ViewGene
Locus Name:
GeneID:
Location:

GeneID:117
TrivialName: PA14_72490
AnnotatorUID:
Modification Date/Time:2006-04-06 13:01:23
LocusName:PA14_72490
PAO1 Ortholog Locus:PA5493
Sequence Length:2742
Protein Length:913
Start: 6459436
Stop: 6456695
Strand: -
Type:
ChromosomeID:2
Status: ACTIVE
Frame Discrepancy: FALSE
Missense Discrepancy:FALSE
Comments:
Homology: gb|AAG08878.1|AE004962_2 (AE004962) DNA polymerase I [Pseudomonas aeruginosa PAO1]
Identities = 911/913 (99%), Positives = 911/913 (99%)
Sequence:
ATGAGCCAAGCGCCCCTCGTCCTGGTGGACGGTTCCTCGTACCTGTACCGCGCCTTCCATGCCCTGCCGCCG
CTGACCACTTCGACCGGCAAGCCCACCGGTGCGGTGAAGGGCGTGCTGAACATGCTCCTGAGCCTGCGCAAG
CAGTACCCGGACAGCCCGTTCGCGGTGGTCTTCGACGCCAAGGGCCCGACCTTCCGCGACGAGCTGTTCGCC
GAGTACAAGGCCAATCGGCCGTCGATGCCCGACGACCTGCGGGTCCAGGTCGAGCCGCTGCATGCCAGCGTC
CGCGCCCTCGGCCTGCCGTTGCTGTGCGTGGAGGGGGTCGAGGCCGACGACGTGATCGGCACCCTGGCGCGC
AGCAGCGCCGCGGCCGGCCGCCCGGTAGTGATTTCCACCGGCGACAAGGACATGGCGCAACTGGTCGACGGG
CACATTACGCTGGTCAACACCATGACCGGTAGCCGCCTCGACGTGGATGGCGTGAAAGAGAAATTCGGCGTC
GGTCCTGAGCTGATCATCGATTTCCTCGCCCTGATGGGCGACAAGGTCGACAACATCCCCGGCGTTCCGGGT
GTCGGCGAGAAAACCGCGCTGGGCCTGCTGACCGGTGTCGGTGGCGGCCTGGAGGTGCTCTACGCCAGCCTG
GACAAGGTGCCCGAGCTACCGATCCGCGGCGCCAAGGGCTTGCCGGCGAAGCTCGAGGAAAATCGCGAGCAG
GCGTTCCTGTCCTATCAACTGGCGACCATCAAGACCGACGTCGAACTGGACGTGGAGATCGACAAGCTGTAT
CCCGGCGAGCCGCAGCGCGAAGCGCTGATCGCCCTGTACCGCGAGCTGGAGTTCAAGAACTGGCTGGACGAC
CTCCTGCGCGAGGCCAAGGAGGCCGGCGAGAACGGCGAGGCGGAAACGCCTATCCAGGCCGAGGTCGACTAC
GACGTGGTGCTCGACCAGGCCGGGTTCGACGCCTGGCTGAAGAAGCTGGAGGAGGCCGAGCTGATCGCCTTC
GATACCGAGACCACCAGCATCGACGCCCAGCAGGCGCAGGTGGTGGGGGTGTCCTTCGCCGTGAAGGAGGGC
GAGGCCGCCTACGTGCCGCTGGCCCACAGCTATATGGGCGTTCCCGAGCAACTGGACCGTGACGCGGTGCTG
CGTGCATTGAAACCGCTGCTGGAGGATCCGAAGAAGCTCAAGGTCGGCCAGCATGCCAAGTACGACATCAAT
GTCCTGGCCAATGCCAGCACCCCCATCGCGCTGCGGGGCGTAGCCTACGACACCATGCTCGAGTCCTATGTG
CTGGACTCCACCGCCACTCGCCACGACATGGACAGCCTGGCCCTGAAGTACCTCGGCCACAGCACCATCCGT
TTCGAGGACATCGCCGGCAAGGGCGCCAAGCAACTGACCTTCGACCAGATCGCCATCGAACAGGCCGGGCCC
TATGCGGCGGAGGACGCCGACGTGACCCTGCGCCTGCACCAGGCCCTGTGGCAGAAGCTGGAGGCGATCCCG
TCCCTGGCCAGGGTCCTGACCGACATCGAGATGCCGCTGGTACCGGTGCTGGCGCGGATCGAGCGCAACGGC
GCGCTGGTCGACGCCAACCTGCTGGGCATCCAGAGCCGCGAACTGGGCGAGAAGATGGTCGCCCTGGAGCGC
CAGGCATACGACCTGGCGGGGCAGGAATTCAACCTCGGCTCGCCCAAGCAGCTCGGCGCGATCCTCTACGAC
