ViewGene
Locus Name:
GeneID:
Location:

GeneID:1680
TrivialName: PA14_47460
AnnotatorUID:
Modification Date/Time:2006-04-06 13:01:23
LocusName:PA14_47460
PAO1 Ortholog Locus:PA1294
Sequence Length:1125
Protein Length:374
Start: 4229267
Stop: 4228143
Strand: -
Type:
ChromosomeID:2
Status: ACTIVE
Frame Discrepancy: FALSE
Missense Discrepancy:FALSE
Comments:
Homology: gb|AAG04683.1|AE004559_2 (AE004559) ribonuclease D [Pseudomonas aeruginosa PAO1]
Identities = 371/374 (99%), Positives = 373/374 (99%)
Sequence:
GTGACCGCGCCCGAAATCCAGTGGATCCGCGATGATGCCAGCCTGGCGCAGCAATGCCGGGAATGGCGCACA
CAGCCGTACCTCGCGCTCGATACCGAGTTCATGCGCGTCGATACCTTCTATCCCGCGGCCGGTCTGGTGCAG
GTGGGCGATGGCCGGCAGGAGTGGCTGATCGATCCGCTGCTGATCCAGGACTGGAGTCCCTTCGCCGAACTG
CTCGAAGACGAGCGGGTGGTGAAGGTGCTGCACGCCTGTAGCGAAGACCTCGAGGTGTTCCTGCGCCTCACC
GGCAGCCTGCCGGTGCCGCTGTTCGATACGCAGTTGGCCGCCGCCTATCTCGGTATGGCCCATTCGATGGGC
TATTCGAAGCTGGTGAAGGAGGTGCTGGACATCGACCTGCCCAAGGACGAGACCCGTTCCGACTGGTTGCAA
CGGCCGCTCACCGAGATGCAGATGCGCTACGCCGCCGACGACGTCCAGCACCTCGCCCAGGTCTACCTGGCC
CTGGATGCGCGGCTGAGCGAGGAGAAACGCGCCTGGCTGCTGGAGGACGGCGCCGAACTGGTCGCCAACCTC
TGCCGCGAGAGCGATCCGCGCGAGGCCTACCGCGAGGTCAAGCTGGGTTGGCGGCTGCGTCCGCAGCAACTG
GCGGTGCTCCGCGAACTCTGCGCCTGGCGCGAGGAGCAGGCACGCCTGCGCAACCGGCCGCGCAACCACGTG
CTGCGCGAACGCACCCTGTGGCCGCTGGCGCGCCTGCTGCCGAAGAACAAGACCGACCTGGCGGCGATCGAG
GACATGCATCCGCGCACCGTGCGCCAGGACGGCGACTTCCTCATCGAACTGATCGCCCAGGCTGCGCGCCTG
CCGCAGAGCGAATGGCCCGAGGCGCTGCCCGAGCCGCTGCCGCCGGAGGTCACCCCGCTGCTCAAGAGCCTG
CGCGCCATCGGCCAGCGCGAAGCGGAGACCCTGGGCATGGCGCCCGAGCTGATGCTGCGCAAGAAGATCCTC
GAGGCACTGCTCAAGAGCGGCTATCCCGAAGGTCCCTACGAACTGCCCGATTCCCTCCGCGGCTGGCGCCGC
GAACGCATGGGCCAGGCCCTGCTGGACGCCCTGGAGAGCGCATGA
Translation:
MTAPEIQWIRDDASLAQQCREWRTQPYLALDTEFMRVDTFYPAAGLVQVGDGRQEWLIDPLLIQDWSPFAEL
LEDERVVKVLHACSEDLEVFLRLTGSLPVPLFDTQLAAAYLGMAHSMGYSKLVKEVLDIDLPKDETRSDWLQ
RPLTEMQMRYAADDVQHLAQVYLALDARLSEEKRAWLLEDGAELVANLCRESDPREAYREVKLGWRLRPQQL
AVLRELCAWREEQARLRNRPRNHVLRERTLWPLARLLPKNKTDLAAIEDMHPRTVRQDGDFLIELIAQAARL
PQSEWPEALPEPLPPEVTPLLKSLRAIGQREAETLGMAPELMLRKKILEALLKSGYPEGPYELPDSLRGWRR
ERMGQALLDALESA*
AnnotationID:1689GeneID:1680
AnnotatorUID: diggins
Modification Date/Time: 2005-04-27 08:08:37
Gene Name:rnd
Confidence Code:2
GeneProduct:ribonuclease D
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:COG0349,pfam01612,cd00007
Secondary Functional Category(ies):translation, ribosomal structure and biogenesis
EC Number:3.1.26.3
Status:ACTIVE
Pathway:






