ViewGene
Locus Name:
GeneID:
Location:

GeneID:2265
TrivialName: PA14_61210
AnnotatorUID:
Modification Date/Time:2006-04-06 13:01:23
LocusName:PA14_61210
PAO1 Ortholog Locus:PA4626
Sequence Length:972
Protein Length:323
Start: 5465175
Stop: 5466146
Strand: +
Type:
ChromosomeID:2
Status: ACTIVE
Frame Discrepancy: FALSE
Missense Discrepancy:FALSE
Comments:
Homology: gb|AAG08014.1|AE004877_1 (AE004877) glycerate dehydrogenase [Pseudomonas aeruginosa PAO1]
Identities = 319/323 (98%), Positives = 321/323 (99%)
Sequence:
ATGAGCCATGCCCTGCGCGCCGTTTTCCTCGACCATGCCTCCCTCGACCTCGGCGACCTGGACATGCGCCCC
CTGCGCGCCGCCTTCGACGAGCTGCAACTGCATGCCGCCAGCCAACCGCAGGAAGTCGCCGCGCGGCTGCAC
GGTGCGCGGGTCGCGATCAGCAACAAGGCGCCGATCGACGCGCAATGCATCGCCGCCTGCCCAGAGCTGGAA
CTGATCCTGGTCAGCGCTACCGGCACCAACAACATCGATCTCGCTGCCGCTCGCGAGCGCGGTATCGTCGTC
GCCAACTGCCATGGCTACGGCACGCCCTCGGTAGCCCAGCACACCCTCGCGTTGCTACTGGCCCTGGCTACG
CGCCTGCCGGACTACCAGCAGGCGGTACGCAGCGGCCGCTGGCAGCAATCCAGCCAGTTCTGCCTGCTGGAC
TTCCCCATCGTCGAACTGGAAGGCAAGACCCTCGGCCTGCTCGGCCATGGCGAACTGGGCGGGGCGGTGGCG
CGGCTGGCGGAGGCGTTCGGCATGCGCGTGCTGCTCGGTCAGTTGCCAGGACGGCCCGCCCGGGCGGACCGC
CTGCCGCTTGGCGAACTCCTGCCACGGGTCGACGCCCTGACCCTGCACTGCCCGCTGACCGAGGACACCCGC
GGGATGCTCGGCGCCGCCGAACTGGCGCTGATGAAGCCTGGCGCCTTCCTGGTCAATACCGCCCGTGGCGGC
CTGGTCGACGAACAGGCGCTGGCCGACGCCCTGCGCGGCGGCCACCTGGGCGGCGCCGCCACCGACGTGCTC
AGCGTCGAGCCGCCGAGAAACGGCAATCCGCTGCTGGCCCCCGACATCCCGCGCCTGATCGTCACCCCCCAT
AACGCCTGGGGCAGTCGCGAGGCGCGGCAGCGCATCGTCGGCCAACTGGCGGAAAACGCAGAGGCATGGAAG
GCCGGGCGCGCCCTGCGGGTAGTCAACGCCGGCTGA
Translation:
MSHALRAVFLDHASLDLGDLDMRPLRAAFDELQLHAASQPQEVAARLHGARVAISNKAPIDAQCIAACPELE
LILVSATGTNNIDLAAARERGIVVANCHGYGTPSVAQHTLALLLALATRLPDYQQAVRSGRWQQSSQFCLLD
FPIVELEGKTLGLLGHGELGGAVARLAEAFGMRVLLGQLPGRPARADRLPLGELLPRVDALTLHCPLTEDTR
GMLGAAELALMKPGAFLVNTARGGLVDEQALADALRGGHLGGAATDVLSVEPPRNGNPLLAPDIPRLIVTPH
NAWGSREARQRIVGQLAENAEAWKAGRALRVVNAG*
AnnotationID:2273GeneID:2265
AnnotatorUID: diggins
Modification Date/Time: 2005-05-06 13:01:19
Gene Name:hprA
Confidence Code:2
GeneProduct:glycerate dehydrogenase
Cell Localization:()
Synonyms:
Cell Localization Confidence Code:5
MolecularFunction:
Functional Category:(8) Central intermediary metabolism
Alternate Gene Product Name:
Functional Category Confidence Code:5
COGs:COG1052,COG0111
Secondary Functional Category(ies):
EC Number:1.1.1.29
Status:ACTIVE
Pathway:






