ViewGene
Locus Name:
GeneID:
Location:

GeneID:1770
TrivialName: PA14_68170
AnnotatorUID:
Modification Date/Time:2006-04-06 13:01:23
LocusName:PA14_68170
PAO1 Ortholog Locus:PA5161
Sequence Length:1059
Protein Length:352
Start: 6082452
Stop: 6083510
Strand: +
Type:
ChromosomeID:2
Status: ACTIVE
Frame Discrepancy: FALSE
Missense Discrepancy:FALSE
Comments:
Homology: gb|AAG08546.1|AE004929_1 (AE004929) dTDP-D-glucose 4,6-dehydratase [Pseudomonas aeruginosa PAO1]
Identities = 352/352 (100%), Positives = 352/352 (100%)
Sequence:
ATGACGATTCTCGTGACCGGCAGCGCCGGCTTCATCGGCGCCAATTTCGTGCTCGACTGGCTGGCCCTGCAT
GACGAGCCGGTGGTCAGCCTCGACAAGCTCACCTACGCCGGCAACCGGCAGAACCTCGCCAGCCTCGACGGC
GACGCCCGGCACACCTTCGTCGCCGGCGATATCGGCGATAGCCAGCTGGTAGCCCGCCTGCTCGCCGAGCAC
CAGCCGCGGGCGATCCTCAACTTCGCCGCGGAATCTCATGTGGACCGCTCGATCCACGGCCCCGAGGACTTC
ATCCAGACCAACATCGTCGGCACCTTCCGCCTGCTGGAAGAAGTGCGCGCCTACTGGGGCGCGCTGGAGCCG
GAAGCGAAGGCGGCATTCCGCTTCCTCCACGTCTCCACCGACGAAGTCTATGGCTCGCTGGCACCGAGCGAT
CCGGCCTTCACCGAGAACAACCGCTACGAGCCGAACAGTCCCTACTCGGCGTCCAAGGCGGCCTCCGACCAC
CTGGTGCGGGCCTATCACCACACCTACGGGCTGCCGGTGCTGACCACCAACTGCTCGAACAACTACGGCCCG
TACCACTTCCCGGAAAAGCTCATCCCACTGGTGATCCACAACGCCCTGGCCGGCAAGCCGCTGCCGATCTAC
GGCGACGGCCAGCAGATCCGCGACTGGCTCTACGTCAAGGACCATTGCAGCGCCATCCGCCGGGTCCTCGAA
GCCGGGCAACTGGGCGAGACCTACAATGTCGGCGGCTGGAACGAAAAGGCCAACCTCGACGTGGTCGAGACC
CTCTGCGCCATCCTCGACCAGGAGCAGCCGCGCGCCGACGGCCGCAGCTATCGCGAGCAGATCACCTTCGTC
AAGGATCGTCCGGGCCATGATCGCCGCTACGCCATCGATGCCACGCGCCTGGAGCGCGAGCTGGGCTGGAAG
CCGGCGGAAACCTTCGAGACCGGCATCCGCAAGACCGTGCGCTGGTACCTGGACAACCAGGACTGGGTGGCC
AACGTAACCAGCGGTGCCTACCGCGAGTGGGTGGGTAAGCAGTACGCATGA
Translation:
MTILVTGSAGFIGANFVLDWLALHDEPVVSLDKLTYAGNRQNLASLDGDARHTFVAGDIGDSQLVARLLAEH
QPRAILNFAAESHVDRSIHGPEDFIQTNIVGTFRLLEEVRAYWGALEPEAKAAFRFLHVSTDEVYGSLAPSD
PAFTENNRYEPNSPYSASKAASDHLVRAYHHTYGLPVLTTNCSNNYGPYHFPEKLIPLVIHNALAGKPLPIY
GDGQQIRDWLYVKDHCSAIRRVLEAGQLGETYNVGGWNEKANLDVVETLCAILDQEQPRADGRSYREQITFV
KDRPGHDRRYAIDATRLERELGWKPAETFETGIRKTVRWYLDNQDWVANVTSGAYREWVGKQYA*
AnnotationID:1779GeneID:1770
AnnotatorUID: diggins
Modification Date/Time: 2005-04-26 13:01:21
Gene Name:rmlB
Confidence Code:2
GeneProduct:dTDP-D-glucose 4,6-dehydratase
Cell Localization:()
Synonyms:rfbB
Cell Localization Confidence Code:5
MolecularFunction:
Functional Category:(7) Cell wall / LPS / capsule
Alternate Gene Product Name:
Functional Category Confidence Code:5
COGs:COG1088,pfam01370
Secondary Functional Category(ies):carbon compound catabolism
EC Number:4.2.1.46
Status:ACTIVE
Pathway:






 
Homology:
>emb|CAD84380.1| (BX321857) NAD dependent epimerase/dehydratase family [Nitrosomonas
           europaea ATCC 19718]
          Length = 352

 Score =  563 bits (1451), Expect = e-160
 Identities = 264/349 (75%), Positives = 299/349 (85%)

>emb|CAD14212.1| (AL646060) PROBABLE DTDP-GLUCOSE 4,6-DEHYDRATASE PROTEIN [Ralstonia
           solanacearum]
          Length = 354

 Score =  548 bits (1412), Expect = e-155
 Identities = 262/351 (74%), Positives = 299/351 (85%), Gaps = 2/351 (0%)

>gb|AAD05454.1| (AF064070) putative dTDP-D-glucose 4,6-dehydratase [Burkholderia
           pseudomallei]
          Length = 353

 Score =  546 bits (1406), Expect = e-155
 Identities = 259/350 (74%), Positives = 291/350 (83%), Gaps = 1/350 (0%)








