGCCCTGGCGGTG
CTGAAGAAGCGTGGCGCGCTCAAGGGCAATCCGCTGAAGCAGATGGTCGCCGCCGTTTCCGTGGGCATCTAC
CAGGGCGTGCCGGTCCTCGACCTGGACTACCTGGAGGATTCCGCCGCGGAAACCGACCTGAACGTAGTGATG
ACCGATGCCGGCGGCTTCATCGAGGTGCAGGGAACCGCCGAAGGCGCGCCGTTCCGTCCCGCCGAGCTGAAC
GCCATGCTCGAACTGGCCCAGCAGGGCATGCAGGAGCTGTTCGAACTTCAGCGCGCCGCGCTGGCCGAATGA
Translation:
MNRPSGRAADQLRPIRITRHYTKHAEGSVLVEFGDTKVICTVSAESGVPRFLKGQGQGWLTAEYGMLPRSTG
ERNQREASRGKQGGRTLEIQRLIGRSLRAALDLSKLGENTLYIDCDVIQADGGTRTASITGATVALIDALAV
LKKRGALKGNPLKQMVAAVSVGIYQGVPVLDLDYLEDSAAETDLNVVMTDAGGFIEVQGTAEGAPFRPAELN
AMLELAQQGMQELFELQRAALAE*
AnnotationID:3415GeneID:3407
AnnotatorUID: danlee
Modification Date/Time: 2006-01-31 16:04:52
Gene Name:rph
Confidence Code:2
GeneProduct:ribonuclease PH
Cell Localization:()
Synonyms:
Cell Localization Confidence Code:5
MolecularFunction:
Functional Category:(24) Transcription, RNA processing and degradation
Alternate Gene Product Name:tRNA nucleotidyltransferase
Functional Category Confidence Code:5
COGs:COG0689
Secondary Functional Category(ies):
EC Number:2.7.7.56
Status:ACTIVE
Pathway:






 
Homology:
>gb|AAO53631.1| (AE016856) ribonuclease PH [Pseudomonas syringae pv. tomato str.
           DC3000]
          Length = 240

 Score =  415 bits (1066), Expect = e-115
 Identities = 212/240 (88%), Positives = 226/240 (94%), Gaps = 1/240 (0%)

>gb|AAN70859.1|AE016730_5 (AE016794) ribonuclease PH [Pseudomonas putida KT2440]
          Length = 240

 Score =  409 bits (1052), Expect = e-114
 Identities = 209/240 (87%), Positives = 223/240 (92%), Gaps = 1/240 (0%)

>gb|AAM42521.1| (AE012442) ribonuclease PH [Xanthomonas campestris pv. campestris
           str. ATCC 33913]
          Length = 241

 Score =  335 bits (858), Expect = 2e-91
 Identities = 168/237 (70%), Positives = 200/237 (84%)








 
Structural Features:
COG0689, Rph, RNase PH [Translation, ribosomal structure and biogenesis]
CD-Length = 230 residues,  97.8% aligned
Score =  297 bits (761), Expect = 1e-81
Identities = 152/238 (63%), Positives = 175/238 (73%), Gaps = 16/238 (6%)






   
Genomic Context:






   
Comment:


















    ReferenceID:6817




  
Author/Investigator(s):
        GenNotator





  
Title:
        




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:BLASTP 







    
Data:


    		




 
URL:

















    ReferenceID:23959




  
Author/Investigator(s):
        GenNotator





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:RPSBLAST 







    
Data:


    		




 
URL:

















    ReferenceID:34775




  
Author/Investigator(s):
        





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:Misc (text/plain)







    
Data:3407_cdd.html


    		




 
URL:

















    ReferenceID:35693




  
Author/Investigator(s):
        MacGregor CH, Arora SK, Hager PW, Dail MB, Phibbs PV Jr.





  
Title:
        The nucleotide sequence of the Pseudomonas aeruginosa pyrE-crc-rph region and the purification of the crc gene product.




