ViewGene
Locus Name:
GeneID:
Location:

GeneID:4039
TrivialName: PA14_65410
AnnotatorUID:
Modification Date/Time:2006-04-06 13:01:23
LocusName:PA14_65410
PAO1 Ortholog Locus:PA4951
Sequence Length:543
Protein Length:180
Start: 5828213
Stop: 5827671
Strand: -
Type:
ChromosomeID:2
Status: ACTIVE
Frame Discrepancy: FALSE
Missense Discrepancy:FALSE
Comments:
Homology: gb|AAG08336.1|AE004908_2 (AE004908) oligoribonuclease [Pseudomonas aeruginosa PAO1]
Identities = 180/180 (100%), Positives = 180/180 (100%)
Sequence:
ATGCAGAACCCGCAGAACCTTATCTGGATCGACCTGGAGATGACCGGCCTCGATCCGGACCGGGACGTCATC
ATCGAGATGGCCACCATCGTCACCGACAGTGACCTCAACACCCTGGCCGAAGGACCGGTGATCGCCATCCAC
CAGCCAGAGGAAATCCTCGCCGGCATGGACGAGTGGAATACCCGCCAGCACGGCCAGTCCGGCCTGACCCAG
AGGGTTCGGGAAAGTACCGTGAGCATGGCCGAGGCCGAGGCGCAGACCCTGGCCTTCCTCGAGCAGTGGGTG
CCCAAGCGCAGCTCGCCGATCTGCGGCAACAGCATCTGCCAGGACCGCCGCTTCCTCTATAGGCACATGCCC
AGGCTGGAAGGCTACTTCCACTACCGCAACCTCGACGTCTCCACCCTCAAGGAGCTGGCTGCGCGCTGGGCG
CCGCAGGTCCGCGAGAGCTTCAAGAAGGGTAACACCCACCTGGCGCTGGACGATATCCGCGAGTCGATCGCC
GAGCTGCGCCACTATCGCGACCACTTCATCAAGCTCTGA
Translation:
MQNPQNLIWIDLEMTGLDPDRDVIIEMATIVTDSDLNTLAEGPVIAIHQPEEILAGMDEWNTRQHGQSGLTQ
RVRESTVSMAEAEAQTLAFLEQWVPKRSSPICGNSICQDRRFLYRHMPRLEGYFHYRNLDVSTLKELAARWA
PQVRESFKKGNTHLALDDIRESIAELRHYRDHFIKL*
AnnotationID:4046GeneID:4039
AnnotatorUID: diggins
Modification Date/Time: 2005-04-26 08:08:46
Gene Name:orn
Confidence Code:2
GeneProduct:oligoribonuclease
Cell Localization:()
Synonyms:yjeR
Cell Localization Confidence Code:5
MolecularFunction:
Functional Category:(24) Transcription, RNA processing and degradation
Alternate Gene Product Name:3'->5' exoribonuclease
Functional Category Confidence Code:5
COGs:COG1949,pfam00929
Secondary Functional Category(ies):
EC Number:3.1.-.-
Status:ACTIVE
Pathway:






 
Homology:
>gb|AAN70469.1|AE016688_8 (AE016792) oligoribonuclease [Pseudomonas putida KT2440]
          Length = 180

 Score =  331 bits (849), Expect = 1e-90
 Identities = 161/180 (89%), Positives = 167/180 (92%)

>gb|AAO58378.1| (AE016873) oligoribonuclease [Pseudomonas syringae pv. tomato str.
           DC3000]
          Length = 178

 Score =  316 bits (810), Expect = 4e-86
 Identities = 153/179 (85%), Positives = 167/179 (93%), Gaps = 2/179 (1%)

>gb|AAN83671.1|AE016771_182 (AE016771) Oligoribonuclease [Escherichia coli CFT073]
          Length = 220

 Score =  251 bits (641), Expect = 1e-66
 Identities = 120/178 (67%), Positives = 142/178 (79%)






 
Structural Features:
COG1949, Orn, Oligoribonuclease (3'->5' exoribonuclease) 
[RNA processing and modification]
CD-Length = 184 residues,  97.8% aligned
Score =  320 bits (822), Expect = 6e-89
Identities = 134/180 (74%), Positives = 153/180 (85%)

pfam00929, Exonuc_X-T, Exonuclease.
CD-Length = 162 residues, 100.0% aligned
Score =  110 bits (276), Expect = 1e-25
Identities = 48/167 (28%), Positives = 65/167 (38%), Gaps = 8/167 (4%)






