ViewGene
Locus Name:
GeneID:
Location:

GeneID:393
TrivialName: PA14_59180
AnnotatorUID:
Modification Date/Time:2006-04-06 13:01:23
LocusName:PA14_59180
PAO1 Ortholog Locus:
Sequence Length:1926
Protein Length:641
Start: 5268174
Stop: 5270099
Strand: +
Type:
ChromosomeID:2
Status: ACTIVE
Frame Discrepancy: FALSE
Missense Discrepancy:FALSE
Comments:
Homology: gb|AAP84217.1| (AY273869) topoisomerase I [Pseudomonas aeruginosa]
Identities = 641/641 (100%), Positives = 641/641 (100%)
Sequence:
ATGCACATCGTAATCATTGAAGCCCCGGGCAAGCTGAAAAAGCTGAGGTCCCTTCTCCCCTCGATTCGTCCC
GACGTGACCTGGCAGGTCGAGGCGACAGCCGGCCACATCAGAGACCTACCCGTTCACGGGCAGGATCCGCAG
ATGCTCACCGTCGGCGTGGGCCAGGATTTCAAACCGCACTACCAGATCCTCTCGGGCAAGGAAAAAACCGTC
GCACGGCTGAAGGAGCTGCGGCAGAAAGCCGTGGAAATCTACGTCGCATCGGACCCGGATCGCGAAGGCGAA
AGCATTGGCTGGCACATCCTCCAAGCTGCCGGGATCAAGAACTACAAGCGCGTTGCCTTCAAAGAAATCACA
AAGTCATGCATCACCGCCGAACTCAGCTCGCCGCGTCGCCTGGACCTCCCGAAGGTCGCCTCGCAGGAATGC
CGTCGCGTCATCGATCGCCTGGTGGGGTATCTGGTCACGCCAGAGTTGCGGCGCGTGATGGGTAGGCCGACC
ACCGCCGGGCGCGTGCAGTCCGTCGCGGTGTACCTGGTGGTCCTGCGAGAGCGGGAGATCCGCGCCTTCACA
GCAATCAAGCACTTCGGGGTGGAACTGACCTTCGTTTCGCCCAGCGACGGCCGTACCTGGACGGCGGAATGG
GATCCAGTGCCCGTGTTTGCCAGCGAGGAGTTCCCGTATGTCCAGGATCGTCAACTCGCAGAACTGGTGGGG
GCTATACGTAATGTCATCGTCGAGACCTGCATTGATAGCGAAGAAACCGATGCGCCTCCGGCACCGTTCATC
TCCTCCTCGCTCCAGATGGCCGCCGGGAATGCGCTGAAGTGGTCACCCGACAAGACGATGAAGGTCGCCCAG
CGGCTGTATGAACAGGGGCTCATCACCTACCACCGGACGGACAACCCCAATATCTCGAAGGACTCGATGCCG
GATATCCGTGCTGTCGCCAAAGCCTTGGGGCTGAAGTGTGTTGAGCAACAGCGGATGTTCAAAGCGGACCAA
GACGCCCAGGAAGGCCACCCCGCCATCACCCCTACCGACTGGATGGCCGCTGCCGCCGGTGAAACTGCTGAT
GAGCAGGCGCTGTACCAGCTCATTCGAGTCCGCGCGCTTGCCAGTCAGATCGAAGCTGCCGTGTACGCAGTG
AGAACCATCACCCTCCTGGGCGTCGGCCCCGACAAAAAGCCGCTGCGCTTCGGCGCCAAAGGGAAGCTGTTG
AACGTGCCTGGCTGGAGAAAACTGCTGCAGGGTGATGACGCCGAGGAGCAGAAGAACGAAACGCCTTCAAAC
