ViewGene
Locus Name:
GeneID:
Location:

GeneID:3980
TrivialName: PA14_68210
AnnotatorUID:
Modification Date/Time:2006-04-06 13:01:23
LocusName:PA14_68210
PAO1 Ortholog Locus:PA5164
Sequence Length:546
Protein Length:181
Start: 6085293
Stop: 6085838
Strand: +
Type:
ChromosomeID:2
Status: ACTIVE
Frame Discrepancy: FALSE
Missense Discrepancy:FALSE
Comments:
Homology: gb|AAG08549.1|AE004929_4 (AE004929) dTDP-4-dehydrorhamnose 3,5-epimerase [Pseudomonas aeruginosa PAO1]
Identities = 181/181 (100%), Positives = 181/181 (100%)
Sequence:
ATGAAAGCGACCCGCCTGGCAATCCCCGACGTCATCCTCTTCGAACCCCGGGTGTTCGGCGACGATCGCGGA
TTCTTCTTCGAAAGCTACAACCAGCGCGCCTTCGAGGAGGCCTGCGGTCATCCGGTCAGCTTCGTCCAGGAC
AACCATTCGCGTTCCGCCCGTGGCGTCCTCCGCGGCCTGCACTACCAGATCCGGCAAGCCCAGGGAAAACTG
GTGCGCGCCACCCTCGGCGAGGTATTCGACGTGGCCGTCGACCTGCGTCGCGGCTCGCCGACCTTCGGCCAG
TGGGTAGGCGAACGCCTGAGCGCGGAGAACAAGCGCCAGATGTGGATTCCGGCCGGCTTCGCGCACGGCTTC
GTGGTGCTCAGCGAATACGCCGAGTTCCTCTACAAGACCACCGACTTCTGGGCGCCGGAACACGAACGCTGC
ATCGTCTGGAACGATCCCGAGCTGAAGATCGACTGGCCGCTGCAGGATGCCCCCCTGCTTTCGGAGAAGGAC
CGCCAGGGCAAGGCATTCGCCGACGCCGACTGCTTCCCCTGA
Translation:
MKATRLAIPDVILFEPRVFGDDRGFFFESYNQRAFEEACGHPVSFVQDNHSRSARGVLRGLHYQIRQAQGKL
VRATLGEVFDVAVDLRRGSPTFGQWVGERLSAENKRQMWIPAGFAHGFVVLSEYAEFLYKTTDFWAPEHERC
IVWNDPELKIDWPLQDAPLLSEKDRQGKAFADADCFP*
AnnotationID:3987GeneID:3980
AnnotatorUID: diggins
Modification Date/Time: 2005-04-26 13:01:48
Gene Name:rmlC
Confidence Code:2
GeneProduct:dTDP-4-dehydrorhamnose 3,5-epimerase
Cell Localization:()
Synonyms:rfbC
Cell Localization Confidence Code:5
MolecularFunction:
Functional Category:(7) Cell wall / LPS / capsule
Alternate Gene Product Name:dTDP-6-deoxy-L-mannose-dehydrogenase
Functional Category Confidence Code:5
COGs:pfam00908,COG1898
Secondary Functional Category(ies):cell envelope biogenesis, outer membrane
EC Number:5.1.3.13
Status:ACTIVE
Pathway:






 
Homology:
>gb|AAO54606.1| (AE016859) dTDP-4-dehydrorhamnose 3,5-epimerase [Pseudomonas
           syringae pv. tomato str. DC3000]
          Length = 181

 Score =  283 bits (725), Expect = 3e-76
 Identities = 130/180 (72%), Positives = 151/180 (83%)

>emb|CAD84589.1| (BX321858) dTDP-4-dehydrorhamnose 3,5-epimerase [Nitrosomonas
           europaea ATCC 19718]
          Length = 181

 Score =  275 bits (704), Expect = 7e-74
 Identities = 127/180 (70%), Positives = 149/180 (82%)

>emb|CAD14215.1| (AL646060) PROBABLE DTDP-4-DEHYDRORHAMNOSE 3,5-EPIMERASE PROTEIN
           [Ralstonia solanacearum]
          Length = 183

 Score =  268 bits (686), Expect = 9e-72
 Identities = 124/174 (71%), Positives = 145/174 (83%)