AAGCTCGGCCTGCCGGTGCTGAGCAAGACCGCGACCGGCCAGCCGTCCACCGCCGAGGCGGTGCTCGCCGAA
CTGGCCGAGCAGGACTTCGAGCTGCCCAAGGTGATCATGCAGTACCGCTCCATGAGCAAGCTCAAGAGCACC
TACACCGACCGCCTGCCCGAGCAGATCAACCCGCGCACCGGGCGCATCCATACCTCATACCACCAGGCGGTG
GCGGCTACCGGGCGGCTGTCGTCGAGCGACCCGAACCTGCAGAACATCCCGATCCGCACCGCGGAGGGCCGG
CGCATCCGCCAGGCGTTCGTCGCGCCGCAGGGCTACAAGCTATTGGCCGCGGACTACTCGCAGATCGAGCTG
CGGATCATGGCCCACCTGGCCAAGGACGACGGCCTGCTGGATGCCTTCCGCCACGACCTGGACGTACACCGC
GCCACCGCGGCGGAAGTCTTCGGCGTGCCGCTGGAAGACGTCAGCGGCGACCAGCGACGCAGCGCCAAGGCG
ATCAACTTCGGATTGATCTACGGCATGAGCGCCTTCGGCCTGGCCAAGCAGATCGGCGTCGAGCGCAAGGAG
GCCCAGGCCTACATCGACCGTTACTTCGCCCGCTACCCCGGCGTCCTGGCGTACATGGAACGGACCCGCGCC
CAGGCCGCGGAGCAGGGCTTCGTCGAAACCCTGTTCGGCCGTCGCCTGTACCTGCCGGAGATCCATTCGAAG
AACGGTGCCATGCGCAAGGCCGCCGAGCGCACCGCGATCAACGCGCCGATGCAGGGCACCGCGGCGGACATC
ATGAAGCGCGCCATGGTCGCTGTGGATAACTGGCTGCAGGAAAGCGGCCTCGATGCCCGGGTGATCCTCCAG
GTGCACGACGAACTGGTGCTGGAAGTGCGCGAGGACCTGGTCGAGCAGGTGCGCGAGGGAATCCGCCCGCTG
ATGAGCGGCGCGGCGACCCTGGACGTACCGCTGGTGGTCGAGGCGGGTGTCGGTTCGAACTGGGACGAAGCC
CACTGA
Translation:
MSQAPLVLVDGSSYLYRAFHALPPLTTSTGKPTGAVKGVLNMLLSLRKQYPDSPFAVVFDAKGPTFRDELFA
EYKANRPSMPDDLRVQVEPLHASVRALGLPLLCVEGVEADDVIGTLARSSAAAGRPVVISTGDKDMAQLVDG
HITLVNTMTGSRLDVDGVKEKFGVGPELIIDFLALMGDKVDNIPGVPGVGEKTALGLLTGVGGGLEVLYASL
DKVPELPIRGAKGLPAKLEENREQAFLSYQLATIKTDVELDVEIDKLYPGEPQREALIALYRELEFKNWLDD
LLREAKEAGENGEAETPIQAEVDYDVVLDQAGFDAWLKKLEEAELIAFDTETTSIDAQQAQVVGVSFAVKEG
EAAYVPLAHSYMGVPEQLDRDAVLRALKPLLEDPKKLKVGQHAKYDINVLANASTPIALRGVAYDTMLESYV
LDSTATRHDMDSLALKYLGHSTIRFEDIAGKGAKQLTFDQIAIEQAGPYAAEDADVTLRLHQALWQKLEAIP
SLARVLTDIEMPLVPVLARIERNGALVDANLLGIQSRELGEKMVALERQAYDLAGQEFNLGSPKQLGAILYD
KLGLPVLSKTATGQPSTAEAVLAELAEQDFELPKVIMQYRSMSKLKSTYTDRLPEQINPRTGRIHTSYHQAV
AATGRLSSSDPNLQNIPIRTAEGRRIRQAFVAPQGYKLLAADYSQIELRIMAHLAKDDGLLDAFRHDLDVHR
ATAAEVFGVPLEDVSGDQRRSAKAINFGLIYGMSAFGLAKQIGVERKEAQAYIDRYFARYPGVLAYMERTRA
QAAEQGFVETLFGRRLYLPEIHSKNGAMRKAAERTAINAPMQGTAADIMKRAMVAVDNWLQESGLDARVILQ
VHDELVLEVREDLVEQVREGIRPLMSGAATLDVPLVVEAGVGSNWDEAH*
AnnotationID:127GeneID:117
AnnotatorUID: diggins
Modification Date/Time: 2005-03-21 08:08:25
Gene Name:polA
Confidence Code:2
GeneProduct:DNA polymerase I
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:COG0749,pfam00476
Secondary Functional Category(ies):
EC Number:
Status:ACTIVE
Pathway:






 
Homology:
>gb|AAN65757.1|AE016201_9 (AE016774) DNA polymerase I [Pseudomonas putida KT2440]
          Length = 915

 Score = 1439 bits (3726), Expect = 0.0
 Identities = 742/915 (81%), Positives = 813/915 (88%), Gaps = 2/915 (0%)

>gb|AAO53889.1| (AE016857) DNA polymerase I [Pseudomonas syringae pv. tomato str.
           DC3000]
          Length = 925

 Score = 1405 bits (3636), Expect = 0.0
 Identities = 718/921 (77%), Positives = 807/921 (87%), Gaps = 8/921 (0%)

>gb|AAB02998.1| (L19201) DNA polymerase I [Escherichia coli]
          Length = 928

 Score = 1111 bits (2873), Expect = 0.0
 Identities = 577/927 (62%), Positives = 699/927 (75%), Gaps = 20/927 (2%)








 
Structural Features:
COG0749, PolA, DNA polymerase I - 3'-5' exonuclease and polymerase domains 
[DNA replication, recombination, and repair]
CD-Length = 593 residues, 100.0% aligned
Score =  822 bits (2126), Expect = 0.0
Identities = 365/605 (60%), Positives = 448/605 (74%), Gaps = 13/605 (2%)

pfam00476, DNA_pol_A, DNA polymerase family A.
CD-Length = 383 residues, 100.0% aligned
Score =  463 bits (1192), Expect = 5e-131
Identities = 218/383 (56%), Positives = 282/383 (73%), Gaps = 1/383 (0%)







   
Genomic Context:






   
Comment:


















    ReferenceID:237




  
Author/Investigator(s):
        GenNotator





  
Title:
        




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:BLASTP 







    
Data:


    		




 
URL:

















    ReferenceID:17379




  
Author/Investigator(s):
        GenNotator





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:RPSBLAST 







    
Data:


    		




 
URL:

















    ReferenceID:33249




  
Author/Investigator(s):
        





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:Misc (text/plain)







    
Data:117_cdd.html


    		




 
URL:

















    ReferenceID:35599




  
Author/Investigator(s):
        Joyce CM, Kelley WS, Grindley ND.





  
Title:
        Nucleotide sequence of the Escherichia coli polA gene and primary structure of DNA polymerase I.




  
PubMed:
        6276402


MedLine:
        




    
Source:
J Biol Chem. 1982 Feb 25;257(4):1958-64.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=6276402

















    ReferenceID:35600




  
Author/Investigator(s):
        Lopez P, Martinez S, Diaz A, Espinosa M, Lacks SA.





  
Title:
        Characterization of the polA gene of Streptococcus pneumoniae and comparison of the DNA polymerase I it encodes to homologous enzymes from Escherichia coli and phage T7.




  
PubMed:
        2537309


MedLine:
        




    
Source:
J Biol Chem. 1989 Mar 5;264(7):4255-63.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=2537309

















    ReferenceID:35601




  
Author/Investigator(s):
        Huberts P, Mizrahi V.





  
Title:
        Cloning and sequence analysis of the gene encoding the DNA polymerase I from Mycobacterium tuberculosis.




  
PubMed:
        7590302


MedLine:
        




    
Source:
Gene. 1995 Oct 16;164(1):133-6.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=7590302

















    ReferenceID:35602




  
Author/Investigator(s):
        Tvermyr M, Kristiansen BE, Kristensen T.





  
Title:
        Cloning, sequence analysis and expression in E. coli of the DNA polymerase I gene from Chloroflexus aurantiacus, a green nonsulfur eubacterium.




