ViewGene
Locus Name:
GeneID:
Location:

GeneID:1203
TrivialName: PA14_58870
AnnotatorUID:
Modification Date/Time:2006-04-06 13:01:23
LocusName:PA14_58870
PAO1 Ortholog Locus:PA4538
Sequence Length:1308
Protein Length:435
Start: 5242281
Stop: 5243588
Strand: +
Type:
ChromosomeID:2
Status: ACTIVE
Frame Discrepancy: FALSE
Missense Discrepancy:FALSE
Comments:
Homology: gb|AAG07926.1|AE004867_12 (AE004867) NADH dehydrogenase [Pseudomonas aeruginosa PAO1]
Identities = 435/435 (100%), Positives = 435/435 (100%)
Sequence:
ATGTCCCATCGCATCGTGATCGTCGGCGGCGGCGCCGGCGGGCTGGAGCTCGCCACCCGTCTCGGCCGCACC
CTGGGTAAACGCGGCAAGGCCCAGGTCACCCTGGTCGACGCCAACCTCACCCACATCTGGAAACCCCTGCTG
CACGAAGTCGCTGCCGGCTCGCTCAACTCCTCCGAGGACGAGCTGAACTACGTCGCCCAGGCGAAATGGAAC
CACTTCGAATTCCAGCTCGGCCGCATGCAGGGCCTGGATCGCGCCGGCAAGCGGGTCCGCCTGGCCGCACTG
GTGGACGAGAATGGCGTTGAGCTGGTTCCCGAGCGCGACATCGCCTACGACACCCTGGTGATCGCCGTCGGC
AGCACCACCAACGACTTCGGCACCGAGGGCGCTGCGGAACACTGCATTTTCCTCGATACCCGCGCCCAGGCC
GAACGCTTCCACCGCCAGCTGCTCGGCCAGTACCTGCGTGCGCATACCGGGCACGACGCGAACAACAACGCA
GTGAGTATCGCCATCATCGGCGCCGGCGCCACCGGCGTCGAACTGGCTGCGGAACTGCACCACGCCGCGCAG
ATGCTGGCCGCCTACGGGCTCGACCGGATCCGCCCGGAAGACCTGCACATCAGCCTGGTCGAAGCCGGCCCA
CGGGTGCTGCCGGCGCTGCCCGAACGTATCAGCCAGCCGGTGCACCAGACCCTGAGCAAGCTCGGCGTACGG
GTGATGACCGGCTCGGCGGTGAGCAAGGTAGATGCGGACGGCCTCTGGACCGGCGACGGCGAGTTCGTCCCG
GCGACGCTCAAGGTCTGGGCGGCGGGCATCCGGGCTCCGGCCTTCCTCAAGGAACTCGACGGCCTGGAAAGC
AACCGTATCAACCAACTGGTGGTCCGCCCGACCCTGCAGACCACCCGCGACGATGACATCTTCGCCTTCGGC
GACTGCGCCGCCTGTCCCCAGCCGGCGCAACCGGGAGAGCAACCGCGCAACGTGCCGCCACGCGCCCAGGCC
GCGCACCAGCAGGCCTCGCTGCTGGTGAAATCGCTGCGTGCCCGTCTCGAAGGCAAGCCGCTGGGCGAATAT
CACTACCGCGACTACGGTTCGTTGATCTCGCTGTCGCGCTTCAGCGCAGTCGGCAATCTGATGGGCAATCTG
ATGGGTAGCGTCATGCTCGAAGGCTGGCTAGCGCGGATGTTCTACGTATCGCTATACCGCATGCACCAGATG
GCGTTGTACGGTCCGCTGCGCACCGCGATGCTGATGCTCAGCGGCCGCCTGCGCAGCACCGAGCCACGCCTC
AAGCTGCACTGA
Translation:
MSHRIVIVGGGAGGLELATRLGRTLGKRGKAQVTLVDANLTHIWKPLLHEVAAGSLNSSEDELNYVAQAKWN
HFEFQLGRMQGLDRAGKRVRLAALVDENGVELVPERDIAYDTLVIAVGSTTNDFGTEGAAEHCIFLDTRAQA
ERFHRQLLGQYLRAHTGHDANNNAVSIAIIGAGATGVELAAELHHAAQMLAAYGLDRIRPEDLHISLVEAGP
RVLPALPERISQPVHQTLSKLGVRVMTGSAVSKVDADGLWTGDGEFVPATLKVWAAGIRAPAFLKELDGLES
NRINQLVVRPTLQTTRDDDIFAFGDCAACPQPAQPGEQPRNVPPRAQAAHQQASLLVKSLRARLEGKPLGEY
HYRDYGSLISLSRFSAVGNLMGNLMGSVMLEGWLARMFYVSLYRMHQMALYGPLRTAMLMLSGRLRSTEPRL
KLH*
AnnotationID:1212GeneID:1203
AnnotatorUID: diggins
Modification Date/Time: 2005-05-04 17:05:34
Gene Name:ndh
Confidence Code:2
GeneProduct: NADH dehydrogenase
Cell Localization:()
Synonyms:
Cell Localization Confidence Code:5
MolecularFunction:
Functional Category:(12) Energy metabolism
Alternate Gene Product Name:
Functional Category Confidence Code:5
COGs:COG1252,KOG2495,pfam00070
Secondary Functional Category(ies):
EC Number:1.6.99.3
Status:ACTIVE
Pathway:






