ViewGene
Locus Name:
GeneID:
Location:

GeneID:125
TrivialName: PA14_25110
AnnotatorUID:
Modification Date/Time:2006-04-06 13:01:23
LocusName:PA14_25110
PAO1 Ortholog Locus:PA3011
Sequence Length:2607
Protein Length:868
Start: 2196651
Stop: 2199257
Strand: +
Type:
ChromosomeID:2
Status: ACTIVE
Frame Discrepancy: FALSE
Missense Discrepancy:FALSE
Comments:
Homology: gb|AAG06399.1|AE004726_5 (AE004726) DNA topoisomerase I [Pseudomonas aeruginosa PAO1]
Identities = 868/868 (100%), Positives = 868/868 (100%)
Sequence:
ATGGGTAAATCGCTGGTCATCGTGGAATCCCCGGCCAAGGCCAAGACCATCAACAAGTACCTGGGTAGCCAG
TACGTGGTGAAGTCGAGCATCGGCCACATCCGTGACCTGCCCACCAGTGGTTCGTCGAGTTCCAAGGAGCCG
GCGGCCAAGGGCCGCAAGAGCGCCTCCGAGGCGCCGGCGCTGTCACCGAAGGAGAAGGCCAGGCGCCAACTG
GTCTCGCGCATGGGGGTCGACCCCGAGCATGGCTGGAAGGCCAAGTACGAGATCCTGCCCGGCAAGGAAAAG
GTCATCGACGAGCTGCGCCGCCTGGCCAAGGACGCCGACACCGTCTATCTCGCGACCGACTTGGACCGCGAA
GGGGAGGCCATCGCCTGGCACCTGCGGGAAGCCATCGGCGGTGACGAAAGCCGCTACAAGCGCGTGGTATTC
AACGAAATCACCAAGAAGGCCATTCAGGAGGCCTTCTCCCAGCCCGGCGAGCTCGATATCAACCGGGTGAAC
GCCCAGCAGGCGCGGCGTTTCCTCGACCGCGTGGTCGGCTACATGGTCTCGCCGCTGCTCTGGCAGAAGATT
GCCCGCGGGTTGTCCGCCGGCCGCGTGCAGTCGGTGGCGGTGAAGCTGGTGGTGGAGCGCGAACGCGAGATC
CGCGCCTTCGTCCCGGAAGAGTACTGGGAGGTGCATGCCGACCTCGGTACCGCCAAGGGCGCCAACGTGCGC
TTCGAGGTTACCCGTGAGAAGGGCGAGGCCTTCAAGCCGCTCAACGAAGCCCAGGCCATGGCGGCCCTGGAA
AAGCTCAAGGCGTCGGCCTATAGCGTCGCCAAGCGCGAGGACCGGCCGACCTCCAGCCGACCCTCGGCGCCG
TTCATCACTTCCACCCTGCAGCAGGCGGCGAGCAACCGCCTGGGCTTCGGGGTGAAGAAGACCATGATGATG
GCCCAGCGTCTCTACGAGGCCGGCTACATCACCTACATGCGTACCGACTCGACCAACCTGTCGGCCGATGCC
ATTGGCATGGTCCGCGGTTTCATCGAGGACGAGTTCGGCCAGAAGTACCTGCCGGGCAAGGCCAACGTCTAC
TCGAGCAAGGAGGGCGCCCAGGAAGCGCACGAGGCGATCCGTCCTTCCGACGTCAACCTCAAGCCGACCCAG
CTGTCCGGCATGGAGCGCGACGCCGAGCGCCTGTACGACCTGATCTGGCGCCAATTCGTGGCGTGCCAGATG
ACCCCGGCCGAATACCTCTCGACCAGCGTGAGCGTCACCGCCGGCGATTTCGAACTGCGCGCCAAGGGCCGC
ATCCTCAAGTTCGACGGTTATACCCGGGTACTGCCGCAGCAGAGCAAGCCGGGCGAGGACGACGTCCTGCCG
GAAATGAAGGAAGGCGAGAACCTCAAGCTGATCAAGCTCGATCCGAGCCAGCACTTCACCAAGCCGCCGGCG
CGCTACTCCGAAGCGAGCCTGGTCAAGGAACTGGAGAAGCGCGGTATCGGCCGCCCCTCGACCTACGCGGCG
ATCATCTCCACCATCCAGGAGCGCGGCTACGTAACCACCCACAACCGCCGCTTCTATGCGGAGAAGATGGGC
GACATCGTCACCGATCGGCTCAACGAGAGCTTTGCCAACCTGATGGACTACGGTTTCACCGCCGGGATGGAG
