ViewGene
Locus Name:
GeneID:
Location:

GeneID:2404
TrivialName: PA14_69450
AnnotatorUID:
Modification Date/Time:2006-04-06 13:01:23
LocusName:PA14_69450
PAO1 Ortholog Locus:PA5260
Sequence Length:942
Protein Length:313
Start: 6194649
Stop: 6193708
Strand: -
Type:
ChromosomeID:2
Status: ACTIVE
Frame Discrepancy: FALSE
Missense Discrepancy:FALSE
Comments:
Homology: gb|AAG08645.1|AE004938_7 (AE004938) porphobilinogen deaminase [Pseudomonas aeruginosa PAO1]
Identities = 312/313 (99%), Positives = 313/313 (100%)
Sequence:
ATGTCGTCCCGCGAAATCCGCATCGCCACTCGCCAGAGCGCCCTCGCCTTGTGGCAGGCCGAATACGTCAAG
GCGCGCCTGGAGCAGGCTCATCCTGGCCTGACCGTCACCCTGCTGCCGATGACCAGTCGCGGCGACAAGCTG
CTCGACGCACCGCTGGCGAAGATCGGCGGCAAGGGCCTGTTCGTCAAGGAACTGGAAACCGCCCTGCTCGAA
GGCGCCGCCGACATCGCGGTGCATTCGATGAAGGACGTGCCGATGGACTTTCCCGAGGGGCTCGGCCTCTAC
ACCATCTGCGAGCGCGAAGACCCGCGTGACGCTTTCGTCTCGAACACCTACGCCAGCCTCGAGCAACTGCCA
GCCGGCAGCGTGGTCGGCACCTCCAGCCTGCGCCGCCAGGCGCAGCTGCTGGCGCGCCGGCCGGACCTGCAG
ATCCGTTTCCTGCGGGGCAACGTCAATACCCGCCTGGCCAAGCTGGATGCCGGCGAATACGACGCGATCATC
CTCGCCGCCGCCGGCCTGATCCGCCTCGGCTTCGAGTCGCGCATCCGCTCCTCGATCAGTGTCGACGACAGC
CTGCCCGCCGGCGGACAAGGCGCCGTCGGCATCGAATGTCGTACTGCCGACAGCGACTTGCATGCCTTGCTG
GAACCCTTGCACCATTCCGACACGGCTCTGCGGGTCACTGCCGAGCGCGCGCTGAACAAGCGACTCAACGGC
GGTTGCCAGGTGCCGATCGCCTGCTACGCCATCCGCGAGGGCGACCAGCTGTGGCTGCGCGGCCTGGTCGGC
CAGCCTGATGGCACCCAGTTGCTGCGCGCCGAGGGGCGGGCGCCACTGGCGGAAGCCGAGGCGCTGGGCGTG
CGGGTGGCCGAGGACCTGCTGGAGCAGGGCGCCGAAGCGATTCTCGAAGCCGTCTACGGCGAGGCCGGACAT
CCGTGA
Translation:
MSSREIRIATRQSALALWQAEYVKARLEQAHPGLTVTLLPMTSRGDKLLDAPLAKIGGKGLFVKELETALLE
GAADIAVHSMKDVPMDFPEGLGLYTICEREDPRDAFVSNTYASLEQLPAGSVVGTSSLRRQAQLLARRPDLQ
IRFLRGNVNTRLAKLDAGEYDAIILAAAGLIRLGFESRIRSSISVDDSLPAGGQGAVGIECRTADSDLHALL
EPLHHSDTALRVTAERALNKRLNGGCQVPIACYAIREGDQLWLRGLVGQPDGTQLLRAEGRAPLAEAEALGV
RVAEDLLEQGAEAILEAVYGEAGHP*
AnnotationID:2412GeneID:2404
AnnotatorUID: diggins
Modification Date/Time: 2005-04-26 14:02:11
Gene Name:hemC
Confidence Code:2
GeneProduct:porphobilinogen deaminase
Cell Localization:()
Synonyms:
Cell Localization Confidence Code:5
MolecularFunction:
Functional Category:(8) Central intermediary metabolism
Alternate Gene Product Name:hydroxymethylbilane synthase
Functional Category Confidence Code:5
COGs:cd00494,pfam03900
Secondary Functional Category(ies):biosynthesis of cofactors, prosthetic groups and carriers
EC Number:4.3.1.8
Status:ACTIVE
Pathway:






 
Homology:
>gb|AAN65819.1|AE016210_7 (AE016774) porphobilinogen deaminase [Pseudomonas putida KT2440]
          Length = 313

 Score =  534 bits (1375), Expect = e-151
 Identities = 274/313 (87%), Positives = 288/313 (92%)

>gb|AAO53682.1| (AE016856) porphobilinogen deaminase [Pseudomonas syringae pv.
           tomato str. DC3000]
          Length = 313

 Score =  511 bits (1316), Expect = e-144
 Identities = 258/312 (82%), Positives = 282/312 (90%)

>gb|AAF93298.1| (AE004102) porphobilinogen deaminase [Vibrio cholerae]
          Length = 317

 Score =  417 bits (1072), Expect = e-116
 Identities = 213/307 (69%), Positives = 244/307 (79%)






 
Structural Features:
cd00494, HMBS, Hydroxymethylbilane synthase (HMBS), 
also known as porphobilinogen deaminase (PBGD)
CD-Length = 292 residues, 100.0% aligned
Score =  421 bits (1085), Expect = 4e-119
Identities = 177/292 (60%), Positives = 213/292 (72%), Gaps = 1/292 (0%)

pfam03900, Porphobil_deamC, Porphobilinogen deaminase, C-terminal domain.
CD-Length = 75 residues, 100.0% aligned
Score = 89.6 bits (222), Expect = 4e-19
Identities = 38/75 (50%), Positives = 49/75 (65%), Gaps = 1/75 (1%)







   
Genomic Context:






   
Comment:


















    ReferenceID:4811




  
Author/Investigator(s):
        GenNotator





  
Title:
        




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:BLASTP 







    
Data:


    		




 
URL:

















    ReferenceID:21957




  
Author/Investigator(s):
        GenNotator





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:RPSBLAST 







    
Data:


    		




 
URL:

















    ReferenceID:34820




  
Author/Investigator(s):
        





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:Misc (text/plain)







    
Data:2404_cdd.html


    		




 
URL:

















    ReferenceID:35734




  
Author/Investigator(s):
        Mohr CD, Sonsteby SK, Deretic V.





  
Title:
        The Pseudomonas aeruginosa homologs of hemC and hemD are linked to the gene encoding the regulator of mucoidy AlgR.




  
PubMed:
        8159168


MedLine:
        




    
Source:
Mol Gen Genet. 1994 Jan;242(2):177-84.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=8159168

















    ReferenceID:35735




  
Author/Investigator(s):
        Thomas SD, Jordan PM.





  
Title:
        Nucleotide sequence of the hemC locus encoding porphobilinogen deaminase of Escherichia coli K12.




  
PubMed:
        3529035


MedLine:
        




    
Source:
Nucleic Acids Res. 1986 Aug 11;14(15):6215-26.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=3529035

















    ReferenceID:35739




  
Author/Investigator(s):
        Alefounder PR, Abell C, Battersby AR.





  
Title:
        The sequence of hemC, hemD and two additional E. coli genes.




  
PubMed:
        3054815


MedLine:
        




    
Source:
Nucleic Acids Res. 1988 Oct 25;16(20):9871.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=3054815

















    ReferenceID:35740




  
Author/Investigator(s):
        Majumdar D, Wyche JH.





  
Title:
        Molecular cloning and nucleotide sequence of the porphobilinogen deaminase gene, hemC, from Chlorobium vibrioforme.