 
Homology:
>gb|AAF97237.1|AF281147_2 (AF281147) NADH dehydrogenase II [Pseudomonas fluorescens]
          Length = 432

 Score =  677 bits (1748), Expect = 0.0
 Identities = 343/436 (78%), Positives = 377/436 (86%), Gaps = 5/436 (1%)

>gb|AAK19737.1|AF346487_2 (AF346487) uncoupled NADH:quinone oxidoreductase [Azotobacter
           vinelandii]
          Length = 432

 Score =  584 bits (1505), Expect = e-166
 Identities = 302/437 (69%), Positives = 354/437 (81%), Gaps = 7/437 (1%)







 
Structural Features:
COG1252, Ndh, NADH dehydrogenase, FAD-containing subunit 
[Energy production and conversion]
CD-Length = 405 residues,  99.8% aligned
Score =  403 bits (1038), Expect = 4e-113
Identities = 177/428 (41%), Positives = 234/428 (54%), Gaps = 27/428 (6%)

KOG2495, NADH-dehydrogenase (ubiquinone) [Energy production and conversion]
CD-Length = 491 residues,  82.5% aligned
Score =  165 bits (418), Expect = 3e-41
Identities = 107/432 (24%), Positives = 180/432 (41%), Gaps = 59/432 (13%)

pfam00070, Pyr_redox, Pyridine nucleotide-disulphide oxidoreductase.
CD-Length = 288 residues,  98.6% aligned
Score =  133 bits (337), Expect = 6e-32
Identities = 90/329 (27%), Positives = 128/329 (38%), Gaps = 57/329 (17%)







   
Genomic Context:






   
Comment:


















    ReferenceID:2409




  
Author/Investigator(s):
        GenNotator





  
Title:
        




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:BLASTP 







    
Data:


    		




 
URL:

















    ReferenceID:19552




  
Author/Investigator(s):
        GenNotator





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:RPSBLAST 







    
Data:


    		




 
URL:

















    ReferenceID:31579




  
Author/Investigator(s):
        





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:Misc (text/plain)







    
Data:1203_cdd.html


    		




 
URL:

















    ReferenceID:32989




  
Author/Investigator(s):
        Jackson L, Blake T, Green J.





  
Title:
        Regulation of ndh expression in Escherichia coli by Fis.




  
PubMed:
        14766919


MedLine:
        




    
Source:
Microbiology. 2004 Feb;150(Pt 2):407-13.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14766919

















    ReferenceID:32990




  
Author/Investigator(s):
        Yano T, Ohnishi T.