GAGCATCTCGACGACGTGGCCCAGGGCGAGCGCGACTGGAAGCACCTGCTCGACGAGTTCTACGGCGATTTC
AAGAAGAAGCTCGAGGTGGCCGAAGTCAGCGAGAAGGGGATGCGCGCCAACCAGCCGACCCTGACCAACATT
CCCTGCCGCGAGTGCGGCCGGCCGATGATGATTCGTACCGCCTCCACCGGCGTGTTCCTCGGCTGCTCGGGC
TACAGCCTGCCGCCGAAGGAACGTTGCAAGGCGACCGTCAACCTGATTCCCGGCGACGAGATCGCCGCGGAC
GACGAGGGCGAGTCCGAGTCGCGGGTGTTGCGTGGCAAGCATCGCTGCCCGATCTGCAGTACCGCGATGGAC
GCCTACCTGCTGGACGAGAAACACAAGCTGCATATCTGCGGCAACAACCCCGACTGTCCGGGCTACGAGATC
GAGGAAGGCCAGTACCGGATCAAGGGCTACGAAGGGCCGAGCCTGGAATGCGACAAGTGTGGCAGCGAGATG
CAGTTGAAGACCGGCCGTTTCGGCAAGTTCTTCGGTTGCACCAATCCGACCTGCAAGAACACCCGCAAGCTG
CTGAAGAATGGCGAGGCGGCGCCGCCGAAGATGGACGCCATCCGCATGCCTGAATTGAAGTGCGAGAAGGTG
GACGATATCTACGTGCTGCGCGACGGCGCTTCGGGCATGTTCCTGGCCGCCAGCCAGTTCCCGAAGAACCGC
GAGACCCGCGCGCCGTTGGTGAGCGAGATCATCCCGCACAAGGCCGAGCTGGATCCCAAGTACCATTACCTC
TGCGACGCCCCGCAGAAAGACCCGGACGGCCGTCCCGCGGTGATCCGTTTCAGCCGCAAGACCAAGGAGCAA
TACGTGCAGTCCGAGGTCGATGGCAAGCCCACCGGCTGGCGCGCCTTCTACGATGGCGGCAAGTGGAAGGTC
GAAGACAAGCGCTGA
Translation:
MGKSLVIVESPAKAKTINKYLGSQYVVKSSIGHIRDLPTSGSSSSKEPAAKGRKSASEAPALSPKEKARRQL
VSRMGVDPEHGWKAKYEILPGKEKVIDELRRLAKDADTVYLATDLDREGEAIAWHLREAIGGDESRYKRVVF
NEITKKAIQEAFSQPGELDINRVNAQQARRFLDRVVGYMVSPLLWQKIARGLSAGRVQSVAVKLVVEREREI
RAFVPEEYWEVHADLGTAKGANVRFEVTREKGEAFKPLNEAQAMAALEKLKASAYSVAKREDRPTSSRPSAP
FITSTLQQAASNRLGFGVKKTMMMAQRLYEAGYITYMRTDSTNLSADAIGMVRGFIEDEFGQKYLPGKANVY
SSKEGAQEAHEAIRPSDVNLKPTQLSGMERDAERLYDLIWRQFVACQMTPAEYLSTSVSVTAGDFELRAKGR
ILKFDGYTRVLPQQSKPGEDDVLPEMKEGENLKLIKLDPSQHFTKPPARYSEASLVKELEKRGIGRPSTYAA
IISTIQERGYVTTHNRRFYAEKMGDIVTDRLNESFANLMDYGFTAGMEEHLDDVAQGERDWKHLLDEFYGDF
KKKLEVAEVSEKGMRANQPTLTNIPCRECGRPMMIRTASTGVFLGCSGYSLPPKERCKATVNLIPGDEIAAD
DEGESESRVLRGKHRCPICSTAMDAYLLDEKHKLHICGNNPDCPGYEIEEGQYRIKGYEGPSLECDKCGSEM
QLKTGRFGKFFGCTNPTCKNTRKLLKNGEAAPPKMDAIRMPELKCEKVDDIYVLRDGASGMFLAASQFPKNR
ETRAPLVSEIIPHKAELDPKYHYLCDAPQKDPDGRPAVIRFSRKTKEQYVQSEVDGKPTGWRAFYDGGKWKV
EDKR*
AnnotationID:135GeneID:125
AnnotatorUID: diggins
Modification Date/Time: 2005-04-11 18:06:34
Gene Name:topA
Confidence Code:2
GeneProduct:DNA topoisomerase 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:COG0550,cd00186
Secondary Functional Category(ies):
EC Number:5.99.1.2
Status:ACTIVE
Pathway:






 
Homology:
>gb|AAN67752.1|AE016406_7 (AE016782) DNA topoisomerase I [Pseudomonas putida KT2440]
          Length = 869

 Score = 1590 bits (4118), Expect = 0.0
 Identities = 778/869 (89%), Positives = 828/869 (95%), Gaps = 1/869 (0%)

>gb|AAO56989.1| (AE016868) DNA topoisomerase I [Pseudomonas syringae pv. tomato
           str. DC3000]
          Length = 869

 Score = 1547 bits (4006), Expect = 0.0
 Identities = 754/870 (86%), Positives = 819/870 (94%), Gaps = 3/870 (0%)

>gb|AAN55733.1|AE015710_1 (AE015710) DNA topoisomerase I [Shewanella oneidensis MR-1]
          Length = 878

 Score = 1197 bits (3096), Expect = 0.0
 Identities = 600/875 (68%), Positives = 700/875 (80%), Gaps = 15/875 (1%)








 
Structural Features:
COG0550, TopA, Topoisomerase IA 
[DNA replication, recombination, and repair]
CD-Length = 570 residues,  98.1% aligned
Score =  673 bits (1737), Expect = 0.0
Identities = 288/593 (48%), Positives = 371/593 (62%), Gaps = 41/593 (6%)

cd00186, TOP1Ac, DNA Topoisomerase, subtype IA
CD-Length = 418 residues, 100.0% aligned
Score =  461 bits (1188), Expect = 1e-130
Identities = 188/423 (44%), Positives = 268/423 (63%), Gaps = 11/423 (2%)






   
Genomic Context:






   
Comment:


















    ReferenceID:253




  
Author/Investigator(s):
        GenNotator





  
Title:
        




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:BLASTP 







    
Data:


    		




 
URL:

















    ReferenceID:17395




  
Author/Investigator(s):
        GenNotator





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:RPSBLAST 







    
Data:


    		




 
URL:

















    ReferenceID:36036




  
Author/Investigator(s):
        





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:Misc (text/plain)







    
Data:125_cdd.html


    		




 
URL:

















    ReferenceID:36477




  
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









           
Homologs By Global Alignment 

           

       



     
Gene ID:125
           
Identity:

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

                           

     
HomologID
                           Accession
                           Description
                           Length
                           PctIdentity
                           PctSimilarity
                           Gaps
                           Score
     

     
     
234
                           PA3011_tr
                           translation of PA3011
                           868
                           99.99
                           99.99
                           0
                           4527.0
     