 
Homology:
>gb|AAN66387.1|AE016266_9 (AE016776) glycerate dehydrogenase [Pseudomonas putida KT2440]
          Length = 321

 Score =  484 bits (1245), Expect = e-136
 Identities = 242/316 (76%), Positives = 275/316 (87%)

>emb|CAD84012.1| (BX321856) D-isomer specific 2-hydroxyacid dehydrogenase
           [Nitrosomonas europaea ATCC 19718]
          Length = 322

 Score =  278 bits (711), Expect = 3e-74
 Identities = 145/301 (48%), Positives = 191/301 (63%), Gaps = 1/301 (0%)






 
Structural Features:
COG1052, LdhA, Lactate dehydrogenase and related dehydrogenases
[Energy production and conversion / Coenzyme metabolism]
CD-Length = 324 residues,  99.4% aligned
Score =  278 bits (713), Expect = 1e-75
Identities = 132/326 (40%), Positives = 176/326 (53%), Gaps = 12/326 (3%)

COG0111, SerA, Phosphoglycerate dehydrogenase and related dehydrogenases 
[Amino acid transport and metabolism]
CD-Length = 324 residues,  90.7% aligned
Score =  239 bits (612), Expect = 6e-64
Identities = 124/302 (41%), Positives = 166/302 (54%), Gaps = 14/302 (4%)






   
Genomic Context:






   
Comment:


















    ReferenceID:4533




  
Author/Investigator(s):
        GenNotator





  
Title:
        




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:BLASTP 







    
Data:


    		




 
URL:

















    ReferenceID:21679




  
Author/Investigator(s):
        GenNotator





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:RPSBLAST 







    
Data:


    		




 
URL:

















    ReferenceID:31594




  
Author/Investigator(s):
        





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:Misc (text/plain)







    
Data:2265_cdd.html


    		




 
URL:

















    ReferenceID:33297




  
Author/Investigator(s):
        Koo JT, Choe J, Moseley SL.





  
Title:
        HrpA, a DEAH-box RNA helicase, is involved in mRNA processing of a fimbrial operon in Escherichia coli.




  
PubMed:
        15186427


MedLine:
        




    
Source:
Mol Microbiol. 2004 Jun;52(6):1813-26.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15186427

















    ReferenceID:33298




  
Author/Investigator(s):
        Hienonen E, Roine E, Romantschuk M, Taira S.





  
Title:
        mRNA stability and the secretion signal of HrpA, a pilin secreted by the type III system in Pseudomonas syringae.




  
PubMed:
        11862491


MedLine:
        




    
Source:
Mol Genet Genomics. 2002 Feb;266(6):973-8. Epub 2001 Dec 01.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11862491

















    ReferenceID:33299




  
Author/Investigator(s):
        Tabira Y, Ohara N, Yamada T.





  
Title:
        Identification and characterization of the ribosome-associated protein, HrpA, of Bacillus Calmette-Guerin.




  
PubMed:
        10993740


MedLine:
        




    
Source:
Microb Pathog. 2000 Oct;29(4):213-22.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10993740

















    ReferenceID:33300




  
Author/Investigator(s):
        Taira S, Tuimala J, Roine E, Nurmiaho-Lassila EL, Savilahti H, Romantschuk M.





  
Title:
        Mutational analysis of the Pseudomonas syringae pv. tomato hrpA gene encoding Hrp pilus subunit.




  
PubMed:
        10564513


MedLine:
        




    
Source:
Mol Microbiol. 1999 Nov;34(4):737-44.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10564513

















    ReferenceID:33301




  
Author/Investigator(s):
        Kim JF, Wei ZM, Beer SV.





  
Title:
        The hrpA and hrpC operons of Erwinia amylovora encode components of a type III pathway that secretes harpin.




  
PubMed:
        9045830


MedLine:
        




    
Source:
J Bacteriol. 1997 Mar;179(5):1690-7.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=9045830

















    ReferenceID:33302




  
Author/Investigator(s):
        Kim JF, Wei ZM, Beer SV.





  
Title:
        The hrpA and hrpC operons of Erwinia amylovora encode components of a type III pathway that secretes harpin.




  
PubMed:
        9045830


MedLine:
        




    
Source:
J Bacteriol. 1997 Mar;179(5):1690-7.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=9045830

















    ReferenceID:33303




  
Author/Investigator(s):
        Moriya H, Kasai H, Isono K.





  
Title:
        Cloning and characterization of the hrpA gene in the terC region of Escherichia coli that is highly similar to the DEAH family RNA helicase genes of Saccharomyces cerevisiae.