 
Structural Features:
pfam00908, dTDP_sugar_isom, dTDP-4-dehydrorhamnose 3,5-epimerase.
CD-Length = 177 residues, 100.0% aligned
Score =  261 bits (669), Expect = 3e-71
Identities = 117/178 (65%), Positives = 135/178 (75%), Gaps = 4/178 (2%)

COG1898, RfbC, dTDP-4-dehydrorhamnose 3,5-epimerase and related enzymes 
[Cell envelope biogenesis, outer membrane]
CD-Length = 173 residues, 100.0% aligned
Score =  235 bits (601), Expect = 2e-63
Identities = 104/176 (59%), Positives = 127/176 (72%), Gaps = 3/176 (1%)







   
Genomic Context:






   
Comment:


















    ReferenceID:7962




  
Author/Investigator(s):
        GenNotator





  
Title:
        




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:BLASTP 







    
Data:


    		




 
URL:

















    ReferenceID:25105




  
Author/Investigator(s):
        GenNotator





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:RPSBLAST 







    
Data:


    		




 
URL:

















    ReferenceID:34909




  
Author/Investigator(s):
        





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:Misc (text/plain)







    
Data:3980_cdd.html


    		




 
URL:

















    ReferenceID:35771




  
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:3980
           
Identity:

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

                           

     
HomologID
                           Accession
                           Description
                           Length
                           PctIdentity
                           PctSimilarity
                           Gaps
                           Score
     

     
     
6218
                           PA5164_tr
                           translation of PA5164
                           181
                           99.99
                           99.99
                           0
                           977.0
     

     
     
172163
                           gb|AAG08549.1|AE004929_4
                           (AE004929) dTDP-4-dehydrorhamnose 3,5-epimerase [Pseudomonas aeruginosa PAO1]
                           181
                           99.99
                           99.99
                           0
                           977.0
     

     
     
172164
                           emb|CAC82199.1|
                           (AJ298594) dTDP-4-keto-6-deoxy-D-glucose 3,5 epimerase [Pseudomonas aeruginosa]
                           181
                           99.99
                           99.99
                           0
                           977.0
     

     
     
172165
                           gb|AAO54606.1|
                           (AE016859) dTDP-4-dehydrorhamnose 3,5-epimerase [Pseudomonas syringae pv. tomato str. DC3000]
                           181
                           71.82
                           83.42
                           0
                           724.0
     

     
     
172166
                           emb|CAD84589.1|
                           (BX321858) dTDP-4-dehydrorhamnose 3,5-epimerase [Nitrosomonas europaea ATCC 19718]
                           181
                           70.16
                           82.32
                           0
                           703.0
     

     






      

          
GC ORFID: 46982How Found: BLASTX

          
GC_TrimmedSeqID: 69Blast Result ID

          
Subject Sequence Name: t_PA5164Glimmer Score: 

          
Start: 5348979Stop: 5349524

          
Length: 546


          
Start Codon: ATGTruncated Start:

          
Stop Codon: TGATruncated Stop: 

          
Homolog: t_PA5164 translation of PA5164Homolog Bit Score 380.0

          
Other Homologs:  psyr_15may02_Scaffold14_revised_gene2284 (ORF: BLASTX 252.0), t_PA5164 (ORF: GLIMMER)

          
GC ORF Sequence

           
ATGAAAGCGACCCGCCTGGCAATCCCCGACGTCATCCTCTTCGAACCCCGGGTGTTCGGCGACGATCGCGGA 
TTCTTCTTCGAAAGCTACAACCAGCGCGCCTTCGAGGAGGCCTGCGGTCATCCGGTCAGCTTCGTCCAGGAC 
AACCATTCGCGTTCCGCCCGTGGCGTCCTCCGCGGCCTGCACTACCAGATCCGGCAAGCCCAGGGAAAACTG 
GTGCGCGCCACCCTCGGCGAGGTATTCGACGTGGCCGTCGACCTGCGTCGCGGCTCGCCGACCTTCGGCCAG 
TGGGTAGGCGAACGCCTGAGCGCGGAGAACAAGCGCCAGATGTGGATTCCGGCCGGCTTCGCGCACGGCTTC 
GTGGTGCTCAGCGAATACGCCGAGTTCCTCTACAAGACCACCGACTTCTGGGCGCCGGAACACGAACGCTGC 
ATCGTCTGGAACGATCCCGAGCTGAAGATCGACTGGCCGCTGCAGGATGCCCCCCTGCTTTCGGAGAAGGAC 
CGCCAGGGCAAGGCATTCGCCGACGCCGACTGCTTCCCCTGA