  
PubMed:
        9526698


MedLine:
        




    
Source:
Genet Anal. 1998 Jan;14(3):75-83.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=9526698

















    ReferenceID:35603




  
Author/Investigator(s):
        Rodes B, Liu H, Johnson S, George R, Steiner B.





  
Title:
        Molecular cloning of a gene (poIA) coding for an unusual DNA polymerase I from Treponema pallidum.




  
PubMed:
        10882092


MedLine:
        




    
Source:
J Med Microbiol. 2000 Jul;49(7):657-67.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10882092









           
Homologs By Global Alignment 

           

       



     
Gene ID:117
           
Identity:

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

                           

     
HomologID
                           Accession
                           Description
                           Length
                           PctIdentity
                           PctSimilarity
                           Gaps
                           Score
     

     
     
222
                           PA5493_tr
                           translation of PA5493
                           913
                           99.78
                           99.78
                           0
                           4581.0
     

     
     
16596
                           gb|AAG08878.1|AE004962_2
                           (AE004962) DNA polymerase I [Pseudomonas aeruginosa PAO1]
                           913
                           99.78
                           99.78
                           0
                           4581.0
     

     
     
16597
                           gb|AAN65757.1|AE016201_9
                           (AE016774) DNA polymerase I [Pseudomonas putida KT2440]
                           915
                           81.09
                           88.85
                           2
                           3728.0
     

     
     
16598
                           gb|AAO53889.1|
                           (AE016857) DNA polymerase I [Pseudomonas syringae pv. tomato str. DC3000]
                           925
                           77.62
                           87.24
                           12
                           3643.0
     

     
     
16599
                           gb|AAG43102.1|AF038542_1
                           (AF038542) DNA polymerase I [Pseudomonas fluorescens]
                           939
                           76.67
                           85.19
                           26
                           3609.0
     

     






      

          
GC ORFID: 43119How Found: BLASTX

          
GC_TrimmedSeqID: 69Blast Result ID

          
Subject Sequence Name: t_PA5493Glimmer Score: 

          
Start: 5723125Stop: 5720384

          
Length: 2742


          
Start Codon: ATGTruncated Start:

          
Stop Codon: TGATruncated Stop: 

          
Homolog: t_PA5493 translation of PA5493Homolog Bit Score 1769.0

          
Other Homologs:  psyr_15may02_Scaffold2_revised_gene3897 (ORF: BLASTX 1411.0), t_PA5493 (ORF: GLIMMER)