  
PubMed:
        7899078


MedLine:
        




    
Source:
Nucleic Acids Res. 1995 Feb 25;23(4):595-8.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=7899078









           
Homologs By Global Alignment 

           

       



     
Gene ID:2265
           
Identity:

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

                           

     
HomologID
                           Accession
                           Description
                           Length
                           PctIdentity
                           PctSimilarity
                           Gaps
                           Score
     

     
     
3853
                           PA4626_tr
                           translation of PA4626
                           323
                           98.76
                           99.38
                           0
                           1630.0
     

     
     
118258
                           gb|AAG08014.1|AE004877_1
                           (AE004877) glycerate dehydrogenase [Pseudomonas aeruginosa PAO1]
                           323
                           98.76
                           99.38
                           0
                           1630.0
     

     
     
118259
                           gb|AAN66387.1|AE016266_9
                           (AE016776) glycerate dehydrogenase [Pseudomonas putida KT2440]
                           323
                           75.23
                           85.44
                           2
                           1245.0
     

     
     
118260
                           gb|AAQ61451.1|
                           (AE016923) probable glycerate dehydrogenase [Chromobacterium violaceum ATCC 12472]
                           329
                           46.80
                           60.18
                           19
                           725.0
     

     
     
118263
                           emb|CAB83582.1|
                           (AL162752) putative glycerate dehydrogenase [Neisseria meningitidis Z2491]
                           331
                           44.41
                           57.70
                           17
                           669.0
     

     






      

          
GC ORFID: 45267How Found: BLASTX

          
GC_TrimmedSeqID: 69Blast Result ID

          
Subject Sequence Name: t_PA4626Glimmer Score: 

          
Start: 4728855Stop: 4729826

          
Length: 972


          
Start Codon: ATGTruncated Start:

          
Stop Codon: TGATruncated Stop: 

          
Homolog: t_PA4626 translation of PA4626Homolog Bit Score 632.0

          
Other Homologs:  t_PA4626 (ORF: GLIMMER)

          
GC ORF Sequence

           
ATGAGCCATGCCCTGCGCGCCGTTTTCCTCGACCATGCCTCCCTCGACCTCGGCGACCTGGACATGCGCCCC 
CTGCGCGCCGCCTTCGACGAGCTGCAACTGCATGCCGCCAGCCAACCGCAGGAAGTCGCCGCGCGGCTGCAC 
GGTGCGCGGGTCGCGATCAGCAACAAGGCGCCGATCGACGCGCAATGCATCGCCGCCTGCCCAGAGCTGGAA 
CTGATCCTGGTCAGCGCTACCGGCACCAACAACATCGATCTCGCTGCCGCTCGCGAGCGCGGTATCGTCGTC 
GCCAACTGCCATGGCTACGGCACGCCCTCGGTAGCCCAGCACACCCTCGCGTTGCTACTGGCCCTGGCTACG 
CGCCTGCCGGACTACCAGCAGGCGGTACGCAGCGGCCGCTGGCAGCAATCCAGCCAGTTCTGCCTGCTGGAC 
TTCCCCATCGTCGAACTGGAAGGCAAGACCCTCGGCCTGCTCGGCCATGGCGAACTGGGCGGGGCGGTGGCG 
CGGCTGGCGGAGGCGTTCGGCATGCGCGTGCTGCTCGGTCAGTTGCCAGGACGGCCCGCCCGGGCGGACCGC 
CTGCCGCTTGGCGAACTCCTGCCACGGGTCGACGCCCTGACCCTGCACTGCCCGCTGACCGAGGACACCCGC 
GGGATGCTCGGCGCCGCCGAACTGGCGCTGATGAAGCCTGGCGCCTTCCTGGTCAATACCGCCCGTGGCGGC 
CTGGTCGACGAACAGGCGCTGGCCGACGCCCTGCGCGGCGGCCACCTGGGCGGCGCCGCCACCGACGTGCTC 
AGCGTCGAGCCGCCGAGAAACGGCAATCCGCTGCTGGCCCCCGACATCCCGCGCCTGATCGTCACCCCCCAT 
AACGCCTGGGGCAGTCGCGAGGCGCGGCAGCGCATCGTCGGCCAACTGGCGGAAAACGCAGAGGCATGGAAG 
GCCGGGCGCGCCCTGCGGGTAGTCAACGCCGGCTGA