ViewGene
Locus Name:
GeneID:
Location:

GeneID:534
TrivialName: PA14_70940
AnnotatorUID:
Modification Date/Time:2006-04-06 13:01:23
LocusName:PA14_70940
PAO1 Ortholog Locus:PA5372
Sequence Length:1686
Protein Length:561
Start: 6321968
Stop: 6320283
Strand: -
Type:
ChromosomeID:2
Status: ACTIVE
Frame Discrepancy: FALSE
Missense Discrepancy:FALSE
Comments:
Homology: gb|AAG08757.1|AE004949_4 (AE004949) choline dehydrogenase [Pseudomonas aeruginosa PAO1]
Identities = 558/561 (99%), Positives = 559/561 (99%)
Sequence:
ATGTCCCAGGAATTCGACTACATCATCATCGGAGCCGGCTCTGCCGGTAACGTACTCGCTACCCGCCTCACC
GAAGATGCCGACGTCAGCGTCCTGCTGCTCGAAGCCGGCGGTCCCGACTACCGCTTCGACTTCCGCACCCAG
ATGCCGGCGGCCCTTGCCTTCCCGCTGCAGGGGCGGCGCTATAACTGGGCCTACGAGACCGACCCCGAGCCC
TACATGAACAACCGCCGCATGGAGTGCGGTCGCGGCAAGGGCCTGGGCGGCTCCTCGCTGATCAACGGCATG
TGCTACATCCGCGGCAACGCCCTGGACTTCGACGGCTGGGCCAAGGAGCCGGGCCTCGAGGACTGGAGCTAC
CTCGACTGCCTGCCGTACTTCCGCAAGGCGGAAACCCGGGACATCGGCCCCAACGACTACCATGGCGGCGAC
GGCCCGGTCAGCGTGACCACGCCGAAGGCCGGCAACAACCCACTGTTCCATGCGATGGTCGAGGCCGGCGTG
CAGGCCGGCTACCCGCGAACCGATGACCTCAACGGCTACCAGCAGGAAGGCTTCGGCCCCATGGACCGGACC
GTCACCCCGGAGGGCCGTCGCGCCGCCACCGGGCGCGGCTACCTGGACCAGGCCCGCGGCCGGCCCAACCTG
ACCATCGTCACCCACGCCCTGAGCGACCGCATCCTGTTCAGCGGCAAACGCGCTATCGGCGTCTCCTACCTG
GTGGGCAACGGCGACAACCCGGCCACCGCCCACGCCCGCCGCGAAGTATTGGTGTGCAGCGGCGCGATCGCC
TCGCCGCAATTGCTGCAACGCTCCGGCGTCGGCCCGGCGGCCCTGCTGCGCGACCTGGACATCCCGGCGGTG
CATGACCTGCCGGGCGTCGGCGCCAACCTACAGGATCACCTGGAACTCTACCTGCAGTACGCCTGCAAGCAG
CCGGTGTCGATCTACCCGGCGACCAAATGGTGGAACCAGCCGGCCATCGGTGCCCAGTGGCTGTTCCTCGGC
AAGGGCCTCGGCGCCAGCAACCAGTTCGAGGCTGGCGGCTTCATCCGAACCCGCGAAGCGTTCGAATGGCCG
AACATCCAGTTCCATTTCCTCCCGGTGGCGATCAACTACAACGGCAGCAAGGGCGTGCAGGAGCACGGCTTC