  
PubMed:
        9058548


MedLine:
        




    
Source:
Curr Microbiol. 1997 Apr;34(4):258-63.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=9058548









           
Homologs By Global Alignment 

           

       



     
Gene ID:2404
           
Identity:

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

                           

     
HomologID
                           Accession
                           Description
                           Length
                           PctIdentity
                           PctSimilarity
                           Gaps
                           Score
     

     
     
4055
                           PA5260_tr
                           translation of PA5260
                           313
                           99.68
                           99.99
                           0
                           1569.0
     

     
     
121698
                           gb|AAG08645.1|AE004938_7
                           (AE004938) porphobilinogen deaminase [Pseudomonas aeruginosa PAO1]
                           313
                           99.68
                           99.99
                           0
                           1569.0
     

     
     
121699
                           gb|AAA18907.1|
                           (M74844) porophorbilinogen deaminase [Pseudomonas aeruginosa]
                           314
                           97.13
                           98.40
                           1
                           1527.0
     

     
     
121700
                           gb|AAN65819.1|AE016210_7
                           (AE016774) porphobilinogen deaminase [Pseudomonas putida KT2440]
                           313
                           87.53
                           92.01
                           0
                           1375.0
     

     
     
121701
                           gb|AAO53682.1|
                           (AE016856) porphobilinogen deaminase [Pseudomonas syringae pv. tomato str. DC3000]
                           313
                           82.42
                           90.09
                           0
                           1315.0
     

     






      

          
GC ORFID: 45406How Found: BLASTX

          
GC_TrimmedSeqID: 69Blast Result ID

          
Subject Sequence Name: t_PA5260Glimmer Score: 

          
Start: 5458336Stop: 5457395

          
Length: 942


          
Start Codon: ATGTruncated Start:

          
Stop Codon: TGATruncated Stop: 

          
Homolog: t_PA5260 translation of PA5260Homolog Bit Score 608.0

          
Other Homologs:  psyr_15may02_Scaffold2_revised_gene4066 (ORF: BLASTX 520.0), t_PA5260 (ORF: GLIMMER)

          
GC ORF Sequence

           
ATGTCGTCCCGCGAAATCCGCATCGCCACTCGCCAGAGCGCCCTCGCCTTGTGGCAGGCCGAATACGTCAAG 
GCGCGCCTGGAGCAGGCTCATCCTGGCCTGACCGTCACCCTGCTGCCGATGACCAGTCGCGGCGACAAGCTG 
CTCGACGCACCGCTGGCGAAGATCGGCGGCAAGGGCCTGTTCGTCAAGGAACTGGAAACCGCCCTGCTCGAA 
GGCGCCGCCGACATCGCGGTGCATTCGATGAAGGACGTGCCGATGGACTTTCCCGAGGGGCTCGGCCTCTAC 
ACCATCTGCGAGCGCGAAGACCCGCGTGACGCTTTCGTCTCGAACACCTACGCCAGCCTCGAGCAACTGCCA 
GCCGGCAGCGTGGTCGGCACCTCCAGCCTGCGCCGCCAGGCGCAGCTGCTGGCGCGCCGGCCGGACCTGCAG 
ATCCGTTTCCTGCGGGGCAACGTCAATACCCGCCTGGCCAAGCTGGATGCCGGCGAATACGACGCGATCATC 
CTCGCCGCCGCCGGCCTGATCCGCCTCGGCTTCGAGTCGCGCATCCGCTCCTCGATCAGTGTCGACGACAGC 
CTGCCCGCCGGCGGACAAGGCGCCGTCGGCATCGAATGTCGTACTGCCGACAGCGACTTGCATGCCTTGCTG 
GAACCCTTGCACCATTCCGACACGGCTCTGCGGGTCACTGCCGAGCGCGCGCTGAACAAGCGACTCAACGGC 
GGTTGCCAGGTGCCGATCGCCTGCTACGCCATCCGCGAGGGCGACCAGCTGTGGCTGCGCGGCCTGGTCGGC 
CAGCCTGATGGCACCCAGTTGCTGCGCGCCGAGGGGCGGGCGCCACTGGCGGAAGCCGAGGCGCTGGGCGTG 
CGGGTGGCCGAGGACCTGCTGGAGCAGGGCGCCGAAGCGATTCTCGAAGCCGTCTACGGCGAGGCCGGACAT 
CCGTGA