CCCATCCCGATCCCGGCGCTGGAGCCACGCCAGATACTCAAGGTCTACAGCGGCGAGGTCCTGGAGAAGAAA
ACCACCCCTCCCAAGCGATTCACCGACGCCAGCCTGGTGGGCGAGATGAAGCGCCGCGGGATTGGTCGGCCA
TCCTCCTACGCCTCGATCGTGAAGAACATCATCGACAAGGGCCAGGTGCAGATGAAGGGGCGAAGCCTGATC
CCCGGCGAGCTGGGAGAGGCCACCATCGCGCTCCTGGAGCACAACTTCAGCTTCCTCAGCCTCGACTTCACC
CGCAACCTCGAGGTCGCCTTGGACCGGATCGCCAACAGCGAGGACACCTACATGAACGTGGTCCAGCAGTTC
TACCAGCTACTACAGACAGAGCTGCAGACACTCCGCGCGCTCCCCAGCGCACAGGACGAACCACGCGCAAGC
TCCACCGCCAGTATCTCCTCGGCGCCGACCAGCGACTTCCTTTGCGGCAAGTGCGGTCTGCCCCTGGTTCAC
CGCAAGAAAGCCGGCAAAGGCGGCTTCGACTTCTGGGGTTGCAGCGGCTATCGAACAACAGGGTGCAAGGTT
AGCTACCCCACCAAGAGCGGCCGGCCTGACTTCGACAACCCGCGCGGGCTATAG
Translation:
MHIVIIEAPGKLKKLRSLLPSIRPDVTWQVEATAGHIRDLPVHGQDPQMLTVGVGQDFKPHYQILSGKEKTV
ARLKELRQKAVEIYVASDPDREGESIGWHILQAAGIKNYKRVAFKEITKSCITAELSSPRRLDLPKVASQEC
RRVIDRLVGYLVTPELRRVMGRPTTAGRVQSVAVYLVVLREREIRAFTAIKHFGVELTFVSPSDGRTWTAEW
DPVPVFASEEFPYVQDRQLAELVGAIRNVIVETCIDSEETDAPPAPFISSSLQMAAGNALKWSPDKTMKVAQ
RLYEQGLITYHRTDNPNISKDSMPDIRAVAKALGLKCVEQQRMFKADQDAQEGHPAITPTDWMAAAAGETAD
EQALYQLIRVRALASQIEAAVYAVRTITLLGVGPDKKPLRFGAKGKLLNVPGWRKLLQGDDAEEQKNETPSN
PIPIPALEPRQILKVYSGEVLEKKTTPPKRFTDASLVGEMKRRGIGRPSSYASIVKNIIDKGQVQMKGRSLI
PGELGEATIALLEHNFSFLSLDFTRNLEVALDRIANSEDTYMNVVQQFYQLLQTELQTLRALPSAQDEPRAS
STASISSAPTSDFLCGKCGLPLVHRKKAGKGGFDFWGCSGYRTTGCKVSYPTKSGRPDFDNPRGL*
AnnotationID:402GeneID:393
AnnotatorUID: danlee
Modification Date/Time: 2006-02-03 18:06:54
Gene Name:
Confidence Code:3
GeneProduct:topoisomerase I - like protein
Cell Localization:(1) Cytoplasmic
Synonyms:
Cell Localization Confidence Code:1
MolecularFunction:
Functional Category:(11) DNA replication, recombination, modification and repair
Alternate Gene Product Name:
Functional Category Confidence Code:5
COGs:COG0550,cd00186,pfam01131,smart00437
Secondary Functional Category(ies):
EC Number:5.99.1.2
Status:ACTIVE
Pathway:






 
Homology:
>gb|AAF85572.1|AE003851_3 (AE003851) topoisomerase I [Xylella fastidiosa]
          Length = 660

 Score =  538 bits (1385), Expect = e-152
 Identities = 295/673 (43%), Positives = 399/673 (59%), Gaps = 47/673 (6%)

>gb|AAN80207.1|AE016760_66 (AE016760) DNA topoisomerase I [Escherichia coli CFT073]
          Length = 879

 Score =  320 bits (819), Expect = 2e-86
 Identities = 229/656 (34%), Positives = 342/656 (52%), Gaps = 79/656 (12%)

>gb|AAP16774.1| (AE016982) DNA topoisomerase type I, omega protein [Shigella
           flexneri 2a str. 2457T]
          Length = 865

 Score =  318 bits (814), Expect = 9e-86
 Identities = 228/656 (34%), Positives = 341/656 (51%), Gaps = 79/656 (12%)






 
Structural Features:
COG0550, TopA, Topoisomerase IA 
[DNA replication, recombination, and repair]
CD-Length = 570 residues,  97.5% aligned
Score =  440 bits (1134), Expect = 2e-124
Identities = 218/581 (37%), Positives = 318/581 (54%), Gaps = 41/581 (7%)

cd00186, TOP1Ac, DNA Topoisomerase, subtype IA
CD-Length = 418 residues,  99.0% aligned
Score =  309 bits (794), Expect = 5e-85
Identities = 149/433 (34%), Positives = 227/433 (52%), Gaps = 31/433 (7%)

pfam01131, Topoisom_bac, DNA topoisomerase.
CD-Length = 409 residues, 100.0% aligned
Score =  272 bits (697), Expect = 9e-74
Identities = 145/422 (34%), Positives = 221/422 (52%), Gaps = 27/422 (6%)

smart00437, TOP1Ac, Bacterial DNA topoisomerase I DNA-binding domain
CD-Length = 260 residues,  99.6% aligned
Score =  205 bits (522), Expect = 2e-53
Identities = 103/273 (37%), Positives = 151/273 (55%), Gaps = 25/273 (9%)








   
Genomic Context:






   
Comment:
Similar to topA (PA3011 and PA14_25110).


















    ReferenceID:789




  
Author/Investigator(s):
        GenNotator





  
Title:
        




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:BLASTP 







    
Data:


    		




 
URL:

















    ReferenceID:17931




  
Author/Investigator(s):
        GenNotator





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:RPSBLAST 







    
Data:


    		




 
URL:

















    ReferenceID:38279




  
Author/Investigator(s):
        





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:Misc (text/plain)







    
Data:393_cdd.html


    		




 
URL:

















    ReferenceID:38280




  
Author/Investigator(s):
        Head NE, Yu H.





  
Title:
        Cross-sectional analysis of clinical and environmental isolates of Pseudomonas aeruginosa: biofilm formation, virulence, and genome diversity.




  
PubMed:
        14688090


MedLine:
        




    
Source:
Infect Immun. 2004 Jan;72(1):133-44.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.pubmedcentral.gov/articlerender.fcgi?tool=pubmed&pubmedid=14688090

















    ReferenceID:38281




  
Author/Investigator(s):
        Tse-Dinh YC, Wang JC.





  
Title:
        Complete nucleotide sequence of the topA gene encoding Escherichia coli DNA topoisomerase I.




  
PubMed:
        3029379


MedLine:
        




    
Source:
J Mol Biol. 1986 Oct 5;191(3):321-31.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=3029379&query_hl=5&itool=pubmed_DocSum

















    ReferenceID:38282




  
Author/Investigator(s):
        Wang JC, Becherer K





  
Title:
        Cloning of the gene topA encoding for DNA topoisomerase I and the physical mapping of the cysB-topA-trp region of Escherichia coli.




  
PubMed:
        6300778


MedLine:
        




    
Source:
Nucleic Acids Res. 1983 Mar 25;11(6):1773-90.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.pubmedcentral.gov/articlerender.fcgi?tool=pubmed&pubmedid=6300778









           
Homologs By Global Alignment 

           

       



     
Gene ID:393
           
Identity:

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

                           

     
HomologID
                           Accession
                           Description
                           Length
                           PctIdentity
                           PctSimilarity
                           Gaps
                           Score
     

     
     
30480
                           gb|AAP84217.1|
                           (AY273869) topoisomerase I [Pseudomonas aeruginosa]
                           641
                           99.99
                           99.99
                           0
                           3303.0
     

     
     
30481
                           gb|AAF85572.1|AE003851_3
                           (AE003851) topoisomerase I [Xylella fastidiosa]
                           675
                           43.70
                           59.11
                           49
                           1420.0
     

     






      

          
GC ORFID: 43395How Found: BLASTX

          
GC_TrimmedSeqID: 69Blast Result ID

          
Subject Sequence Name: t_RL092Glimmer Score: 

          
Start: 4531853Stop: 4533778

          
Length: 1926


          
Start Codon: ATGTruncated Start:

          
Stop Codon: TAGTruncated Stop: 

          
Homolog: t_RL092 topA 641 Homolog: XFa0003 / Topoisomerase I; DNA replication / X.fastidiosa / 9a5c (AAF85572) translation of RL092Homolog Bit Score 1276.0

          
Other Homologs:  t_RL092 (ORF: GLIMMER)

