ViewGene
Locus Name:
GeneID:
Location:

GeneID:2525
TrivialName: PA14_68190
AnnotatorUID:
Modification Date/Time:2006-04-06 13:01:23
LocusName:PA14_68190
PAO1 Ortholog Locus:PA5162
Sequence Length:909
Protein Length:302
Start: 6083507
Stop: 6084415
Strand: +
Type:
ChromosomeID:2
Status: ACTIVE
Frame Discrepancy: FALSE
Missense Discrepancy:FALSE
Comments:
Homology: gb|AAG08547.1|AE004929_2 (AE004929) dTDP-4-dehydrorhamnose reductase [Pseudomonas aeruginosa PAO1]
Identities = 298/302 (98%), Positives = 298/302 (98%)
Sequence:
ATGAACCGGATCCTTCTCCTCGGCGCCAACGGCCAGGTCGGCTGGGAGCTGCAGCGCGCCCTGGCGCCGCTG
GGCGAACTGCTGGTCTGCGACCGCCGGCGCGCCGATCTCGCCGACCCCGAAGGCCTGGCGCGACTGGTTCGC
GCCGAGCGGCCGCAGTTCATCGTCAACGCCGGCGCCTACACCGCGGTGGACAAGGCCGAGAGCGATGCCGAC
AACGCCCGCCTGATCAATGCCCGCGCCGTCGCGGTACTGGCCGAGGAGGCCGCGGCCTGCGGCGCCTGGCTG
GTGCATTACTCCACCGACTACGTGTTCGACGGCGCGGGCAGCGCGCCTTTCGCCGAGGACGCGCCGACCGGC
CCGCTGAGCGTCTACGGGCAGACCAAGCTGGAAGGCGAGCAGGCCATCCGCGCCAGCGGCTGCCGCCACCTG
ATCTTCCGCACCAGTTGGGTCTACGCCGCGCGCGGCGGGAACTTCGCCAAGACCATGCTGCGCCTGGCCGGG
CAACGCGACGAACTCAAGGTCGTGGCCGACCAGTTCGGCGCGCCGACCAGCGCCGAGCTGATCGCCGACGTC
ACCGCCCAGGCCCTGCAGCGTCTGCGCTGGGATGCCGAGCTGGCAGCACGGGCCAGCGGCACCTACCACCTG
GTCGCCAGCGGCGAGACGTCCTGGCACCTCTATGCGCGCTTCGTCATCGAACAGGCGCTGGAGCGGGGCTGG
GAATTGCAGGCGACGCCGCAGCGGGTCCTGCCGATTGCCACCGAGGATTACCCGGTGCCGGCGAAGCGCCCG
GCCAATTCGCGCCTCGACAACCACAAGCTGCAACAGGTCTTCGGCCTGGTACTGCCCGACTGGCGCTACCAT
GCCGGACGCATGATCCAGGAACTGAGCGAGCAGGGACCACTATGA
Translation:
MNRILLLGANGQVGWELQRALAPLGELLVCDRRRADLADPEGLARLVRAERPQFIVNAGAYTAVDKAESDAD
NARLINARAVAVLAEEAAACGAWLVHYSTDYVFDGAGSAPFAEDAPTGPLSVYGQTKLEGEQAIRASGCRHL
IFRTSWVYAARGGNFAKTMLRLAGQRDELKVVADQFGAPTSAELIADVTAQALQRLRWDAELAARASGTYHL
VASGETSWHLYARFVIEQALERGWELQATPQRVLPIATEDYPVPAKRPANSRLDNHKLQQVFGLVLPDWRYH
AGRMIQELSEQGPL*
AnnotationID:2533GeneID:2525
AnnotatorUID: diggins
Modification Date/Time: 2005-04-26 13:01:12
Gene Name:rmlD
Confidence Code:2
GeneProduct:dTDP-4-dehydrorhamnose reductase
Cell Localization:()
Synonyms:rfbD
Cell Localization Confidence Code:5
MolecularFunction:
Functional Category:(7) Cell wall / LPS / capsule
Alternate Gene Product Name:dTDP-4-keto-L-rhamnose reductase
Functional Category Confidence Code:5
COGs:COG1091,pfam04321
Secondary Functional Category(ies):cell envelope biogenesis, outer membrane
EC Number:1.1.1.133
Status:ACTIVE
Pathway:






 
Homology:
>gb|AAN67404.1|AE016367_4 (AE016780) dTDP-4-dehydrorhamnose reductase [Pseudomonas putida
           KT2440]
          Length = 300

 Score =  340 bits (872), Expect = 6e-93
 Identities = 180/299 (60%), Positives = 216/299 (72%), Gaps = 6/299 (2%)

>emb|CAD14213.1| (AL646060) PROBABLE DTDP-4-DEHYDRORHAMNOSE REDUCTASE OXIDOREDUCTASE
           PROTEIN [Ralstonia solanacearum]
          Length = 305

 Score =  320 bits (821), Expect = 5e-87
 Identities = 162/294 (55%), Positives = 204/294 (69%)

>gb|AAN60455.1| (AF529080) dTDP-6-deoxy-L-mannose-dehydrogenase [Escherichia coli]
          Length = 299

 Score =  311 bits (796), Expect = 4e-84
 Identities = 165/297 (55%), Positives = 202/297 (68%), Gaps = 10/297 (3%)








