ViewGene
Locus Name:
GeneID:
Location:

GeneID:1799
TrivialName: PA14_11400
AnnotatorUID:
Modification Date/Time:2006-04-06 13:01:23
LocusName:PA14_11400
PAO1 Ortholog Locus:PA4056
Sequence Length:1122
Protein Length:373
Start: 988435
Stop: 989556
Strand: +
Type:
ChromosomeID:2
Status: ACTIVE
Frame Discrepancy: FALSE
Missense Discrepancy:FALSE
Comments:
Homology: gb|AAG07443.1|AE004822_3 (AE004822) riboflavin-specific deaminase/reductase [Pseudomonas aeruginosa PAO1]
Identities = 369/373 (98%), Positives = 370/373 (99%)
Sequence:
ATGAACGCCGCCGACCCGCTGTACATGGCCCGCGCCCTGGAACTGGCGCGCCAGGGGCTGTACTCCACCCAT
CCGAATCCGCGCGTCGGCTGCGTGCTGGTCAAGGACGGCCAGGTGGTCGGCGAGGGCTGGCACGTCCGCGCC
GGCGAGCCGCACGCCGAGGTCCATGCCCTGCGCCAGGCCGGCGAGAATGCACGCGGCGCCACCGCCTACGTG
ACCCTCGAGCCCTGCAGCCACTTCGGCCGCACCCCGCCGTGCGCCGACGCGCTGGTGGGCGCCGGGGTGGCG
CGGGTGGTCGCGGCGATGCAGGATCCCAACCCCGAGGTCGCCGGTCGCGGCCTGCTGCGTCTGATGCAGGCC
GGCATCGCGGTGCAGAGCGGGGTCCTCGAAGCCGAGGCGCGGGAACTCAACATCGGTTTCATCAAGCGCATG
GAACATGGCCTGCCGTTCGTCCGGGTCAAGCTGGCGATGAGCCTGGACGGGCGCACCGCCATGGCCAGCGGG
GAAAGCCAGTGGATCACCGGGCCCTCTGCGCGTTCGGCGGTGCAGCGCTTGCGCGCTCGCTCCAGCGTGGTG
TTGTCCGGCGCCGATACGCTGCTGGCGGACGATGCGCGGCTCAACGTACGCCCCGACGAACTGGGCCTGAAC
GCCGAGCTTACCGCGCTCGCCGCGGCTCGCCAGCCGTTGCGGGTGCTGGTCGACGGGCGCCTGCGGGTGCCG
CTGGAGTCGGCGTTCTACCAGGCCGGTCCGGCACTGGTGGCGACCTGCGCCGCCGCCTCGGCGCGCGAACGC
TTCCAGGACGCCGGTCACGAACTGCTGGCGCTGCCCTCCGCCGAGGGGCATGTCGACCTGCACAAGTTGCTC
GTGGAACTGGCGGCGCGCGGCGCCAACGAAGTGCTGGTGGAGGCCGGCCCCCGCCTGGCCGGCGCCTTCGCT
CGACTGGGGCTGGTGGATGAGTACCGGCTGTTCGTCGCGCCGAAGTTCCTCGGCTCCAGCGCCCGTCCTTTG
CTCGACTGGCCGCTGACGCGGATGGCCGATGCGGCGCAGTTGCGGATCGACGACATCCGCGCGGTGGGCGAC
GACTGGCTGGTCACCGCGCGGCCCCATCCGCGGGACGCTTGA
Translation:
MNAADPLYMARALELARQGLYSTHPNPRVGCVLVKDGQVVGEGWHVRAGEPHAEVHALRQAGENARGATAYV
TLEPCSHFGRTPPCADALVGAGVARVVAAMQDPNPEVAGRGLLRLMQAGIAVQSGVLEAEARELNIGFIKRM
EHGLPFVRVKLAMSLDGRTAMASGESQWITGPSARSAVQRLRARSSVVLSGADTLLADDARLNVRPDELGLN
AELTALAAARQPLRVLVDGRLRVPLESAFYQAGPALVATCAAASARERFQDAGHELLALPSAEGHVDLHKLL
VELAARGANEVLVEAGPRLAGAFARLGLVDEYRLFVAPKFLGSSARPLLDWPLTRMADAAQLRIDDIRAVGD
DWLVTARPHPRDA*
AnnotationID:1808GeneID:1799
AnnotatorUID: diggins
Modification Date/Time: 2005-03-29 19:07:32
Gene Name:ribD
Confidence Code:2
GeneProduct:riboflavin-specific deaminase/reductase
Cell Localization:()
Synonyms:
Cell Localization Confidence Code:5
MolecularFunction:
Functional Category:(3) Antibiotic resistance and susceptibility
Alternate Gene Product Name:bifunctional pyrimidine deaminase
Functional Category Confidence Code:5
COGs:COG0117,COG1985,cd01284,pfam01872
Secondary Functional Category(ies):
EC Number:3.5.4.26
Status:ACTIVE
Pathway:






 
Homology:
>gb|AAO54232.1| (AE016858) riboflavin biosynthesis protein RibD [Pseudomonas
           syringae pv. tomato str. DC3000]
          Length = 381

 Score =  571 bits (1471), Expect = e-162
 Identities = 288/366 (78%), Positives = 323/366 (88%)

>gb|AAN66141.1|AE016242_9 (AE016775) riboflavin biosynthesis protein RibD [Pseudomonas putida
           KT2440]
          Length = 378

 Score =  538 bits (1387), Expect = e-152
 Identities = 277/366 (75%), Positives = 311/366 (84%), Gaps = 2/366 (0%)

>gb|AAG54763.1|AE005220_12 (AE005220) bifunctional pyrimidine deaminase/reductase in pathway
           of riboflavin synthesis [Escherichia coli O157:H7
           EDL933]
          Length = 367

 Score =  382 bits (981), Expect = e-105
 Identities = 202/359 (56%), Positives = 253/359 (70%), Gaps = 4/359 (1%)






 
Structural Features:
COG0117, RibD, Pyrimidine deaminase [Coenzyme metabolism]
CD-Length = 146 residues,  98.6% aligned
Score =  223 bits (571), Expect = 2e-59
Identities = 101/144 (70%), Positives = 115/144 (79%)

COG1985, RibD, Pyrimidine reductase, riboflavin biosynthesis [Coenzyme metabolism]
CD-Length = 218 residues, 100.0% aligned
Score =  207 bits (527), Expect = 2e-54
Identities = 104/229 (45%), Positives = 135/229 (58%), Gaps = 15/229 (6%)

cd01284, Riboflavin-specific deaminase.
CD-Length = 115 residues, 100.0% aligned
Score =  157 bits (399), Expect = 2e-39

pfam01872, RibD_C, RibD C-terminal domain. 
CD-Length = 196 residues, 100.0% aligned
Score =  150 bits (381), Expect = 2e-37
Identities = 82/216 (37%), Positives = 112/216 (51%), Gaps = 20/216 (9%)






   
Genomic Context:






   
Comment:


















    ReferenceID:3601




  
Author/Investigator(s):
        GenNotator





  
Title:
        




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:BLASTP 







    
Data:


    		




 
URL:

















    ReferenceID:20748




  
Author/Investigator(s):
        GenNotator





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:RPSBLAST 







    
Data:


    		




 
URL:

















    ReferenceID:36523




  
Author/Investigator(s):
        





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:Misc (text/plain)







    
Data:1799_cdd.html


    		




 
URL:

















    ReferenceID:36593




  
Author/Investigator(s):
        Mironov VN, Kraev AS, Chikindas ML, Chernov BK, Stepanov AI, Skryabin KG.





  
Title:
        Functional organization of the riboflavin biosynthesis operon from Bacillus subtilis SHgw.




  
PubMed:
        8159171


MedLine:
        




    
Source:
Mol Gen Genet. 1994 Jan;242(2):201-8.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=94211210&dopt=Abstract

















    ReferenceID:36594




  
Author/Investigator(s):
        Richter G, Fischer M, Krieger C, Eberhardt S, Luttgen H, Gerstenschlager I, Bacher A.





  
Title:
        Biosynthesis of riboflavin: characterization of the bifunctional deaminase-reductase of Escherichia coli and Bacillus subtilis.




