ViewGene
Locus Name:
GeneID:
Location:

GeneID:2096
TrivialName: PA14_20320
AnnotatorUID:
Modification Date/Time:2006-04-06 13:01:23
LocusName:PA14_20320
PAO1 Ortholog Locus:PA3383
Sequence Length:1005
Protein Length:334
Start: 1749178
Stop: 1750182
Strand: +
Type:
ChromosomeID:2
Status: ACTIVE
Frame Discrepancy: FALSE
Missense Discrepancy:FALSE
Comments:
Homology: gb|AAG06771.1|AE004759_18 (AE004759) binding protein component of ABC phosphonate transporter [Pseudomonas aeruginosa PAO1]
Identities = 332/334 (99%), Positives = 334/334 (100%)
Sequence:
ATGTTGAAACGCTTCAGTCGTGTGCTCGCGGCTTCCGCCCTGCTCGCCGGCTCCCTTGCCGGGATGGCGCAC
GCCGACCAGCCGGTGATCAATTTCGGGATCATCTCCACCGAGTCGTCGCAGAACCTCAAGAGCATCTGGGAG
CCCTTCCTCAAGGACATGAGCCAGCAGACCGGCTACCAGGTGAGGGCCTTCTTCGCCCCCGACTACGCCGGG
ATCATCCAGGGCATGCGTTTCGACAAGGTCGACATCGCCTGGTACGGCAACAAGGCCGCCATGGAAGCGGTG
GATCGCGCCCACGGCGAGATCTTCGCCCAGACCGTCGCCGCCAGCGGCGCGCCGGGCTACTGGAGCCTGCTG
ATCGCCAACAAGGACAGCAAGATCGACAGCGTCGAGGACATGTTGGCGAACGCCAAGAGCCTGACCTTCGGC
AACGGCGATCCGAACTCCACGTCCGGCTACCTGGTGCCCGGCTACTACGTGTTCGCCAAGAACAACGTCGAC
CCGGTCAAGGCCTTCAAGCGCACCCTCAACTCCAGCCATGAGGTCAACGCCCTGGCGGTGGCCAACAAGCAG
GTCGACGTCGCCACCTTCAATACCGAGGGCATGGAGCGCCTGGAACTGACCCAGCCGGAGAAGGCCAGGCAG
CTCAAGGTGATCTGGAAGTCGCCGCTGATCCCGGGCGACCCGCTGGTGTGGCGCAACAACCTGAGCGACGAG
CAGAAGAACAAGCTGCGCGACTTCTTCTTCAAGTACGGCGCCAACGCCGAGCAGAAGAAGGTCCTCGCCGAC
CTGCAATGGTCGAAGTTCCAGCCCTCCGACGACGACCAGTTGCTGCCGATCCGCCAGCTCGAGCTGTTCAAG
CAGCGCACCGACGTGGCGAACAACGCCAACCTCGGCGCCGAGGAGAAGGCCGCCAAGCTGAAGGCCCTCGAC
GAGGAGCTGGCCAAGCTGGAGAAACGCATGGCCGAGCGCGAGCAGAAGACCGCCGCCAACGCCGGCTGA
Translation:
MLKRFSRVLAASALLAGSLAGMAHADQPVINFGIISTESSQNLKSIWEPFLKDMSQQTGYQVRAFFAPDYAG
IIQGMRFDKVDIAWYGNKAAMEAVDRAHGEIFAQTVAASGAPGYWSLLIANKDSKIDSVEDMLANAKSLTFG
NGDPNSTSGYLVPGYYVFAKNNVDPVKAFKRTLNSSHEVNALAVANKQVDVATFNTEGMERLELTQPEKARQ
LKVIWKSPLIPGDPLVWRNNLSDEQKNKLRDFFFKYGANAEQKKVLADLQWSKFQPSDDDQLLPIRQLELFK
QRTDVANNANLGAEEKAAKLKALDEELAKLEKRMAEREQKTAANAG*
AnnotationID:2104GeneID:2096
AnnotatorUID: diggins
Modification Date/Time: 2005-04-18 07:07:50
Gene Name:phnD
Confidence Code:2
GeneProduct:binding protein component of ABC phosphonate transporter
Cell Localization:()
Synonyms:
Cell Localization Confidence Code:5
MolecularFunction:
Functional Category:(27) Transport of small molecules
Alternate Gene Product Name:
Functional Category Confidence Code:5
COGs:COG3221
Secondary Functional Category(ies):
EC Number:
Status:ACTIVE
Pathway:






 
Homology:
>gb|AAO56061.1| (AE016865) phosphonates ABC transporter, periplasmic
           phosphonates-binding protein [Pseudomonas syringae pv.
           tomato str. DC3000]
          Length = 336

 Score =  451 bits (1159), Expect = e-126
 Identities = 227/333 (68%), Positives = 266/333 (79%), Gaps = 1/333 (0%)

>gb|AAN83534.1|AE016771_45 (AE016771) Phosphonates-binding periplasmic protein precursor
           [Escherichia coli CFT073]
          Length = 338

 Score =  389 bits (1000), Expect = e-107
 Identities = 192/316 (60%), Positives = 240/316 (75%), Gaps = 4/316 (1%)

>gb|AAP18656.1| (AE016989) periplasmic binding protein component of phosphonate
           transporter [Shigella flexneri 2a str. 2457T]
          Length = 338

 Score =  383 bits (984), Expect = e-106
 Identities = 192/318 (60%), Positives = 239/318 (75%), Gaps = 8/318 (2%)






 
Structural Features:
COG3221, PhnD, ABC-type phosphate/phosphonate transport system, 
periplasmic component 
[Inorganic ion transport and metabolism]
CD-Length = 299 residues,  97.3% aligned
Score =  260 bits (665), Expect = 2e-70
Identities = 122/296 (41%), Positives = 158/296 (53%), Gaps = 16/296 (5%)






   
Genomic Context:






   
Comment:


















    ReferenceID:4195




  
Author/Investigator(s):
        GenNotator





  
Title:
        




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:BLASTP 







    
Data:


    		




 
URL:

















    ReferenceID:21341




  
Author/Investigator(s):
        GenNotator





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:RPSBLAST 







    
Data:


    		




 
URL:

















    ReferenceID:32178




  
Author/Investigator(s):
        





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:Misc (text/plain)







    
Data:2096_cdd.html


    		




 
URL:

















    ReferenceID:34031




  
Author/Investigator(s):
        Shin HJ, Kim SJ, Kim YC.





  
Title:
        Sequence analysis of the phnD gene encoding 2-hydroxymuconic semialdehyde hydrolase in Pseudomonas sp. strain DJ77.




  
PubMed:
        9125165


MedLine:
        




    
Source:
Biochem Biophys Res Commun. 1997 Mar 17;232(2):288-91.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=9125165

















    ReferenceID:34032




  
Author/Investigator(s):
        Metcalf WW, Wanner BL.





  
Title:
        Evidence for a fourteen-gene, phnC to phnP locus for phosphonate metabolism in Escherichia coli.




  
PubMed:
        8335257


MedLine:
        




    
Source:
Gene. 1993 Jul 15;129(1):27-32.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=8335257

















    ReferenceID:34033




  
Author/Investigator(s):
        Wanner BL, Metcalf WW.





  
Title:
        Molecular genetic studies of a 10.9-kb operon in Escherichia coli for phosphonate uptake and biodegradation.




  
PubMed:
        1335942


MedLine:
        




    
Source:
FEMS Microbiol Lett. 1992 Dec 15;79(1-3):133-9.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=1335942

















    ReferenceID:34034




  
Author/Investigator(s):
        Wanner BL.





  
Title:
        Genes for phosphonate biodegradation in Escherichia coli.




  
PubMed:
        1368181


MedLine:
        




    
Source:
SAAS Bull Biochem Biotechnol. 1992 Jan;5:1-6.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=1368181

















    ReferenceID:34035




  
Author/Investigator(s):
        Metcalf WW, Wanner BL.





  
Title:
        Involvement of the Escherichia coli phn (psiD) gene cluster in assimilation of phosphorus in the form of phosphonates, phosphite, Pi esters, and Pi.




  
PubMed:
        1846145


MedLine:
        




    
Source:
J Bacteriol. 1991 Jan;173(2):587-600.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=1846145

















    ReferenceID:34036




  
Author/Investigator(s):
        Chen CM, Ye QZ, Zhu ZM, Wanner BL, Walsh CT.





  
Title:
        Molecular biology of carbon-phosphorus bond cleavage. Cloning and sequencing of the phn (psiD) genes involved in alkylphosphonate uptake and C-P lyase activity in Escherichia coli B.




