ViewGene
Locus Name:
GeneID:
Location:

GeneID:2320
TrivialName: PA14_47730
AnnotatorUID:
Modification Date/Time:2006-04-06 13:01:23
LocusName:PA14_47730
PAO1 Ortholog Locus:PA1275
Sequence Length:939
Protein Length:312
Start: 4248273
Stop: 4247335
Strand: -
Type:
ChromosomeID:2
Status: ACTIVE
Frame Discrepancy: FALSE
Missense Discrepancy:FALSE
Comments:
Homology: gb|AAG04664.1|AE004557_5 (AE004557) cobalamin biosynthetic protein CobD [Pseudomonas aeruginosa PAO1]
Identities = 308/312 (98%), Positives = 308/312 (98%)
Sequence:
ATGAGCGCACTGCTGGGTATCCTCGGCGTGGCGCTGGATGCGCGCTTCGGCGAGCCGCAGGGCTGGCACCCG
CTGGTCGCCTTCGGCCGCCTGGCCGATCGCCTGGAGCGCCGTTTCAACCGCTCGCGCCTGGCCGGCGAGGGC
GATCCCGGGGTCGGCTGGCGCAGCCACGGGGTGACCGCCTGGGTCCTCGCGGTACTGCCGCTGACCCTGCTG
GCCTGGGCGCTCGCTGAACTTCCCTACCTCGGCTGGCTGGTCCAGGCCCTGGCGCTGTACGCCGCGCTCGGC
CTGCGCAGCCTCGGCGAGCACGCCGAACCGGTGGCACTGGCCTTGCGCGCCGGCGACCTGGACGAGGCGCGG
CGACGTGTCGGCTACCTGGTCAGCCGCGATACCCGCGAGCTGGACCAGGCCGGGGTCGCCCGCGCGGCCACC
GAATCGGTACTGGAGAACGGCAGCGACGCGGTCTACGCCGCGCTGTTCTGGTTCGCCGTGGCCGGCGCGCCG
GGGGTGGTGCTGTATCGCCTGAGCAATACCCTGGACGCGATGTGGGGCTACCGCAACGCGCGCTTCGAGCGC
TTCGGCTGGGCCGCGGCGAAGATCGACGACATCCTCAACTACCTGCCGGCGCGGCTGGTGGCGCTGACCTAC
GCGCTGCTCGGCGGCACCCGCCAGGCCCTGCGCTGCTGGCGCGAGCAGGCGCCGCAATGGGACAGCCCCAAC
GCCGGCCCGGTGATGGCCGCCGGCGCCGGTGCGCTGGGGGTTTCCCTGGGCGGCGCGGCGATCTACCACGGC
GAGCTGCACCAGCGGCCGCTCCTCGGCAGCGGCCCGCAGCCGCAGGGCCGCGACATCTATCGGGCCCTGGCG
CTGGTACGCCAGGGCGTGCTGCTCTGGCTGCTGGTGCTGGCCGGACTCTGGGCCATGGGGTGGCTGCATGCT
TGA
Translation:
MSALLGILGVALDARFGEPQGWHPLVAFGRLADRLERRFNRSRLAGEGDPGVGWRSHGVTAWVLAVLPLTLL
AWALAELPYLGWLVQALALYAALGLRSLGEHAEPVALALRAGDLDEARRRVGYLVSRDTRELDQAGVARAAT
ESVLENGSDAVYAALFWFAVAGAPGVVLYRLSNTLDAMWGYRNARFERFGWAAAKIDDILNYLPARLVALTY
ALLGGTRQALRCWREQAPQWDSPNAGPVMAAGAGALGVSLGGAAIYHGELHQRPLLGSGPQPQGRDIYRALA
LVRQGVLLWLLVLAGLWAMGWLHA*
AnnotationID:2328GeneID:2320
AnnotatorUID: diggins
Modification Date/Time: 2005-02-22 18:06:41
Gene Name:cobD
Confidence Code:2
GeneProduct:cobalamin biosynthetic protein CobD
Cell Localization:()
Synonyms:cbiB
Cell Localization Confidence Code:5
MolecularFunction:
Functional Category:(4) Biosynthesis of cofactors, prosthetic groups and carriers
Alternate Gene Product Name:
Functional Category Confidence Code:5
COGs:COG1270,pfam03186
Secondary Functional Category(ies):coenzyme metabolism
EC Number:
Status:ACTIVE
Pathway:






 
Homology:
>gb|AAO55231.1| (AE016861) cobalamin biosynthesis protein CobD [Pseudomonas
           syringae pv. tomato str. DC3000]
          Length = 302

 Score =  439 bits (1129), Expect = e-122
 Identities = 221/299 (73%), Positives = 241/299 (80%), Gaps = 8/299 (2%)

>gb|AAN67296.1|AE016356_4 (AE016780) cobalamin biosynthesis protein CobD [Pseudomonas putida
           KT2440]
          Length = 307

 Score =  439 bits (1128), Expect = e-122
 Identities = 221/299 (73%), Positives = 242/299 (80%), Gaps = 8/299 (2%)

>gb|AAM42333.1| (AE012421) cobalamin biosynthesis protein [Xanthomonas campestris
           pv. campestris str. ATCC 33913]
          Length = 303

 Score =  325 bits (832), Expect = 3e-88
 Identities = 184/310 (59%), Positives = 206/310 (66%), Gaps = 19/310 (6%)






 
Structural Features:
COG1270, CbiB, Cobalamin biosynthesis protein CobD/CbiB [Coenzyme metabolism]
CD-Length = 320 residues,  99.1% aligned
Score =  294 bits (754), Expect = 8e-81
Identities = 160/323 (49%), Positives = 195/323 (60%), Gaps = 17/323 (5%)

pfam03186, CobD_Cbib, CobD/Cbib protein.
CD-Length = 302 residues,  98.7% aligned
Score =  225 bits (575), Expect = 5e-60
Identities = 138/313 (44%), Positives = 174/313 (55%), Gaps = 24/313 (7%)






   
Genomic Context:






   
Comment:


















    ReferenceID:4643




  
Author/Investigator(s):
        GenNotator





  
Title:
        




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:BLASTP 







    
Data:


    		




 
URL:

















    ReferenceID:21789




  
Author/Investigator(s):
        GenNotator





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:RPSBLAST 







    
Data:


    		




 
URL:

















    ReferenceID:37511




  
Author/Investigator(s):
        





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:Misc (text/plain)







    
Data:2320_cdd.html


    		




 
URL:

















    ReferenceID:38026




  
Author/Investigator(s):
        Crouzet J, Cauchois L, Blanche F, Debussche L, Thibaut D, Rouyez MC, Rigault S, Mayaux JF, Cameron B.





  
Title:
        Nucleotide sequence of a Pseudomonas denitrificans 5.4-kilobase DNA fragment containing five cob genes and identification of structural genes encoding S-adenosyl-L-methionine: uroporphyrinogen III methyltransferase and cobyrinic acid a,c-diamide synthase.




  
PubMed:
        2211520


MedLine:
        




    
Source:
J Bacteriol. 1990 Oct;172(10):5968-79.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=2211520

















    ReferenceID:38031




  
Author/Investigator(s):
        Brushaber KR, O'Toole GA, Escalante-Semerena JC.





  
Title:
        CobD, a novel enzyme with L-threonine-O-3-phosphate decarboxylase activity, is responsible for the synthesis of (R)-1-amino-2-propanol O-2-phosphate, a proposed new intermediate in cobalamin biosynthesis in Salmonella typhimurium LT2.