   
Genomic Context:






   
Comment:


















    ReferenceID:8080




  
Author/Investigator(s):
        GenNotator





  
Title:
        




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:BLASTP 







    
Data:


    		




 
URL:

















    ReferenceID:25223




  
Author/Investigator(s):
        GenNotator





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:RPSBLAST 







    
Data:


    		




 
URL:

















    ReferenceID:35097




  
Author/Investigator(s):
        





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:Misc (text/plain)







    
Data:4039_cdd.html


    		




 
URL:

















    ReferenceID:35897




  
Author/Investigator(s):
        Zhang X, Zhu L, Deutscher MP.





  
Title:
        Oligoribonuclease is encoded by a highly conserved gene in the 3'-5' exonuclease superfamily.




  
PubMed:
        9573169


MedLine:
        




    
Source:
J Bacteriol. 1998 May;180(10):2779-81.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=9573169









           
Homologs By Global Alignment 

           

       



     
Gene ID:4039
           
Identity:

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

                           

     
HomologID
                           Accession
                           Description
                           Length
                           PctIdentity
                           PctSimilarity
                           Gaps
                           Score
     

     
     
6280
                           PA4951_tr
                           translation of PA4951
                           180
                           99.99
                           99.99
                           0
                           947.0
     

     
     
173091
                           gb|AAG08336.1|AE004908_2
                           (AE004908) oligoribonuclease [Pseudomonas aeruginosa PAO1]
                           180
                           99.99
                           99.99
                           0
                           947.0
     

     
     
173092
                           gb|AAN70469.1|AE016688_8
                           (AE016792) oligoribonuclease [Pseudomonas putida KT2440]
                           180
                           89.44
                           92.77
                           0
                           849.0
     

     
     
173093
                           gb|AAO58378.1|
                           (AE016873) oligoribonuclease [Pseudomonas syringae pv. tomato str. DC3000]
                           180
                           85.00
                           92.77
                           2
                           809.0
     

     
     
173097
                           gb|AAF93514.1|
                           (AE004123) oligoribonuclease [Vibrio cholerae O1 biovar eltor str. N16961]
                           181
                           69.61
                           77.34
                           1
                           636.0
     

     






      

          
GC ORFID: 47041How Found: BLASTX

          
GC_TrimmedSeqID: 69Blast Result ID

          
Subject Sequence Name: t_PA4951Glimmer Score: 

          
Start: 5091894Stop: 5091352

          
Length: 543


          
Start Codon: ATGTruncated Start:

          
Stop Codon: TGATruncated Stop: 

          
Homolog: t_PA4951 translation of PA4951Homolog Bit Score 369.0

          
Other Homologs:  psyr_15may02_Scaffold2_revised_gene3421 (ORF: BLASTX 313.0), t_PA4951 (ORF: GLIMMER)

          
GC ORF Sequence

           
ATGCAGAACCCGCAGAACCTTATCTGGATCGACCTGGAGATGACCGGCCTCGATCCGGACCGGGACGTCATC 
ATCGAGATGGCCACCATCGTCACCGACAGTGACCTCAACACCCTGGCCGAAGGACCGGTGATCGCCATCCAC 
CAGCCAGAGGAAATCCTCGCCGGCATGGACGAGTGGAATACCCGCCAGCACGGCCAGTCCGGCCTGACCCAG 
AGGGTTCGGGAAAGTACCGTGAGCATGGCCGAGGCCGAGGCGCAGACCCTGGCCTTCCTCGAGCAGTGGGTG 
CCCAAGCGCAGCTCGCCGATCTGCGGCAACAGCATCTGCCAGGACCGCCGCTTCCTCTATAGGCACATGCCC 
AGGCTGGAAGGCTACTTCCACTACCGCAACCTCGACGTCTCCACCCTCAAGGAGCTGGCTGCGCGCTGGGCG 
CCGCAGGTCCGCGAGAGCTTCAAGAAGGGTAACACCCACCTGGCGCTGGACGATATCCGCGAGTCGATCGCC 
GAGCTGCGCCACTATCGCGACCACTTCATCAAGCTCTGA