  
PubMed:
        2155230


MedLine:
        




    
Source:
J Biol Chem. 1990 Mar 15;265(8):4461-71.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=2155230









           
Homologs By Global Alignment 

           

       



     
Gene ID:2096
           
Identity:

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

                           

     
HomologID
                           Accession
                           Description
                           Length
                           PctIdentity
                           PctSimilarity
                           Gaps
                           Score
     

     
     
3599
                           PA3383_tr
                           translation of PA3383
                           334
                           99.40
                           99.99
                           0
                           1700.0
     

     
     
110547
                           gb|AAG06771.1|AE004759_18
                           (AE004759) binding protein component of ABC phosphonate transporter [Pseudomonas aeruginosa PAO1]
                           334
                           99.40
                           99.99
                           0
                           1700.0
     

     
     
110548
                           gb|AAO56061.1|
                           (AE016865) phosphonates ABC transporter, periplasmic phosphonates-binding protein [Pseudomonas syringae pv. tomato str. DC3000]
                           336
                           68.45
                           80.65
                           2
                           1161.0
     

     
     
110549
                           gb|AAA24340.1|
                           (J05260) phnD protein [Escherichia coli]
                           342
                           56.43
                           72.51
                           12
                           997.0
     

     
     
110555
                           dbj|BAB38510.1|
                           (AP002568) periplasmic binding protein component of Pn transporter [Escherichia coli O157:H7]
                           343
                           56.26
                           72.59
                           14
                           990.0
     

     






      

          
GC ORFID: 45098How Found: BLASTX

          
GC_TrimmedSeqID: 69Blast Result ID

          
Subject Sequence Name: t_PA3383Glimmer Score: 

          
Start: 3204754Stop: 3203750

          
Length: 1005


          
Start Codon: ATGTruncated Start:

          
Stop Codon: TGATruncated Stop: 

          
Homolog: t_PA3383 translation of PA3383Homolog Bit Score 659.0

          
Other Homologs:  psyr_15may02_Scaffold1_revised_gene1217 (ORF: BLASTX 442.0), t_PA3383 (ORF: GLIMMER)

          
GC ORF Sequence

           
ATGTTGAAACGCTTCAGTCGTGTGCTCGCGGCTTCCGCCCTGCTCGCCGGCTCCCTTGCCGGGATGGCGCAC 
GCCGACCAGCCGGTGATCAATTTCGGGATCATCTCCACCGAGTCGTCGCAGAACCTCAAGAGCATCTGGGAG 
CCCTTCCTCAAGGACATGAGCCAGCAGACCGGCTACCAGGTGAGGGCCTTCTTCGCCCCCGACTACGCCGGG 
ATCATCCAGGGCATGCGTTTCGACAAGGTCGACATCGCCTGGTACGGCAACAAGGCCGCCATGGAAGCGGTG 
GATCGCGCCCACGGCGAGATCTTCGCCCAGACCGTCGCCGCCAGCGGCGCGCCGGGCTACTGGAGCCTGCTG 
ATCGCCAACAAGGACAGCAAGATCGACAGCGTCGAGGACATGTTGGCGAACGCCAAGAGCCTGACCTTCGGC 
AACGGCGATCCGAACTCCACGTCCGGCTACCTGGTGCCCGGCTACTACGTGTTCGCCAAGAACAACGTCGAC 
CCGGTCAAGGCCTTCAAGCGCACCCTCAACTCCAGCCATGAGGTCAACGCCCTGGCGGTGGCCAACAAGCAG 
GTCGACGTCGCCACCTTCAATACCGAGGGCATGGAGCGCCTGGAACTGACCCAGCCGGAGAAGGCCAGGCAG 
CTCAAGGTGATCTGGAAGTCGCCGCTGATCCCGGGCGACCCGCTGGTGTGGCGCAACAACCTGAGCGACGAG 
CAGAAGAACAAGCTGCGCGACTTCTTCTTCAAGTACGGCGCCAACGCCGAGCAGAAGAAGGTCCTCGCCGAC 
CTGCAATGGTCGAAGTTCCAGCCCTCCGACGACGACCAGTTGCTGCCGATCCGCCAGCTCGAGCTGTTCAAG 
CAGCGCACCGACGTGGCGAACAACGCCAACCTCGGCGCCGAGGAGAAGGCCGCCAAGCTGAAGGCCCTCGAC 
GAGGAGCTGGCCAAGCTGGAGAAACGCATGGCCGAGCGCGAGCAGAAGACCGCCGCCAACGCCGGCTGA