ViewGene
Locus Name:
GeneID:
Location:

GeneID:2462
TrivialName: PA14_16040
AnnotatorUID:
Modification Date/Time:2006-04-06 13:01:23
LocusName:PA14_16040
PAO1 Ortholog Locus:PA3738
Sequence Length:897
Protein Length:298
Start: 1366492
Stop: 1367388
Strand: +
Type:
ChromosomeID:2
Status: ACTIVE
Frame Discrepancy: FALSE
Missense Discrepancy:FALSE
Comments:
Homology: gb|AAG07125.1|AE004793_2 (AE004793) integrase/recombinase XerD [Pseudomonas aeruginosa PAO1]
Identities = 298/298 (100%), Positives = 298/298 (100%)
Sequence:
ATGAGTACCCTCGAACATCCCCTGATCGACCGTTTCCTCGATGCCCTGTGGCTGGAAAAAGGCCTTGCCGAC
AACACCCGCGAGGCTTATCGCAACGACCTCCAGCAGTTCAACGCCTGGCTCGATGGCCGCGGGCTGCGCCTG
GAGGGCATCGGCCGCGACGCCATCCTCGATCACCTGGCCTGGCGCCTGGAACAGGGCTACAAGGCTCGCTCG
ACCGCGCGCTTCCTCTCCGGCCTGCGTGGCTTCTACCGCTATTGCCTGCGCGATGGCCTGATCGCCGAGGAT
CCCACCTTGCAGGTGGACCTGCCGCAACTGGGCAAGCCGTTGCCGAAATCCCTCTCCGAAGCGGACGTCGAG
GCATTGCTGGCGGCGCCGGAAGTCGACGACCCGCTGGGCCTGCGCGATCGCACCATGCTCGAAGTGCTGTAT
GCCTGCGGCCTGCGGGTCAGCGAACTGGTCGGCCTGACCCTGGAGCAGGTCAACCTGCGCCAGGGCGTGGTC
AAGGTCTTCGGCAAGGGCAGCAAGGAGCGCCTGGTGCCGCTCGGCGAGGAAGCCATCGGCTGGCTCGAACGC
TACCTGCGCGAGGCGCGCGGCGACCTGCTCGGCGGGCGGCCCAGCGACGTGCTGTTCCCCAGCCTGCGCGGC
GAACAGATGACCCGCCAGACCTTCTGGCATCGCATCAAGCATCACGCGCAggTGGCGGCGATCGGTACGTCG
ATTTCGCCGCACACCCTGCGCCACGCCTTCGCCACCCACCTGCTCAACCATGGCGCCGACCTGCGGGTGGTG
CAGATGCTGCTCGGCCACAGCGACCTGTCGACCACCCAGATCTATACCCATATCGCCCGGGCCCGCCTCCAG
GATCTGCACGCACGCCACCACCCGCGAGGCTGA
Translation:
MSTLEHPLIDRFLDALWLEKGLADNTREAYRNDLQQFNAWLDGRGLRLEGIGRDAILDHLAWRLEQGYKARS
TARFLSGLRGFYRYCLRDGLIAEDPTLQVDLPQLGKPLPKSLSEADVEALLAAPEVDDPLGLRDRTMLEVLY
ACGLRVSELVGLTLEQVNLRQGVVKVFGKGSKERLVPLGEEAIGWLERYLREARGDLLGGRPSDVLFPSLRG
EQMTRQTFWHRIKHHAQVAAIGTSISPHTLRHAFATHLLNHGADLRVVQMLLGHSDLSTTQIYTHIARARLQ
DLHARHHPRG*
AnnotationID:2470GeneID:2462
AnnotatorUID: diggins
Modification Date/Time: 2005-04-22 08:08:09
Gene Name:xerD
Confidence Code:2
GeneProduct:integrase/recombinase XerD
Cell Localization:()
Synonyms:
Cell Localization Confidence Code:5
MolecularFunction:
Functional Category:(11) DNA replication, recombination, modification and repair
Alternate Gene Product Name:site-specific recombinase
Functional Category Confidence Code:5
COGs:COG4974,COG4973
Secondary Functional Category(ies):
EC Number:
Status:ACTIVE
Pathway:






 
Homology:
>gb|AAO54999.1| (AE016861) integrase/recombinase XerD [Pseudomonas syringae pv.
           tomato str. DC3000]
          Length = 298

 Score =  493 bits (1268), Expect = e-139
 Identities = 234/298 (78%), Positives = 267/298 (89%)

>gb|AAB87499.1| (AF033497) site-specific recombinase [Proteus mirabilis]
          Length = 313

 Score =  358 bits (920), Expect = 2e-98
 Identities = 180/292 (61%), Positives = 225/292 (77%), Gaps = 1/292 (0%)

>gb|AAN81922.1|AE016766_10 (AE016766) Integrase/recombinase xerD [Escherichia coli CFT073]
          Length = 298

 Score =  357 bits (915), Expect = 6e-98
 Identities = 185/290 (63%), Positives = 215/290 (74%), Gaps = 1/290 (0%)










 
Structural Features:
COG4974, XerD, Site-specific recombinase XerD 
[DNA replication, recombination, and repair]
CD-Length = 300 residues, 100.0% aligned
Score =  414 bits (1066), Expect = 1e-116
Identities = 178/300 (59%), Positives = 222/300 (74%), Gaps = 2/300 (0%)