  
PubMed:
        8824606


MedLine:
        




    
Source:
J Bacteriol. 1996 Oct;178(19):5627-35.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=8824606

















    ReferenceID:35694




  
Author/Investigator(s):
        Hoshiko S, Nojiri C, Matsunaga K, Katsumata K, Satoh E, Nagaoka K.





  
Title:
        Nucleotide sequence of the ribostamycin phosphotransferase gene and of its control region in Streptomyces ribosidificus.




  
PubMed:
        2851496


MedLine:
        




    
Source:
Gene. 1988 Sep 7;68(2):285-96.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=2851496









           
Homologs By Global Alignment 

           

       



     
Gene ID:3407
           
Identity:

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

                           

     
HomologID
                           Accession
                           Description
                           Length
                           PctIdentity
                           PctSimilarity
                           Gaps
                           Score
     

     
     
5442
                           PA5334_tr
                           translation of PA5334
                           239
                           99.99
                           99.99
                           0
                           1197.0
     

     
     
151694
                           gb|AAG08719.1|AE004946_3
                           (AE004946) ribonuclease PH [Pseudomonas aeruginosa PAO1]
                           239
                           99.99
                           99.99
                           0
                           1197.0
     

     
     
151695
                           gb|AAC44429.1|
                           (U38241) RNase PH [Pseudomonas aeruginosa]
                           239
                           94.56
                           95.81
                           0
                           1120.0
     

     
     
151696
                           gb|AAO53631.1|
                           (AE016856) ribonuclease PH [Pseudomonas syringae pv. tomato str. DC3000]
                           240
                           88.33
                           94.16
                           1
                           1068.0
     

     
     
151697
                           gb|AAN70859.1|AE016730_5
                           (AE016794) ribonuclease PH [Pseudomonas putida KT2440]
                           240
                           87.08
                           92.91
                           1
                           1054.0
     

     






      

          
GC ORFID: 46409How Found: BLASTX

          
GC_TrimmedSeqID: 69Blast Result ID

          
Subject Sequence Name: t_PA5334Glimmer Score: 

          
Start: 5540704Stop: 5539985

          
Length: 720


          
Start Codon: ATGTruncated Start:

          
Stop Codon: TGATruncated Stop: 

          
Homolog: t_PA5334 translation of PA5334Homolog Bit Score 465.0

          
Other Homologs:  psyr_15may02_Scaffold2_revised_gene3141 (ORF: BLASTX 416.0), t_PA5334 (ORF: GLIMMER)

          
GC ORF Sequence

           
ATGAATCGTCCCAGTGGCCGTGCCGCCGACCAGCTGCGCCCGATCCGCATCACCCGCCATTACACCAAGCAC 
GCAGAAGGTTCGGTGCTGGTCGAGTTCGGCGATACCAAGGTGATCTGCACCGTCAGCGCCGAGTCCGGGGTG 
CCGCGCTTCCTCAAGGGCCAGGGGCAGGGTTGGCTGACCGCCGAGTACGGCATGCTGCCGCGCTCCACCGGC 
GAGCGTAACCAGCGCGAGGCCAGCCGCGGCAAGCAGGGCGGTCGTACCCTGGAGATCCAGCGCCTGATCGGC 
CGTTCCCTGCGAGCGGCGCTGGACCTCAGCAAGCTCGGCGAGAACACCCTGTACATCGACTGCGACGTGATC 
CAGGCCGACGGCGGCACCCGCACCGCCTCGATCACCGGCGCCACCGTGGCGCTGATCGACGCCCTGGCGGTG 
CTGAAGAAGCGTGGCGCGCTCAAGGGCAATCCGCTGAAGCAGATGGTCGCCGCCGTTTCCGTGGGCATCTAC 
CAGGGCGTGCCGGTCCTCGACCTGGACTACCTGGAGGATTCCGCCGCGGAAACCGACCTGAACGTAGTGATG 
ACCGATGCCGGCGGCTTCATCGAGGTGCAGGGAACCGCCGAAGGCGCGCCGTTCCGTCCCGCCGAGCTGAAC 
GCCATGCTCGAACTGGCCCAGCAGGGCATGCAGGAGCTGTTCGAACTTCAGCGCGCCGCGCTGGCCGAATGA