CAGGCGCACATGGGCTCGATGCGCTCGCCGAGCCGCGGGCGCATCCACCTGAAGTCCAGGGACCCGCGCCAG
CATCCGAGCATCCTGTTCAACTACATGTCCCACGAGCAGGACTGGCAGGAGTTCCGCGACGGCATCCGGCTG
ACCCGCGAGATCATGAACCAGCCGGCGCTGGACCCCTATCGGGGCCGCGAGTTGAGCCCAGGGGTGAACGTG
CAGTCGGACGCCGAACTCGACGAGTTCATCCGCAACCATGCGGAGACCGCTTTCCACCCATCCTGCTCGTGC
AAGATGGGCAGCGACGACATGGCGGTGGTCGATGGCCAGGGACGGGTCCACGGCATGGAAGGACTGCGAGTG
GTGGATGCGTCGATCATGCCGCTGATCATCACCGGCAACCTCAATGCCACCACCATCATGATGGCCGAGAAG
ATCGCCGACAGGATCCGCGGTCGCCAGCCGCTGCCGCGCAGCACGGCGAAGTACTACGTGGCCGGGGATGCG
CCGGTACGCGGCAACCCCGTGCGGGCCTGA
Translation:
MSQEFDYIIIGAGSAGNVLATRLTEDADVSVLLLEAGGPDYRFDFRTQMPAALAFPLQGRRYNWAYETDPEP
YMNNRRMECGRGKGLGGSSLINGMCYIRGNALDFDGWAKEPGLEDWSYLDCLPYFRKAETRDIGPNDYHGGD
GPVSVTTPKAGNNPLFHAMVEAGVQAGYPRTDDLNGYQQEGFGPMDRTVTPEGRRAATGRGYLDQARGRPNL
TIVTHALSDRILFSGKRAIGVSYLVGNGDNPATAHARREVLVCSGAIASPQLLQRSGVGPAALLRDLDIPAV
HDLPGVGANLQDHLELYLQYACKQPVSIYPATKWWNQPAIGAQWLFLGKGLGASNQFEAGGFIRTREAFEWP
NIQFHFLPVAINYNGSKGVQEHGFQAHMGSMRSPSRGRIHLKSRDPRQHPSILFNYMSHEQDWQEFRDGIRL
TREIMNQPALDPYRGRELSPGVNVQSDAELDEFIRNHAETAFHPSCSCKMGSDDMAVVDGQGRVHGMEGLRV
VDASIMPLIITGNLNATTIMMAEKIADRIRGRQPLPRSTAKYYVAGDAPVRGNPVRA*
AnnotationID:543GeneID:534
AnnotatorUID: diggins
Modification Date/Time: 2005-04-26 20:08:44
Gene Name:betA
Confidence Code:2
GeneProduct:choline dehydrogenase
Cell Localization:()
Synonyms:
Cell Localization Confidence Code:5
MolecularFunction:
Functional Category:(2) Amino acid biosynthesis and metabolism
Alternate Gene Product Name:
Functional Category Confidence Code:5
COGs:COG2303,pfam00732,pfam05199
Secondary Functional Category(ies):adaptation, protection
EC Number:1.1.99.1
Status:ACTIVE
Pathway:






 
Homology:
>gb|AAN70629.1|AE016706_4 (AE016793) choline dehydrogenase [Pseudomonas putida KT2440]
          Length = 565

 Score = 1020 bits (2638), Expect = 0.0
 Identities = 481/560 (85%), Positives = 524/560 (93%)

>gb|AAO53987.1| (AE016857) choline dehydrogenase [Pseudomonas syringae pv. tomato
           str. DC3000]
          Length = 568

 Score = 1005 bits (2598), Expect = 0.0
 Identities = 466/557 (83%), Positives = 519/557 (93%)

>emb|CAC90006.1| (AJ414146) choline dehydrogenase [Yersinia pestis CO92]
          Length = 567

 Score =  968 bits (2502), Expect = 0.0
 Identities = 460/557 (82%), Positives = 502/557 (90%)






 
Structural Features:
COG2303, BetA, Choline dehydrogenase and related flavoproteins 
[Amino acid transport and metabolism]
CD-Length = 542 residues,  98.9% aligned
Score =  514 bits (1325), Expect = 1e-146
Identities = 266/545 (48%), Positives = 341/545 (62%), Gaps = 15/545 (2%)

pfam00732, GMC_oxred_N, GMC oxidoreductase.
CD-Length = 291 residues, 100.0% aligned
Score =  358 bits (921), Expect = 7e-100 
Identities = 159/294 (54%), Positives = 193/294 (65%), Gaps = 6/294 (2%)

pfam05199, GMC_oxred_C, GMC oxidoreductase.
CD-Length = 202 residues, 100.0% aligned
Score =  239 bits (612), Expect = 5e-64
Identities = 100/202 (49%), Positives = 129/202 (63%), Gaps = 5/202 (2%)







   
Genomic Context:






   
Comment:


















    ReferenceID:1071




  
Author/Investigator(s):
        GenNotator





  
Title:
        




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:BLASTP 







    
Data:


    		




 
URL:

















    ReferenceID:18213




  
Author/Investigator(s):
        GenNotator





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:RPSBLAST 







    
Data:


    		




 
URL:

















    ReferenceID:34728




  
Author/Investigator(s):
        





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:Misc (text/plain)







    
Data:534_cdd.html


    		




 
URL:

















    ReferenceID:35659




  
Author/Investigator(s):
        Lamark T, Kaasen I, Eshoo MW, Falkenberg P, McDougall J, Strom AR.





  
Title:
        DNA sequence and analysis of the bet genes encoding the osmoregulatory choline-glycine betaine pathway of Escherichia coli.




  
PubMed:
        1956285


MedLine:
        




    
Source:
Mol Microbiol. 1991 May;5(5):1049-64.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=1956285

















    ReferenceID:35661




  
Author/Investigator(s):
        Canovas D, Vargas C, Kneip S, Moron MJ, Ventosa A, Bremer E, Nieto JJ.





  
Title:
        Genes for the synthesis of the osmoprotectant glycine betaine from choline in the moderately halophilic bacterium Halomonas elongata DSM 3043, USA.




  
PubMed:
        10708384


MedLine:
        




    
Source:
Microbiology. 2000 Feb;146 ( Pt 2):455-63.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10708384









           
Homologs By Global Alignment 

           

       



     
Gene ID:534
           
Identity:

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

                           

     
HomologID
                           Accession
                           Description
                           Length
                           PctIdentity
                           PctSimilarity
                           Gaps
                           Score
     

     
     
931
                           PA5372_tr
                           translation of PA5372
                           561
                           99.46
                           99.64
                           0
                           2989.0
     

     
     
37426
                           gb|AAG08757.1|AE004949_4
                           (AE004949) choline dehydrogenase [Pseudomonas aeruginosa PAO1]
                           561
                           99.46
                           99.64
                           0
                           2989.0
     

     
     
37427
                           gb|AAN70629.1|AE016706_4
                           (AE016793) choline dehydrogenase [Pseudomonas putida KT2440]
                           565
                           85.13
                           92.74
                           4
                           2637.0
     

     
     
37428
                           gb|AAO53987.1|
                           (AE016857) choline dehydrogenase [Pseudomonas syringae pv. tomato str. DC3000]
                           568
                           82.04
                           91.37
                           7
                           2596.0
     

     
     
37430
                           gb|AAM35607.1|
                           (AE011702) choline dehydrogenase [Xanthomonas axonopodis pv. citri str. 306]
                           561
                           81.63
                           88.23
                           5
                           2482.0
     

     






      

          
GC ORFID: 43536How Found: BLASTX

          
GC_TrimmedSeqID: 69Blast Result ID

          
Subject Sequence Name: t_PA5372Glimmer Score: 

          
Start: 5585657Stop: 5583972

          
Length: 1686


          
Start Codon: ATGTruncated Start:

          
Stop Codon: TGATruncated Stop: 

          
Homolog: t_PA5372 translation of PA5372Homolog Bit Score 1155.0

          
Other Homologs:  psyr_15may02_Scaffold6_revised_gene6626 (ORF: BLASTX 1006.0), t_PA4100 (ORF: BLASTX 367.0), t_PA5372 (ORF: GLIMMER)