 
Homology:
>gb|AAN70164.1|AE016655_9 (AE016791) ribonuclease D [Pseudomonas putida KT2440]
          Length = 377

 Score =  531 bits (1367), Expect = e-150
 Identities = 257/372 (69%), Positives = 302/372 (81%)

>gb|AAO57388.1| (AE016870) ribonuclease D [Pseudomonas syringae pv. tomato str.
           DC3000]
          Length = 377

 Score =  530 bits (1365), Expect = e-150
 Identities = 257/372 (69%), Positives = 303/372 (81%)

>gb|AAP96280.1| (AE017155) ribonuclease D [Haemophilus ducreyi 35000HP]
          Length = 373

 Score =  235 bits (600), Expect = 3e-61
 Identities = 141/373 (37%), Positives = 215/373 (57%), Gaps = 13/373 (3%)








 
Structural Features:
COG0349, Rnd, Ribonuclease D 
[Translation, ribosomal structure and biogenesis]
CD-Length = 361 residues, 100.0% aligned
Score =  342 bits (879), Expect = 4e-95
Identities = 159/368 (43%), Positives = 208/368 (56%), Gaps = 10/368 (2%)

pfam01612, 3_5_exonuc, 3'-5' exonuclease. 
CD-Length = 172 residues,  99.4% aligned
Score =  133 bits (337), Expect = 3e-32
Identities = 61/171 (35%), Positives = 85/171 (49%), Gaps = 3/171 (1%)

cd00007, 35EXOc, 3'-5' exonuclease. 
CD-Length = 155 residues, 100.0% aligned
Score =  103 bits (259), Expect = 3e-23
Identities = 52/155 (33%), Positives = 67/155 (43%), Gaps = 7/155 (4%)







   
Genomic Context:






   
Comment:


















    ReferenceID:14411




  
Author/Investigator(s):
        GenNotator





  
Title:
        




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:BLASTP 







    
Data:


    		




 
URL:

















    ReferenceID:20510




  
Author/Investigator(s):
        GenNotator





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:RPSBLAST 







    
Data:


    		




 
URL:

















    ReferenceID:37498




  
Author/Investigator(s):
        





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:Misc (text/plain)







    
Data:1680_cdd.html


    		




 
URL:

















    ReferenceID:38020




  
Author/Investigator(s):
        Zhang JR, Deutscher MP.





  
Title:
        Escherichia coli RNase D: sequencing of the rnd structural gene and purification of the overexpressed protein.




  
PubMed:
        3041371


MedLine:
        




    
Source:
Nucleic Acids Res. 1988 Jul 25;16(14A):6265-78.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=3041371









           
Homologs By Global Alignment 

           

       



     
Gene ID:1680
           
Identity:

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

                           

     
HomologID
                           Accession
                           Description
                           Length
                           PctIdentity
                           PctSimilarity
                           Gaps
                           Score
     

     
     
2962
                           PA1294_tr
                           translation of PA1294
                           374
                           99.19
                           99.73
                           0
                           1937.0
     

     
     
92529
                           gb|AAG04683.1|AE004559_2
                           (AE004559) ribonuclease D [Pseudomonas aeruginosa PAO1]
                           374
                           98.93
                           99.73
                           0
                           1934.0
     

     
     
