ViewGene
Locus Name:
GeneID:
Location:

GeneID:1829
TrivialName: PA14_69990
AnnotatorUID:
Modification Date/Time:2006-04-06 13:01:23
LocusName:PA14_69990
PAO1 Ortholog Locus:PA5302
Sequence Length:1074
Protein Length:357
Start: 6245008
Stop: 6243935
Strand: -
Type:
ChromosomeID:2
Status: ACTIVE
Frame Discrepancy: FALSE
Missense Discrepancy:FALSE
Comments:
Homology: gb|AAG08687.1|AE004943_3 (AE004943) catabolic alanine racemase [Pseudomonas aeruginosa PAO1]
Identities = 356/357 (99%), Positives = 356/357 (99%)
Sequence:
ATGCGCCCCGCCCGTGCCCTGATCGACCTGCAAGCCCTTCGTCACAACTATCGGCTGGCCCGCGAGGCCACC
GGCGCCCGTGCGCTCGCGGTGATTAAAGCGGACGCATACGGCCACGGCGCGGTGCGCTGTGCCGAAGCGCTG
GCGGCCGAGGCCGATGGCTTCGCCGTGGCCTGCATCGAGGAGGGCCTGGAGCTGCGCGAGGCCGGTATCCGC
CAGCCGATCCTGCTGCTGGAGGGCTTCTTCGAGGCGTCCGAGCTGGAGCTGATCGTCGCCCACGACTTCTGG
TGCGTGGTGCATTGCGCCTGGCAATTGGAGGCGATCGAACGCGCCAGCCTGGCCCGCCCGCTGAACGTCTGG
CTGAAGATGGATTCGGGCATGCACCGCGTCGGCTTCTTCCCCGAGGACTTCCGCGCCGCCCACGAGCGCCTG
CGGGCCAGCGGCAAGGTGGCGAAGATCGTGATGATGAGTCACTTCTCCCGCGCCGACGAACTGGATTGCCCG
CGCACCGAGGAACAGCTCGCCGCCTTCGCGGCCGCGAGCCAGGGCCTGGAAGGCGAGATCAGCCTGCGCAAT
TCGCCAGCCGTGCTCGGCTGGCCGAAGGTGCCCAGCGATTGGGTACGTCCGGGCATCCTGCTCTACGGAGCC
ACGCCGTTCGAGCGCGCACATCCGCTGGCCGACCGCTTGCGCCCGGTGATGACCCTGGAATCGAAGGTGATC
AGCGTCCGCGACCTGCCGGCCGGCGAACCGGTTGGCTACGGCGCGCGCTACAGCACCGAGCGTAGCCAGCGC
ATCGGCGTGGTCGCCATGGGCTACGCCGATGGCTACCCGCGGCACGCCGCCGACGGCACCCTGGTGTTCATC
GACGGCAAGCCGGGGCGCCTGGTTGGCCGGGTATCGATGGACATGCTCACCGTCGACCTTACCGACCATCCC
CAGGCCGGGCTGGGCAGCCGGGTCGAACTATGGGGCCCGAACGTGCCGGTCGGCGCCCTGGCGGCGCAGTTC
GGCAGCATTCCCTACCAACTGCTGTGCAACCTGAAAAGGGTGCCGCGCGTCTATTCCGGGGCTTGA
Translation:
MRPARALIDLQALRHNYRLAREATGARALAVIKADAYGHGAVRCAEALAAEADGFAVACIEEGLELREAGIR
QPILLLEGFFEASELELIVAHDFWCVVHCAWQLEAIERASLARPLNVWLKMDSGMHRVGFFPEDFRAAHERL
RASGKVAKIVMMSHFSRADELDCPRTEEQLAAFAAASQGLEGEISLRNSPAVLGWPKVPSDWVRPGILLYGA
TPFERAHPLADRLRPVMTLESKVISVRDLPAGEPVGYGARYSTERSQRIGVVAMGYADGYPRHAADGTLVFI
DGKPGRLVGRVSMDMLTVDLTDHPQAGLGSRVELWGPNVPVGALAAQFGSIPYQLLCNLKRVPRVYSGA*
AnnotationID:1838GeneID:1829
AnnotatorUID: diggins
Modification Date/Time: 2005-04-26 15:03:39
Gene Name:dadX
Confidence Code:1
GeneProduct:catabolic alanine racemase
Cell Localization:()
Synonyms:alr
Cell Localization Confidence Code:5
MolecularFunction:
Functional Category:(2) Amino acid biosynthesis and metabolism
Alternate Gene Product Name:
Functional Category Confidence Code:5
COGs:COG0787,cd00430,pfam01168,pfam00842
Secondary Functional Category(ies):
EC Number:5.1.1.1
Status:ACTIVE
Pathway:






 
Homology:
>gb|AAO53657.1| (AE016856) alanine racemase, catabolic [Pseudomonas syringae pv.
           tomato str. DC3000]
          Length = 357

 Score =  524 bits (1350), Expect = e-148
 Identities = 258/355 (72%), Positives = 298/355 (83%)

>gb|AAN70834.1|AE016728_3 (AE016793) alanine racemase, catabolic [Pseudomonas putida KT2440]
          Length = 357

 Score =  519 bits (1337), Expect = e-147
 Identities = 255/356 (71%), Positives = 293/356 (82%)

>gb|AAM38530.1| (AE012019) alanine racemase [Xanthomonas axonopodis pv. citri str.
           306]
          Length = 366

 Score =  467 bits (1202), Expect = e-131
 Identities = 232/356 (65%), Positives = 272/356 (76%)






 
Structural Features:
COG0787, Alr, Alanine racemase [Cell envelope biogenesis, outer membrane]
CD-Length = 360 residues,  99.7% aligned
Score =  433 bits (1114), Expect = 2e-122
Identities = 190/362 (52%), Positives = 238/362 (65%), Gaps = 9/362 (2%)

cd00430, Ala_racemase, Alanine racemase. 
CD-Length = 339 residues,  99.7% aligned
Score =  331 bits (850), Expect = 8e-92
Identities = 155/339 (45%), Positives = 205/339 (60%), Gaps = 11/339 (3%)

pfam01168, Ala_racemase_N, Alanine racemase, N-terminal domain.
CD-Length = 227 residues, 100.0% aligned
Score =  212 bits (540), Expect = 6e-56
Identities = 109/228 (47%), Positives = 133/228 (58%), Gaps = 12/228 (5%)

pfam00842, Ala_racemase_C, Alanine racemase, C-terminal domain. 
CD-Length = 126 residues,  99.2% aligned
Score =  175 bits (445), Expect = 8e-45
Identities = 72/125 (57%), Positives = 90/125 (72%), Gaps = 2/125 (1%)







   
Genomic Context:






   
Comment:


















    ReferenceID:3661




  
Author/Investigator(s):
        GenNotator





  
Title:
        




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:BLASTP 







    
Data:


    		




 
URL:

















    ReferenceID:20808




  
Author/Investigator(s):
        GenNotator





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:RPSBLAST 







    
Data:


    		




 
URL:

















    ReferenceID:34797




  
Author/Investigator(s):
        





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:Misc (text/plain)







    
Data:1829_cdd.html


    		




 
URL:

















    ReferenceID:35709




  
Author/Investigator(s):
        Strych U, Huang HC, Krause KL, Benedik MJ.





  
Title:
        Characterization of the alanine racemases from Pseudomonas aeruginosa PAO1.




  
PubMed:
        10977898


MedLine:
        




    
Source:
Curr Microbiol. 2000 Oct;41(4):290-4.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10977898

















    ReferenceID:35710




  
Author/Investigator(s):
        Lobocka M, Hennig J, Wild J, Klopotowski T.





  
Title:
        Organization and expression of the Escherichia coli K-12 dad operon encoding the smaller subunit of D-amino acid dehydrogenase and the catabolic alanine racemase.