     
     
16924
                           gb|AAG06399.1|AE004726_5
                           (AE004726) DNA topoisomerase I [Pseudomonas aeruginosa PAO1]
                           868
                           99.99
                           99.99
                           0
                           4527.0
     

     
     
16925
                           gb|AAN67752.1|AE016406_7
                           (AE016782) DNA topoisomerase I [Pseudomonas putida KT2440]
                           869
                           89.52
                           95.28
                           1
                           4120.0
     

     
     
16926
                           gb|AAO56989.1|
                           (AE016868) DNA topoisomerase I [Pseudomonas syringae pv. tomato str. DC3000]
                           870
                           86.66
                           94.13
                           3
                           4012.0
     

     
     
16927
                           gb|AAN55733.1|AE015710_1
                           (AE015710) DNA topoisomerase I [Shewanella oneidensis MR-1]
                           883
                           67.95
                           79.27
                           20
                           3110.0
     

     






      

          
GC ORFID: 43127How Found: BLASTX

          
GC_TrimmedSeqID: 69Blast Result ID

          
Subject Sequence Name: t_PA3011Glimmer Score: 

          
Start: 2757276Stop: 2754670

          
Length: 2607


          
Start Codon: ATGTruncated Start:

          
Stop Codon: TGATruncated Stop: 

          
Homolog: t_PA3011 translation of PA3011Homolog Bit Score 1748.0

          
Other Homologs:  psyr_15may02_Scaffold9_revised_gene8047 (ORF: BLASTX 1558.0), t_PA3011 (ORF: GLIMMER)