92530
                           gb|AAN70164.1|AE016655_9
                           (AE016791) ribonuclease D [Pseudomonas putida KT2440]
                           378
                           67.98
                           79.89
                           5
                           1366.0
     

     
     
92531
                           gb|AAO57388.1|
                           (AE016870) ribonuclease D [Pseudomonas syringae pv. tomato str. DC3000]
                           378
                           67.98
                           80.15
                           5
                           1364.0
     

     
     
92532
                           dbj|BAA15613.1|
                           (D90825) Ribonuclease D (EC 3.1.13.-) [Escherichia coli]
                           386
                           27.97
                           36.52
                           166
                           473.0
     

     






      

          
GC ORFID: 44682How Found: BLASTX

          
GC_TrimmedSeqID: 69Blast Result ID

          
Subject Sequence Name: t_PA1294Glimmer Score: 

          
Start: 724642Stop: 725766

          
Length: 1125


          
Start Codon: GTGTruncated Start:

          
Stop Codon: TGATruncated Stop: 

          
Homolog: t_PA1294 translation of PA1294Homolog Bit Score 750.0

          
Other Homologs:  psyr_15may02_Scaffold10_revised_gene1735 (ORF: BLASTX 530.0), t_PA1294 (ORF: GLIMMER)

          
GC ORF Sequence

           
GTGACCGCGCCCGAAATCCAGTGGATCCGCGATGATGCCAGCCTGGCGCAGCAATGCCGGGAATGGCGCACA 
CAGCCGTACCTCGCGCTCGATACCGAGTTCATGCGCGTCGATACCTTCTATCCCGCGGCCGGTCTGGTGCAG 
GTGGGCGATGGCCGGCAGGAGTGGCTGATCGATCCGCTGCTGATCCAGGACTGGAGTCCCTTCGCCGAACTG 
CTCGAAGACGAGCGGGTGGTGAAGGTGCTGCACGCCTGTAGCGAAGACCTCGAGGTGTTCCTGCGCCTCACC 
GGCAGCCTGCCGGTGCCGCTGTTCGATACGCAGTTGGCCGCCGCCTATCTCGGTATGGCCCATTCGATGGGC 
TATTCGAAGCTGGTGAAGGAGGTGCTGGACATCGACCTGCCCAAGGACGAGACCCGTTCCGACTGGTTGCAA 
CGGCCGCTCACCGAGATGCAGATGCGCTACGCCGCCGACGACGTCCAGCACCTCGCCCAGGTCTACCTGGCC 
CTGGATGCGCGGCTGAGCGAGGAGAAACGCGCCTGGCTGCTGGAGGACGGCGCCGAACTGGTCGCCAACCTC 
TGCCGCGAGAGCGATCCGCGCGAGGCCTACCGCGAGGTCAAGCTGGGTTGGCGGCTGCGTCCGCAGCAACTG 
GCGGTGCTCCGCGAACTCTGCGCCTGGCGCGAGGAGCAGGCACGCCTGCGCAACCGGCCGCGCAACCACGTG 
CTGCGCGAACGCACCCTGTGGCCGCTGGCGCGCCTGCTGCCGAAGAACAAGACCGACCTGGCGGCGATCGAG 
GACATGCATCCGCGCACCGTGCGCCAGGACGGCGACTTCCTCATCGAACTGATCGCCCAGGCTGCGCGCCTG 
CCGCAGAGCGAATGGCCCGAGGCGCTGCCCGAGCCGCTGCCGCCGGAGGTCACCCCGCTGCTCAAGAGCCTG 
CGCGCCATCGGCCAGCGCGAAGCGGAGACCCTGGGCATGGCGCCCGAGCTGATGCTGCGCAAGAAGATCCTC 
GAGGCACTGCTCAAGAGCGGCTATCCCGAAGGTCCCTACGAACTGCCCGATTCCCTCCGCGGCTGGCGCCGC 
GAACGCATGGGCCAGGCCCTGCTGGACGCCCTGGAGAGCGCATGA