 
Structural Features:
COG1091, RfbD, dTDP-4-dehydrorhamnose reductase 
[Cell envelope biogenesis, outer membrane]
CD-Length = 281 residues,  99.6% aligned
Score =  328 bits (842), Expect = 5e-91
Identities = 142/295 (48%), Positives = 187/295 (63%), Gaps = 15/295 (5%)

pfam04321, RmlD_sub_bind, RmlD substrate binding domain. 
CD-Length = 139 residues,  97.1% aligned
Score =  166 bits (422), Expect = 3e-42
Identities = 75/146 (51%), Positives = 92/146 (63%), Gaps = 11/146 (7%)






   
Genomic Context:






   
Comment:


















    ReferenceID:5053




  
Author/Investigator(s):
        GenNotator





  
Title:
        




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:BLASTP 







    
Data:


    		




 
URL:

















    ReferenceID:22199




  
Author/Investigator(s):
        GenNotator





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:RPSBLAST 







    
Data:


    		




 
URL:

















    ReferenceID:34911




  
Author/Investigator(s):
        





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:Misc (text/plain)







    
Data:2525_cdd.html


    		




 
URL:

















    ReferenceID:35773




  
Author/Investigator(s):
        Rajakumar K, Jost BH, Sasakawa C, Okada N, Yoshikawa M, Adler B.





  
Title:
        Nucleotide sequence of the rhamnose biosynthetic operon of Shigella flexneri 2a and role of lipopolysaccharide in virulence.




  
PubMed:
        8157605


MedLine:
        




    
Source:
J Bacteriol. 1994 Apr;176(8):2362-73.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=8157605









           
Homologs By Global Alignment 

           

       



     
Gene ID:2525
           
Identity:

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

                           

     
HomologID
                           Accession
                           Description
                           Length
                           PctIdentity
                           PctSimilarity
                           Gaps
                           Score
     

     
     
4212
                           PA5162_tr
                           translation of PA5162
                           302
                           98.67
                           98.67
                           0
                           1534.0
     

     
     
124228
                           gb|AAG08547.1|AE004929_2
                           (AE004929) dTDP-4-dehydrorhamnose reductase [Pseudomonas aeruginosa PAO1]
                           302
                           98.67
                           98.67
                           0
                           1534.0
     

     
     
124229
                           emb|CAC82200.1|
                           (AJ298595) dTDP-4-keto-L-rhamnose reductase [Pseudomonas aeruginosa]
                           302
                           98.67
                           98.67
                           0
                           1534.0
     

     
     
124230
                           gb|AAN67404.1|AE016367_4
                           (AE016780) dTDP-4-dehydrorhamnose reductase [Pseudomonas putida KT2440]
                           307
                           58.63
                           70.35
                           12
                           876.0
     

     
     
124236
                           gb|AAQ82926.1|
                           (AY376146) dTDP-4-keto-L-rhamnose reductase [Raoultella terrigena]
                           307
                           55.04
                           67.75
                           16
                           798.0
     

     






      

          
GC ORFID: 45527How Found: BLASTX

          
GC_TrimmedSeqID: 69Blast Result ID

          
Subject Sequence Name: t_PA5162Glimmer Score: 

          
Start: 5347193Stop: 5348101

          
Length: 909


          
Start Codon: ATGTruncated Start:

          
Stop Codon: TGATruncated Stop: 

          
Homolog: t_PA5162 translation of PA5162Homolog Bit Score 595.0

          
Other Homologs:  psyr_15may02_Scaffold3_revised_gene5108 (ORF: BLASTX 357.0), t_PA5162 (ORF: GLIMMER)

          
GC ORF Sequence

           
ATGAACCGGATCCTTCTCCTCGGCGCCAACGGCCAGGTCGGCTGGGAGCTGCAGCGCGCCCTGGCGCCGCTG 
GGCGAACTGCTGGTCTGCGACCGCCGGCGCGCCGATCTCGCCGACCCCGAAGGCCTGGCGCGACTGGTTCGC 
GCCGAGCGGCCGCAGTTCATCGTCAACGCCGGCGCCTACACCGCGGTGGACAAGGCCGAGAGCGATGCCGAC 
AACGCCCGCCTGATCAATGCCCGCGCCGTCGCGGTACTGGCCGAGGAGGCCGCGGCCTGCGGCGCCTGGCTG 
GTGCATTACTCCACCGACTACGTGTTCGACGGCGCGGGCAGCGCGCCTTTCGCCGAGGACGCGCCGACCGGC 
CCGCTGAGCGTCTACGGGCAGACCAAGCTGGAAGGCGAGCAGGCCATCCGCGCCAGCGGCTGCCGCCACCTG 
ATCTTCCGCACCAGTTGGGTCTACGCCGCGCGCGGCGGGAACTTCGCCAAGACCATGCTGCGCCTGGCCGGG 
CAACGCGACGAACTCAAGGTCGTGGCCGACCAGTTCGGCGCGCCGACCAGCGCCGAGCTGATCGCCGACGTC 
ACCGCCCAGGCCCTGCAGCGTCTGCGCTGGGATGCCGAGCTGGCAGCACGGGCCAGCGGCACCTACCACCTG 
GTCGCCAGCGGCGAGACGTCCTGGCACCTCTATGCGCGCTTCGTCATCGAACAGGCGCTGGAGCGGGGCTGG 
GAATTGCAGGCGACGCCGCAGCGGGTCCTGCCGATTGCCACCGAGGATTACCCGGTGCCGGCGAAGCGCCCG 
GCCAATTCGCGCCTCGACAACCACAAGCTGCAACAGGTCTTCGGCCTGGTACTGCCCGACTGGCGCTACCAT 
GCCGGACGCATGATCCAGGAACTGAGCGAGCAGGGACCACTATGA