  
PubMed:
        9068650


MedLine:
        




    
Source:
J Bacteriol. 1997 Mar;179(6):2022-8.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=9068650









           
Homologs By Global Alignment 

           

       



     
Gene ID:1799
           
Identity:

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

                           

     
HomologID
                           Accession
                           Description
                           Length
                           PctIdentity
                           PctSimilarity
                           Gaps
                           Score
     

     
     
3168
                           PA4056_tr
                           translation of PA4056
                           373
                           98.92
                           99.19
                           0
                           1865.0
     

     
     
98431
                           gb|AAG07443.1|AE004822_3
                           (AE004822) riboflavin-specific deaminase/reductase [Pseudomonas aeruginosa PAO1]
                           373
                           98.92
                           99.19
                           0
                           1865.0
     

     
     
98432
                           gb|AAO54232.1|
                           (AE016858) riboflavin biosynthesis protein RibD [Pseudomonas syringae pv. tomato str. DC3000]
                           381
                           75.59
                           84.77
                           8
                           1463.0
     

     
     
98433
                           gb|AAN66141.1|AE016242_9
                           (AE016775) riboflavin biosynthesis protein RibD [Pseudomonas putida KT2440]
                           380
                           73.94
                           82.89
                           9
                           1384.0
     

     
     
98434
                           gb|AAM84581.1|AE013703_11
                           (AE013703) bifunctional pyrimidine deaminase/reductase [Yersinia pestis KIM]
                           378
                           55.55
                           67.98
                           14
                           995.0
     

     






      

          
GC ORFID: 44801How Found: BLASTX

          
GC_TrimmedSeqID: 69Blast Result ID

          
Subject Sequence Name: t_PA4056Glimmer Score: 

          
Start: 3965502Stop: 3964381

          
Length: 1122


          
Start Codon: ATGTruncated Start:

          
Stop Codon: TGATruncated Stop: 

          
Homolog: t_PA4056 translation of PA4056Homolog Bit Score 723.0

          
Other Homologs:  psyr_15may02_Scaffold4_revised_gene5262 (ORF: BLASTX 580.0), t_PA4056 (ORF: GLIMMER)

          
GC ORF Sequence

           
ATGAACGCCGCCGACCCGCTGTACATGGCCCGCGCCCTGGAACTGGCGCGCCAGGGGCTGTACTCCACCCAT 
CCGAATCCGCGCGTCGGCTGCGTGCTGGTCAAGGACGGCCAGGTGGTCGGCGAGGGCTGGCACGTCCGCGCC 
GGCGAGCCGCACGCCGAGGTCCATGCCCTGCGCCAGGCCGGCGAGAATGCACGCGGCGCCACCGCCTACGTG 
ACCCTCGAGCCCTGCAGCCACTTCGGCCGCACCCCGCCGTGCGCCGACGCGCTGGTGGGCGCCGGGGTGGCG 
CGGGTGGTCGCGGCGATGCAGGATCCCAACCCCGAGGTCGCCGGTCGCGGCCTGCTGCGTCTGATGCAGGCC 
GGCATCGCGGTGCAGAGCGGGGTCCTCGAAGCCGAGGCGCGGGAACTCAACATCGGTTTCATCAAGCGCATG 
GAACATGGCCTGCCGTTCGTCCGGGTCAAGCTGGCGATGAGCCTGGACGGGCGCACCGCCATGGCCAGCGGG 
GAAAGCCAGTGGATCACCGGGCCCTCTGCGCGTTCGGCGGTGCAGCGCTTGCGCGCTCGCTCCAGCGTGGTG 
TTGTCCGGCGCCGATACGCTGCTGGCGGACGATGCGCGGCTCAACGTACGCCCCGACGAACTGGGCCTGAAC 
GCCGAGCTTACCGCGCTCGCCGCGGCTCGCCAGCCGTTGCGGGTGCTGGTCGACGGGCGCCTGCGGGTGCCG 
CTGGAGTCGGCGTTCTACCAGGCCGGTCCGGCACTGGTGGCGACCTGCGCCGCCGCCTCGGCGCGCGAACGC 
TTCCAGGACGCCGGTCACGAACTGCTGGCGCTGCCCTCCGCCGAGGGGCATGTCGACCTGCACAAGTTGCTC 
GTGGAACTGGCGGCGCGCGGCGCCAACGAAGTGCTGGTGGAGGCCGGCCCCCGCCTGGCCGGCGCCTTCGCT 
CGACTGGGGCTGGTGGATGAGTACCGGCTGTTCGTCGCGCCGAAGTTCCTCGGCTCCAGCGCCCGTCCTTTG 
CTCGACTGGCCGCTGACGCGGATGGCCGATGCGGCGCAGTTGCGGATCGACGACATCCGCGCGGTGGGCGAC 
GACTGGCTGGTCACCGCGCGGCCCCATCCGCGGGACGCTTGA