          
GC ORF Sequence

           
ATGTCCCAGGAATTCGACTACATCATCATCGGAGCCGGCTCTGCCGGTAACGTACTCGCTACCCGCCTCACC 
GAAGATGCCGACGTCAGCGTCCTGCTGCTCGAAGCCGGCGGTCCCGACTACCGCTTCGACTTCCGCACCCAG 
ATGCCGGCGGCCCTTGCCTTCCCGCTGCAGGGGCGGCGCTATAACTGGGCCTACGAGACCGACCCCGAGCCC 
TACATGAACAACCGCCGCATGGAGTGCGGTCGCGGCAAGGGCCTGGGCGGCTCCTCGCTGATCAACGGCATG 
TGCTACATCCGCGGCAACGCCCTGGACTTCGACGGCTGGGCCAAGGAGCCGGGCCTCGAGGACTGGAGCTAC 
CTCGACTGCCTGCCGTACTTCCGCAAGGCGGAAACCCGGGACATCGGCCCCAACGACTACCATGGCGGCGAC 
GGCCCGGTCAGCGTGACCACGCCGAAGGCCGGCAACAACCCACTGTTCCATGCGATGGTCGAGGCCGGCGTG 
CAGGCCGGCTACCCGCGAACCGATGACCTCAACGGCTACCAGCAGGAAGGCTTCGGCCCCATGGACCGGACC 
GTCACCCCGGAGGGCCGTCGCGCCGCCACCGGGCGCGGCTACCTGGACCAGGCCCGCGGCCGGCCCAACCTG 
ACCATCGTCACCCACGCCCTGAGCGACCGCATCCTGTTCAGCGGCAAACGCGCTATCGGCGTCTCCTACCTG 
GTGGGCAACGGCGACAACCCGGCCACCGCCCACGCCCGCCGCGAAGTATTGGTGTGCAGCGGCGCGATCGCC 
TCGCCGCAATTGCTGCAACGCTCCGGCGTCGGCCCGGCGGCCCTGCTGCGCGACCTGGACATCCCGGCGGTG 
CATGACCTGCCGGGCGTCGGCGCCAACCTACAGGATCACCTGGAACTCTACCTGCAGTACGCCTGCAAGCAG 
CCGGTGTCGATCTACCCGGCGACCAAATGGTGGAACCAGCCGGCCATCGGTGCCCAGTGGCTGTTCCTCGGC 
AAGGGCCTCGGCGCCAGCAACCAGTTCGAGGCTGGCGGCTTCATCCGAACCCGCGAAGCGTTCGAATGGCCG 
AACATCCAGTTCCATTTCCTCCCGGTGGCGATCAACTACAACGGCAGCAAGGGCGTGCAGGAGCACGGCTTC 
CAGGCGCACATGGGCTCGATGCGCTCGCCGAGCCGCGGGCGCATCCACCTGAAGTCCAGGGACCCGCGCCAG 
CATCCGAGCATCCTGTTCAACTACATGTCCCACGAGCAGGACTGGCAGGAGTTCCGCGACGGCATCCGGCTG 
ACCCGCGAGATCATGAACCAGCCGGCGCTGGACCCCTATCGGGGCCGCGAGTTGAGCCCAGGGGTGAACGTG 
CAGTCGGACGCCGAACTCGACGAGTTCATCCGCAACCATGCGGAGACCGCTTTCCACCCATCCTGCTCGTGC 
AAGATGGGCAGCGACGACATGGCGGTGGTCGATGGCCAGGGACGGGTCCACGGCATGGAAGGACTGCGAGTG 
GTGGATGCGTCGATCATGCCGCTGATCATCACCGGCAACCTCAATGCCACCACCATCATGATGGCCGAGAAG 
ATCGCCGACAGGATCCGCGGTCGCCAGCCGCTGCCGCGCAGCACGGCGAAGTACTACGTGGCCGGGGATGCG 
CCGGTACGCGGCAACCCCGTGCGGGCCTGA