          
GC ORF Sequence

           
ATGCACATCGTAATCATTGAAGCCCCGGGCAAGCTGAAAAAGCTGAGGTCCCTTCTCCCCTCGATTCGTCCC 
GACGTGACCTGGCAGGTCGAGGCGACAGCCGGCCACATCAGAGACCTACCCGTTCACGGGCAGGATCCGCAG 
ATGCTCACCGTCGGCGTGGGCCAGGATTTCAAACCGCACTACCAGATCCTCTCGGGCAAGGAAAAAACCGTC 
GCACGGCTGAAGGAGCTGCGGCAGAAAGCCGTGGAAATCTACGTCGCATCGGACCCGGATCGCGAAGGCGAA 
AGCATTGGCTGGCACATCCTCCAAGCTGCCGGGATCAAGAACTACAAGCGCGTTGCCTTCAAAGAAATCACA 
AAGTCATGCATCACCGCCGAACTCAGCTCGCCGCGTCGCCTGGACCTCCCGAAGGTCGCCTCGCAGGAATGC 
CGTCGCGTCATCGATCGCCTGGTGGGGTATCTGGTCACGCCAGAGTTGCGGCGCGTGATGGGTAGGCCGACC 
ACCGCCGGGCGCGTGCAGTCCGTCGCGGTGTACCTGGTGGTCCTGCGAGAGCGGGAGATCCGCGCCTTCACA 
GCAATCAAGCACTTCGGGGTGGAACTGACCTTCGTTTCGCCCAGCGACGGCCGTACCTGGACGGCGGAATGG 
GATCCAGTGCCCGTGTTTGCCAGCGAGGAGTTCCCGTATGTCCAGGATCGTCAACTCGCAGAACTGGTGGGG 
GCTATACGTAATGTCATCGTCGAGACCTGCATTGATAGCGAAGAAACCGATGCGCCTCCGGCACCGTTCATC 
TCCTCCTCGCTCCAGATGGCCGCCGGGAATGCGCTGAAGTGGTCACCCGACAAGACGATGAAGGTCGCCCAG 
CGGCTGTATGAACAGGGGCTCATCACCTACCACCGGACGGACAACCCCAATATCTCGAAGGACTCGATGCCG 
GATATCCGTGCTGTCGCCAAAGCCTTGGGGCTGAAGTGTGTTGAGCAACAGCGGATGTTCAAAGCGGACCAA 
GACGCCCAGGAAGGCCACCCCGCCATCACCCCTACCGACTGGATGGCCGCTGCCGCCGGTGAAACTGCTGAT 
GAGCAGGCGCTGTACCAGCTCATTCGAGTCCGCGCGCTTGCCAGTCAGATCGAAGCTGCCGTGTACGCAGTG 
AGAACCATCACCCTCCTGGGCGTCGGCCCCGACAAAAAGCCGCTGCGCTTCGGCGCCAAAGGGAAGCTGTTG 
AACGTGCCTGGCTGGAGAAAACTGCTGCAGGGTGATGACGCCGAGGAGCAGAAGAACGAAACGCCTTCAAAC 
CCCATCCCGATCCCGGCGCTGGAGCCACGCCAGATACTCAAGGTCTACAGCGGCGAGGTCCTGGAGAAGAAA 
ACCACCCCTCCCAAGCGATTCACCGACGCCAGCCTGGTGGGCGAGATGAAGCGCCGCGGGATTGGTCGGCCA 
TCCTCCTACGCCTCGATCGTGAAGAACATCATCGACAAGGGCCAGGTGCAGATGAAGGGGCGAAGCCTGATC 
CCCGGCGAGCTGGGAGAGGCCACCATCGCGCTCCTGGAGCACAACTTCAGCTTCCTCAGCCTCGACTTCACC 
CGCAACCTCGAGGTCGCCTTGGACCGGATCGCCAACAGCGAGGACACCTACATGAACGTGGTCCAGCAGTTC 
TACCAGCTACTACAGACAGAGCTGCAGACACTCCGCGCGCTCCCCAGCGCACAGGACGAACCACGCGCAAGC 
TCCACCGCCAGTATCTCCTCGGCGCCGACCAGCGACTTCCTTTGCGGCAAGTGCGGTCTGCCCCTGGTTCAC 
CGCAAGAAAGCCGGCAAAGGCGGCTTCGACTTCTGGGGTTGCAGCGGCTATCGAACAACAGGGTGCAAGGTT 
AGCTACCCCACCAAGAGCGGCCGGCCTGACTTCGACAACCCGCGCGGGCTATAG