          
GC ORF Sequence

           
ATGGGTAAATCGCTGGTCATCGTGGAATCCCCGGCCAAGGCCAAGACCATCAACAAGTACCTGGGTAGCCAG 
TACGTGGTGAAGTCGAGCATCGGCCACATCCGTGACCTGCCCACCAGTGGTTCGTCGAGTTCCAAGGAGCCG 
GCGGCCAAGGGCCGCAAGAGCGCCTCCGAGGCGCCGGCGCTGTCACCGAAGGAGAAGGCCAGGCGCCAACTG 
GTCTCGCGCATGGGGGTCGACCCCGAGCATGGCTGGAAGGCCAAGTACGAGATCCTGCCCGGCAAGGAAAAG 
GTCATCGACGAGCTGCGCCGCCTGGCCAAGGACGCCGACACCGTCTATCTCGCGACCGACTTGGACCGCGAA 
GGGGAGGCCATCGCCTGGCACCTGCGGGAAGCCATCGGCGGTGACGAAAGCCGCTACAAGCGCGTGGTATTC 
AACGAAATCACCAAGAAGGCCATTCAGGAGGCCTTCTCCCAGCCCGGCGAGCTCGATATCAACCGGGTGAAC 
GCCCAGCAGGCGCGGCGTTTCCTCGACCGCGTGGTCGGCTACATGGTCTCGCCGCTGCTCTGGCAGAAGATT 
GCCCGCGGGTTGTCCGCCGGCCGCGTGCAGTCGGTGGCGGTGAAGCTGGTGGTGGAGCGCGAACGCGAGATC 
CGCGCCTTCGTCCCGGAAGAGTACTGGGAGGTGCATGCCGACCTCGGTACCGCCAAGGGCGCCAACGTGCGC 
TTCGAGGTTACCCGTGAGAAGGGCGAGGCCTTCAAGCCGCTCAACGAAGCCCAGGCCATGGCGGCCCTGGAA 
AAGCTCAAGGCGTCGGCCTATAGCGTCGCCAAGCGCGAGGACCGGCCGACCTCCAGCCGACCCTCGGCGCCG 
TTCATCACTTCCACCCTGCAGCAGGCGGCGAGCAACCGCCTGGGCTTCGGGGTGAAGAAGACCATGATGATG 
GCCCAGCGTCTCTACGAGGCCGGCTACATCACCTACATGCGTACCGACTCGACCAACCTGTCGGCCGATGCC 
ATTGGCATGGTCCGCGGTTTCATCGAGGACGAGTTCGGCCAGAAGTACCTGCCGGGCAAGGCCAACGTCTAC 
TCGAGCAAGGAGGGCGCCCAGGAAGCGCACGAGGCGATCCGTCCTTCCGACGTCAACCTCAAGCCGACCCAG 
CTGTCCGGCATGGAGCGCGACGCCGAGCGCCTGTACGACCTGATCTGGCGCCAATTCGTGGCGTGCCAGATG 
ACCCCGGCCGAATACCTCTCGACCAGCGTGAGCGTCACCGCCGGCGATTTCGAACTGCGCGCCAAGGGCCGC 
ATCCTCAAGTTCGACGGTTATACCCGGGTACTGCCGCAGCAGAGCAAGCCGGGCGAGGACGACGTCCTGCCG 
GAAATGAAGGAAGGCGAGAACCTCAAGCTGATCAAGCTCGATCCGAGCCAGCACTTCACCAAGCCGCCGGCG 
CGCTACTCCGAAGCGAGCCTGGTCAAGGAACTGGAGAAGCGCGGTATCGGCCGCCCCTCGACCTACGCGGCG 
ATCATCTCCACCATCCAGGAGCGCGGCTACGTAACCACCCACAACCGCCGCTTCTATGCGGAGAAGATGGGC 
GACATCGTCACCGATCGGCTCAACGAGAGCTTTGCCAACCTGATGGACTACGGTTTCACCGCCGGGATGGAG 
GAGCATCTCGACGACGTGGCCCAGGGCGAGCGCGACTGGAAGCACCTGCTCGACGAGTTCTACGGCGATTTC 
AAGAAGAAGCTCGAGGTGGCCGAAGTCAGCGAGAAGGGGATGCGCGCCAACCAGCCGACCCTGACCAACATT 
CCCTGCCGCGAGTGCGGCCGGCCGATGATGATTCGTACCGCCTCCACCGGCGTGTTCCTCGGCTGCTCGGGC 
TACAGCCTGCCGCCGAAGGAACGTTGCAAGGCGACCGTCAACCTGATTCCCGGCGACGAGATCGCCGCGGAC 
GACGAGGGCGAGTCCGAGTCGCGGGTGTTGCGTGGCAAGCATCGCTGCCCGATCTGCAGTACCGCGATGGAC 
GCCTACCTGCTGGACGAGAAACACAAGCTGCATATCTGCGGCAACAACCCCGACTGTCCGGGCTACGAGATC 
GAGGAAGGCCAGTACCGGATCAAGGGCTACGAAGGGCCGAGCCTGGAATGCGACAAGTGTGGCAGCGAGATG 
CAGTTGAAGACCGGCCGTTTCGGCAAGTTCTTCGGTTGCACCAATCCGACCTGCAAGAACACCCGCAAGCTG 
CTGAAGAATGGCGAGGCGGCGCCGCCGAAGATGGACGCCATCCGCATGCCTGAATTGAAGTGCGAGAAGGTG 
GACGATATCTACGTGCTGCGCGACGGCGCTTCGGGCATGTTCCTGGCCGCCAGCCAGTTCCCGAAGAACCGC 
GAGACCCGCGCGCCGTTGGTGAGCGAGATCATCCCGCACAAGGCCGAGCTGGATCCCAAGTACCATTACCTC 
TGCGACGCCCCGCAGAAAGACCCGGACGGCCGTCCCGCGGTGATCCGTTTCAGCCGCAAGACCAAGGAGCAA 
TACGTGCAGTCCGAGGTCGATGGCAAGCCCACCGGCTGGCGCGCCTTCTACGATGGCGGCAAGTGGAAGGTC 
GAAGACAAGCGCTGA