 
Structural Features:
COG1088, RfbB, dTDP-D-glucose 4,6-dehydratase [Cell envelope biogenesis, outer membrane] 
CD-Length = 340 residues, 100.0% aligned
Score =  556 bits (1434), Expect = 1e-159
Identities = 221/353 (62%), Positives = 263/353 (74%), Gaps = 14/353 (3%)

pfam01370, Epimerase, NAD dependent epimerase/dehydratase family.
CD-Length = 310 residues, 100.0% aligned
Score =  396 bits (1020), Expect = 2e-111
Identities = 168/331 (50%), Positives = 210/331 (63%), Gaps = 22/331 (6%)






   
Genomic Context:






   
Comment:


















    ReferenceID:3543




  
Author/Investigator(s):
        GenNotator





  
Title:
        




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:BLASTP 







    
Data:


    		




 
URL:

















    ReferenceID:20690




  
Author/Investigator(s):
        GenNotator





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:RPSBLAST 







    
Data:


    		




 
URL:

















    ReferenceID:34912




  
Author/Investigator(s):
        





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:Misc (text/plain)







    
Data:1770_cdd.html


    		




 
URL:

















    ReferenceID:35774




  
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:1770
           
Identity:

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

                           

     
HomologID
                           Accession
                           Description
                           Length
                           PctIdentity
                           PctSimilarity
                           Gaps
                           Score
     

     
     
3134
                           PA5161_tr
                           translation of PA5161
                           352
                           99.99
                           99.99
                           0
                           1879.0
     

     
     
97160
                           gb|AAG08546.1|AE004929_1
                           (AE004929) dTDP-D-glucose 4,6-dehydratase [Pseudomonas aeruginosa PAO1]
                           352
                           99.99
                           99.99
                           0
                           1879.0
     

     
     
97161
                           emb|CAC82202.1|
                           (AJ298597) dTDP-D-glucose 4,6-dehydratase [Pseudomonas aeruginosa]
                           352
                           99.99
                           99.99
                           0
                           1879.0
     

     
     
97162
                           gb|AAQ61672.1|
                           (AE016924) dTDPglucose 4,6-dehydratase [Chromobacterium violaceum ATCC 12472]
                           352
                           76.13
                           84.65
                           0
                           1461.0
     

     
     
97163
                           emb|CAD84380.1|
                           (BX321857) NAD dependent epimerase/dehydratase family [Nitrosomonas europaea ATCC 19718]
                           353
                           74.78
                           84.70
                           2
                           1450.0
     

     






      

          
GC ORFID: 44772How Found: BLASTX

          
GC_TrimmedSeqID: 69Blast Result ID

          
Subject Sequence Name: t_PA5161Glimmer Score: 

          
Start: 5346138Stop: 5347196

          
Length: 1059


          
Start Codon: ATGTruncated Start:

          
Stop Codon: TGATruncated Stop: 

          
Homolog: t_PA5161 translation of PA5161Homolog Bit Score 728.0

          
Other Homologs:  psyr_15may02_Scaffold3_revised_gene5107 (ORF: BLASTX 546.0), psyr_15may02_Scaffold14_revised_gene2283 (ORF: BLASTX 429.0), t_PA5161 (ORF: GLIMMER)

          
GC ORF Sequence

           
ATGACGATTCTCGTGACCGGCAGCGCCGGCTTCATCGGCGCCAATTTCGTGCTCGACTGGCTGGCCCTGCAT 
GACGAGCCGGTGGTCAGCCTCGACAAGCTCACCTACGCCGGCAACCGGCAGAACCTCGCCAGCCTCGACGGC 
GACGCCCGGCACACCTTCGTCGCCGGCGATATCGGCGATAGCCAGCTGGTAGCCCGCCTGCTCGCCGAGCAC 
CAGCCGCGGGCGATCCTCAACTTCGCCGCGGAATCTCATGTGGACCGCTCGATCCACGGCCCCGAGGACTTC 
ATCCAGACCAACATCGTCGGCACCTTCCGCCTGCTGGAAGAAGTGCGCGCCTACTGGGGCGCGCTGGAGCCG 
GAAGCGAAGGCGGCATTCCGCTTCCTCCACGTCTCCACCGACGAAGTCTATGGCTCGCTGGCACCGAGCGAT 
CCGGCCTTCACCGAGAACAACCGCTACGAGCCGAACAGTCCCTACTCGGCGTCCAAGGCGGCCTCCGACCAC 
CTGGTGCGGGCCTATCACCACACCTACGGGCTGCCGGTGCTGACCACCAACTGCTCGAACAACTACGGCCCG 
TACCACTTCCCGGAAAAGCTCATCCCACTGGTGATCCACAACGCCCTGGCCGGCAAGCCGCTGCCGATCTAC 
GGCGACGGCCAGCAGATCCGCGACTGGCTCTACGTCAAGGACCATTGCAGCGCCATCCGCCGGGTCCTCGAA 
GCCGGGCAACTGGGCGAGACCTACAATGTCGGCGGCTGGAACGAAAAGGCCAACCTCGACGTGGTCGAGACC 
CTCTGCGCCATCCTCGACCAGGAGCAGCCGCGCGCCGACGGCCGCAGCTATCGCGAGCAGATCACCTTCGTC 
AAGGATCGTCCGGGCCATGATCGCCGCTACGCCATCGATGCCACGCGCCTGGAGCGCGAGCTGGGCTGGAAG 
CCGGCGGAAACCTTCGAGACCGGCATCCGCAAGACCGTGCGCTGGTACCTGGACAACCAGGACTGGGTGGCC 
AACGTAACCAGCGGTGCCTACCGCGAGTGGGTGGGTAAGCAGTACGCATGA