COG4973, XerC, Site-specific recombinase XerC 
[DNA replication, recombination, and repair]
CD-Length = 299 residues,  96.7% aligned
Score =  226 bits (578), Expect = 4e-60
Identities = 115/293 (39%), Positives = 166/293 (56%), Gaps = 5/293 (1%)







   
Genomic Context:






   
Comment:


















    ReferenceID:4927




  
Author/Investigator(s):
        GenNotator





  
Title:
        




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:BLASTP 







    
Data:


    		




 
URL:

















    ReferenceID:22073




  
Author/Investigator(s):
        GenNotator





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:RPSBLAST 







    
Data:


    		




 
URL:

















    ReferenceID:31819




  
Author/Investigator(s):
        





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:Misc (text/plain)







    
Data:2462_cdd.html


    		




 
URL:

















    ReferenceID:34260




  
Author/Investigator(s):
        Villion M, Szatmari G.





  
Title:
        Cloning and characterisation of the Proteus mirabilis xerD gene.




  
PubMed:
        9675854


MedLine:
        




    
Source:
FEMS Microbiol Lett. 1998 Jul 1;164(1):83-90.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=9675854









           
Homologs By Global Alignment 

           

       



     
Gene ID:2462
           
Identity:

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

                           

     
HomologID
                           Accession
                           Description
                           Length
                           PctIdentity
                           PctSimilarity
                           Gaps
                           Score
     

     
     
4130
                           PA3738_tr
                           translation of PA3738
                           298
                           99.99
                           99.99
                           0
                           1553.0
     

     
     
123049
                           gb|AAG07125.1|AE004793_2
                           (AE004793) integrase/recombinase XerD [Pseudomonas aeruginosa PAO1]
                           298
                           99.99
                           99.99
                           0
                           1553.0
     

     
     
123050
                           gb|AAO54999.1|
                           (AE016861) integrase/recombinase XerD [Pseudomonas syringae pv. tomato str. DC3000]
                           298
                           78.52
                           89.59
                           0
                           1268.0
     

     
     
123051
                           gb|AAN67090.1|AE016337_13
                           (AE016779) integrase/recombinase XerD [Pseudomonas putida KT2440]
                           298
                           78.18
                           87.58
                           0
                           1243.0
     

     
     
123052
                           gb|AAN54024.1|AE015540_4
                           (AE015540) integrase/recombinase XerD [Shewanella oneidensis MR-1]
                           300
                           62.00
                           76.00
                           2
                           947.0
     

     






      

          
GC ORFID: 45464How Found: BLASTX

          
GC_TrimmedSeqID: 69Blast Result ID

          
Subject Sequence Name: t_PA3738Glimmer Score: 

          
Start: 3587445Stop: 3586549

          
Length: 897


          
Start Codon: ATGTruncated Start:

          
Stop Codon: TGATruncated Stop: 

          
Homolog: t_PA3738 translation of PA3738Homolog Bit Score 602.0

          
Other Homologs:  psyr_15may02_Scaffold3_revised_gene4562 (ORF: BLASTX 491.0), t_PA3738 (ORF: GLIMMER)

          
GC ORF Sequence

           
ATGAGTACCCTCGAACATCCCCTGATCGACCGTTTCCTCGATGCCCTGTGGCTGGAAAAAGGCCTTGCCGAC 
AACACCCGCGAGGCTTATCGCAACGACCTCCAGCAGTTCAACGCCTGGCTCGATGGCCGCGGGCTGCGCCTG 
GAGGGCATCGGCCGCGACGCCATCCTCGATCACCTGGCCTGGCGCCTGGAACAGGGCTACAAGGCTCGCTCG 
ACCGCGCGCTTCCTCTCCGGCCTGCGTGGCTTCTACCGCTATTGCCTGCGCGATGGCCTGATCGCCGAGGAT 
CCCACCTTGCAGGTGGACCTGCCGCAACTGGGCAAGCCGTTGCCGAAATCCCTCTCCGAAGCGGACGTCGAG 
GCATTGCTGGCGGCGCCGGAAGTCGACGACCCGCTGGGCCTGCGCGATCGCACCATGCTCGAAGTGCTGTAT 
GCCTGCGGCCTGCGGGTCAGCGAACTGGTCGGCCTGACCCTGGAGCAGGTCAACCTGCGCCAGGGCGTGGTC 
AAGGTCTTCGGCAAGGGCAGCAAGGAGCGCCTGGTGCCGCTCGGCGAGGAAGCCATCGGCTGGCTCGAACGC 
TACCTGCGCGAGGCGCGCGGCGACCTGCTCGGCGGGCGGCCCAGCGACGTGCTGTTCCCCAGCCTGCGCGGC 
GAACAGATGACCCGCCAGACCTTCTGGCATCGCATCAAGCATCACGCGCAggTGGCGGCGATCGGTACGTCG 
ATTTCGCCGCACACCCTGCGCCACGCCTTCGCCACCCACCTGCTCAACCATGGCGCCGACCTGCGGGTGGTG 
CAGATGCTGCTCGGCCACAGCGACCTGTCGACCACCCAGATCTATACCCATATCGCCCGGGCCCGCCTCCAG 
GATCTGCACGCACGCCACCACCCGCGAGGCTGA