  
PubMed:
        7906689


MedLine:
        




    
Source:
J Bacteriol. 1994 Mar;176(5):1500-10.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=7906689









           
Homologs By Global Alignment 

           

       



     
Gene ID:1829
           
Identity:

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

                           

     
HomologID
                           Accession
                           Description
                           Length
                           PctIdentity
                           PctSimilarity
                           Gaps
                           Score
     

     
     
3210
                           PA5302_tr
                           translation of PA5302
                           357
                           99.71
                           99.71
                           0
                           1845.0
     

     
     
99605
                           gb|AAG08687.1|AE004943_3
                           (AE004943) catabolic alanine racemase [Pseudomonas aeruginosa PAO1]
                           357
                           99.71
                           99.71
                           0
                           1845.0
     

     
     
99606
                           gb|AAD47081.1|AF165881_1
                           (AF165881) catabolic alanine racemase DadX [Pseudomonas aeruginosa]
                           357
                           99.43
                           99.71
                           0
                           1843.0
     

     
     
99607
                           gb|AAO53657.1|
                           (AE016856) alanine racemase, catabolic [Pseudomonas syringae pv. tomato str. DC3000]
                           357
                           72.26
                           83.47
                           0
                           1346.0
     

     
     
99608
                           gb|AAN70834.1|AE016728_3
                           (AE016793) alanine racemase, catabolic [Pseudomonas putida KT2440]
                           357
                           71.42
                           82.07
                           0
                           1336.0
     

     






      

          
GC ORFID: 44831How Found: BLASTX

          
GC_TrimmedSeqID: 69Blast Result ID

          
Subject Sequence Name: t_PA5302Glimmer Score: 

          
Start: 5508697Stop: 5507624

          
Length: 1074


          
Start Codon: ATGTruncated Start:

          
Stop Codon: TGATruncated Stop: 

          
Homolog: t_PA5302 translation of PA5302Homolog Bit Score 715.0

          
Other Homologs:  psyr_15may02_Scaffold2_revised_gene3159 (ORF: BLASTX 520.0), t_PA4930 (ORF: BLASTX 308.0), t_PA5302 (ORF: GLIMMER)

          
GC ORF Sequence

           
ATGCGCCCCGCCCGTGCCCTGATCGACCTGCAAGCCCTTCGTCACAACTATCGGCTGGCCCGCGAGGCCACC 
GGCGCCCGTGCGCTCGCGGTGATTAAAGCGGACGCATACGGCCACGGCGCGGTGCGCTGTGCCGAAGCGCTG 
GCGGCCGAGGCCGATGGCTTCGCCGTGGCCTGCATCGAGGAGGGCCTGGAGCTGCGCGAGGCCGGTATCCGC 
CAGCCGATCCTGCTGCTGGAGGGCTTCTTCGAGGCGTCCGAGCTGGAGCTGATCGTCGCCCACGACTTCTGG 
TGCGTGGTGCATTGCGCCTGGCAATTGGAGGCGATCGAACGCGCCAGCCTGGCCCGCCCGCTGAACGTCTGG 
CTGAAGATGGATTCGGGCATGCACCGCGTCGGCTTCTTCCCCGAGGACTTCCGCGCCGCCCACGAGCGCCTG 
CGGGCCAGCGGCAAGGTGGCGAAGATCGTGATGATGAGTCACTTCTCCCGCGCCGACGAACTGGATTGCCCG 
CGCACCGAGGAACAGCTCGCCGCCTTCGCGGCCGCGAGCCAGGGCCTGGAAGGCGAGATCAGCCTGCGCAAT 
TCGCCAGCCGTGCTCGGCTGGCCGAAGGTGCCCAGCGATTGGGTACGTCCGGGCATCCTGCTCTACGGAGCC 
ACGCCGTTCGAGCGCGCACATCCGCTGGCCGACCGCTTGCGCCCGGTGATGACCCTGGAATCGAAGGTGATC 
AGCGTCCGCGACCTGCCGGCCGGCGAACCGGTTGGCTACGGCGCGCGCTACAGCACCGAGCGTAGCCAGCGC 
ATCGGCGTGGTCGCCATGGGCTACGCCGATGGCTACCCGCGGCACGCCGCCGACGGCACCCTGGTGTTCATC 
GACGGCAAGCCGGGGCGCCTGGTTGGCCGGGTATCGATGGACATGCTCACCGTCGACCTTACCGACCATCCC 
CAGGCCGGGCTGGGCAGCCGGGTCGAACTATGGGGCCCGAACGTGCCGGTCGGCGCCCTGGCGGCGCAGTTC 
GGCAGCATTCCCTACCAACTGCTGTGCAACCTGAAAAGGGTGCCGCGCGTCTATTCCGGGGCTTGA