  
PubMed:
        9446573


MedLine:
        




    
Source:
J Biol Chem. 1998 Jan 30;273(5):2684-91.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=9446573









           
Homologs By Global Alignment 

           

       



     
Gene ID:2320
           
Identity:

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

                           

     
HomologID
                           Accession
                           Description
                           Length
                           PctIdentity
                           PctSimilarity
                           Gaps
                           Score
     

     
     
3950
                           PA1275_tr
                           translation of PA1275
                           312
                           98.71
                           98.71
                           0
                           1604.0
     

     
     
120166
                           gb|AAG04664.1|AE004557_5
                           (AE004557) cobalamin biosynthetic protein CobD [Pseudomonas aeruginosa PAO1]
                           312
                           98.71
                           98.71
                           0
                           1604.0
     

     
     
120167
                           gb|AAO55231.1|
                           (AE016861) cobalamin biosynthesis protein CobD [Pseudomonas syringae pv. tomato str. DC3000]
                           316
                           71.20
                           77.84
                           18
                           1130.0
     

     
     
120168
                           gb|AAN67296.1|AE016356_4
                           (AE016780) cobalamin biosynthesis protein CobD [Pseudomonas putida KT2440]
                           319
                           71.15
                           78.99
                           19
                           1129.0
     

     
     
120169
                           gb|AAQ59251.1|
                           (AE016915) cobalamin biosynthetic protein [Chromobacterium violaceum ATCC 12472]
                           318
                           60.06
                           67.61
                           12
                           911.0
     

     






      

          
GC ORFID: 45322How Found: BLASTX

          
GC_TrimmedSeqID: 69Blast Result ID

          
Subject Sequence Name: t_PA1275Glimmer Score: 

          
Start: 705636Stop: 706574

          
Length: 939


          
Start Codon: ATGTruncated Start:

          
Stop Codon: TGATruncated Stop: 

          
Homolog: t_PA1275 translation of PA1275Homolog Bit Score 622.0

          
Other Homologs:  psyr_15may02_Scaffold5_revised_gene6471 (ORF: BLASTX 440.0), t_PA1275 (ORF: GLIMMER)

          
GC ORF Sequence

           
ATGAGCGCACTGCTGGGTATCCTCGGCGTGGCGCTGGATGCGCGCTTCGGCGAGCCGCAGGGCTGGCACCCG 
CTGGTCGCCTTCGGCCGCCTGGCCGATCGCCTGGAGCGCCGTTTCAACCGCTCGCGCCTGGCCGGCGAGGGC 
GATCCCGGGGTCGGCTGGCGCAGCCACGGGGTGACCGCCTGGGTCCTCGCGGTACTGCCGCTGACCCTGCTG 
GCCTGGGCGCTCGCTGAACTTCCCTACCTCGGCTGGCTGGTCCAGGCCCTGGCGCTGTACGCCGCGCTCGGC 
CTGCGCAGCCTCGGCGAGCACGCCGAACCGGTGGCACTGGCCTTGCGCGCCGGCGACCTGGACGAGGCGCGG 
CGACGTGTCGGCTACCTGGTCAGCCGCGATACCCGCGAGCTGGACCAGGCCGGGGTCGCCCGCGCGGCCACC 
GAATCGGTACTGGAGAACGGCAGCGACGCGGTCTACGCCGCGCTGTTCTGGTTCGCCGTGGCCGGCGCGCCG 
GGGGTGGTGCTGTATCGCCTGAGCAATACCCTGGACGCGATGTGGGGCTACCGCAACGCGCGCTTCGAGCGC 
TTCGGCTGGGCCGCGGCGAAGATCGACGACATCCTCAACTACCTGCCGGCGCGGCTGGTGGCGCTGACCTAC 
GCGCTGCTCGGCGGCACCCGCCAGGCCCTGCGCTGCTGGCGCGAGCAGGCGCCGCAATGGGACAGCCCCAAC 
GCCGGCCCGGTGATGGCCGCCGGCGCCGGTGCGCTGGGGGTTTCCCTGGGCGGCGCGGCGATCTACCACGGC 
GAGCTGCACCAGCGGCCGCTCCTCGGCAGCGGCCCGCAGCCGCAGGGCCGCGACATCTATCGGGCCCTGGCG 
CTGGTACGCCAGGGCGTGCTGCTCTGGCTGCTGGTGCTGGCCGGACTCTGGGCCATGGGGTGGCTGCATGCT 
TGA