          
GC ORF Sequence

           
ATGAGCCAAGCGCCCCTCGTCCTGGTGGACGGTTCCTCGTACCTGTACCGCGCCTTCCATGCCCTGCCGCCG 
CTGACCACTTCGACCGGCAAGCCCACCGGTGCGGTGAAGGGCGTGCTGAACATGCTCCTGAGCCTGCGCAAG 
CAGTACCCGGACAGCCCGTTCGCGGTGGTCTTCGACGCCAAGGGCCCGACCTTCCGCGACGAGCTGTTCGCC 
GAGTACAAGGCCAATCGGCCGTCGATGCCCGACGACCTGCGGGTCCAGGTCGAGCCGCTGCATGCCAGCGTC 
CGCGCCCTCGGCCTGCCGTTGCTGTGCGTGGAGGGGGTCGAGGCCGACGACGTGATCGGCACCCTGGCGCGC 
AGCAGCGCCGCGGCCGGCCGCCCGGTAGTGATTTCCACCGGCGACAAGGACATGGCGCAACTGGTCGACGGG 
CACATTACGCTGGTCAACACCATGACCGGTAGCCGCCTCGACGTGGATGGCGTGAAAGAGAAATTCGGCGTC 
GGTCCTGAGCTGATCATCGATTTCCTCGCCCTGATGGGCGACAAGGTCGACAACATCCCCGGCGTTCCGGGT 
GTCGGCGAGAAAACCGCGCTGGGCCTGCTGACCGGTGTCGGTGGCGGCCTGGAGGTGCTCTACGCCAGCCTG 
GACAAGGTGCCCGAGCTACCGATCCGCGGCGCCAAGGGCTTGCCGGCGAAGCTCGAGGAAAATCGCGAGCAG 
GCGTTCCTGTCCTATCAACTGGCGACCATCAAGACCGACGTCGAACTGGACGTGGAGATCGACAAGCTGTAT 
CCCGGCGAGCCGCAGCGCGAAGCGCTGATCGCCCTGTACCGCGAGCTGGAGTTCAAGAACTGGCTGGACGAC 
CTCCTGCGCGAGGCCAAGGAGGCCGGCGAGAACGGCGAGGCGGAAACGCCTATCCAGGCCGAGGTCGACTAC 
GACGTGGTGCTCGACCAGGCCGGGTTCGACGCCTGGCTGAAGAAGCTGGAGGAGGCCGAGCTGATCGCCTTC 
GATACCGAGACCACCAGCATCGACGCCCAGCAGGCGCAGGTGGTGGGGGTGTCCTTCGCCGTGAAGGAGGGC 
GAGGCCGCCTACGTGCCGCTGGCCCACAGCTATATGGGCGTTCCCGAGCAACTGGACCGTGACGCGGTGCTG 
CGTGCATTGAAACCGCTGCTGGAGGATCCGAAGAAGCTCAAGGTCGGCCAGCATGCCAAGTACGACATCAAT 
GTCCTGGCCAATGCCAGCACCCCCATCGCGCTGCGGGGCGTAGCCTACGACACCATGCTCGAGTCCTATGTG 
CTGGACTCCACCGCCACTCGCCACGACATGGACAGCCTGGCCCTGAAGTACCTCGGCCACAGCACCATCCGT 
TTCGAGGACATCGCCGGCAAGGGCGCCAAGCAACTGACCTTCGACCAGATCGCCATCGAACAGGCCGGGCCC 
TATGCGGCGGAGGACGCCGACGTGACCCTGCGCCTGCACCAGGCCCTGTGGCAGAAGCTGGAGGCGATCCCG 
TCCCTGGCCAGGGTCCTGACCGACATCGAGATGCCGCTGGTACCGGTGCTGGCGCGGATCGAGCGCAACGGC 
GCGCTGGTCGACGCCAACCTGCTGGGCATCCAGAGCCGCGAACTGGGCGAGAAGATGGTCGCCCTGGAGCGC 
CAGGCATACGACCTGGCGGGGCAGGAATTCAACCTCGGCTCGCCCAAGCAGCTCGGCGCGATCCTCTACGAC 
AAGCTCGGCCTGCCGGTGCTGAGCAAGACCGCGACCGGCCAGCCGTCCACCGCCGAGGCGGTGCTCGCCGAA 
CTGGCCGAGCAGGACTTCGAGCTGCCCAAGGTGATCATGCAGTACCGCTCCATGAGCAAGCTCAAGAGCACC 
TACACCGACCGCCTGCCCGAGCAGATCAACCCGCGCACCGGGCGCATCCATACCTCATACCACCAGGCGGTG 
GCGGCTACCGGGCGGCTGTCGTCGAGCGACCCGAACCTGCAGAACATCCCGATCCGCACCGCGGAGGGCCGG 
CGCATCCGCCAGGCGTTCGTCGCGCCGCAGGGCTACAAGCTATTGGCCGCGGACTACTCGCAGATCGAGCTG 
CGGATCATGGCCCACCTGGCCAAGGACGACGGCCTGCTGGATGCCTTCCGCCACGACCTGGACGTACACCGC 
GCCACCGCGGCGGAAGTCTTCGGCGTGCCGCTGGAAGACGTCAGCGGCGACCAGCGACGCAGCGCCAAGGCG 
ATCAACTTCGGATTGATCTACGGCATGAGCGCCTTCGGCCTGGCCAAGCAGATCGGCGTCGAGCGCAAGGAG 
GCCCAGGCCTACATCGACCGTTACTTCGCCCGCTACCCCGGCGTCCTGGCGTACATGGAACGGACCCGCGCC 
CAGGCCGCGGAGCAGGGCTTCGTCGAAACCCTGTTCGGCCGTCGCCTGTACCTGCCGGAGATCCATTCGAAG 
AACGGTGCCATGCGCAAGGCCGCCGAGCGCACCGCGATCAACGCGCCGATGCAGGGCACCGCGGCGGACATC 
ATGAAGCGCGCCATGGTCGCTGTGGATAACTGGCTGCAGGAAAGCGGCCTCGATGCCCGGGTGATCCTCCAG 
GTGCACGACGAACTGGTGCTGGAAGTGCGCGAGGACCTGGTCGAGCAGGTGCGCGAGGGAATCCGCCCGCTG 
ATGAGCGGCGCGGCGACCCTGGACGTACCGCTGGTGGTCGAGGCGGGTGTCGGTTCGAACTGGGACGAAGCC 
CACTGA