  
Title:
        The origin of cluster N2 of the energy-transducing NADH-quinone oxidoreductase: comparisons of phylogenetically related enzymes.




  
PubMed:
        11695831


MedLine:
        




    
Source:
J Bioenerg Biomembr. 2001 Jun;33(3):213-22






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11695831

















    ReferenceID:32991




  
Author/Investigator(s):
        Green J, Anjum MF, Guest JR.





  
Title:
        The ndh-binding protein (Nbp) regulates the ndh gene of Escherichia coli in response to growth phase and is identical to Fis.




  
PubMed:
        8809757


MedLine:
        




    
Source:
Mol Microbiol. 1996 Jun;20(5):1043-55.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=8809757

















    ReferenceID:32992




  
Author/Investigator(s):
        Green J, Guest JR.





  
Title:
        Regulation of transcription at the ndh promoter of Escherichia coli by FNR and novel factors.




  
PubMed:
        8065261


MedLine:
        




    
Source:
Mol Microbiol. 1994 May;12(3):433-44.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=8065261

















    ReferenceID:32993




  
Author/Investigator(s):
        Poulis MI, Shaw DC, Campbell HD, Young IG.





  
Title:
        In vitro synthesis of the respiratory NADH dehydrogenase of Escherichia coli. Role of UUG as initiation codon.




  
PubMed:
        7025892


MedLine:
        




    
Source:
Biochemistry. 1981 Jul 7;20(14):4178-85.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=7025892

















    ReferenceID:32994




  
Author/Investigator(s):
        Jaworowski A, Campbell HD, Poulis MI, Young IG.





  
Title:
        Genetic identification and purification of the respiratory NADH dehydrogenase of Escherichia coli.




  
PubMed:
        6784762


MedLine:
        




    
Source:
Biochemistry. 1981 Mar 31;20(7):2041-7.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=6784762

















    ReferenceID:32995




  
Author/Investigator(s):
        Young IG, Jaworowski A, Poulis MI.





  
Title:
        Amplification of the respiratory NADH dehydrogenase of Escherichia coli by gene cloning.




  
PubMed:
        365690


MedLine:
        




    
Source:
Gene. 1978 Sep;4(1):25-36.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=365690









           
Homologs By Global Alignment 

           

       



     
Gene ID:1203
           
Identity:

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

                           

     
HomologID
                           Accession
                           Description
                           Length
                           PctIdentity
                           PctSimilarity
                           Gaps
                           Score
     

     
     
2181
                           PA4538_tr
                           translation of PA4538
                           435
                           99.99
                           99.99
                           0
                           2234.0
     

     
     
72605
                           gb|AAG07926.1|AE004867_12
                           (AE004867) NADH dehydrogenase [Pseudomonas aeruginosa PAO1]
                           435
                           99.99
                           99.99
                           0
                           2234.0
     

     
     
72607
                           gb|AAF97237.1|AF281147_2
                           (AF281147) NADH dehydrogenase II [Pseudomonas fluorescens]
                           436
                           78.66
                           86.46
                           5
                           1753.0
     

     
     
72606
                           gb|AAN66251.1|AE016253_6
                           (AE016776) NADH dehydrogenase [Pseudomonas putida KT2440]
                           436
                           77.75
                           87.61
                           6
                           1757.0
     

     
     
72608
                           gb|AAO54451.1|
                           (AE016859) NADH dehydrogenase [Pseudomonas syringae pv. tomato str. DC3000]
                           436
                           76.60
                           85.77
                           5
                           1717.0
     

     






      

          
GC ORFID: 44205How Found: BLASTX

          
GC_TrimmedSeqID: 69Blast Result ID

          
Subject Sequence Name: t_PA4538Glimmer Score: 

          
Start: 4505960Stop: 4507267

          
Length: 1308


          
Start Codon: ATGTruncated Start:

          
Stop Codon: TGATruncated Stop: 

          
Homolog: t_PA4538 translation of PA4538Homolog Bit Score 865.0

          
Other Homologs:  psyr_15may02_Scaffold15_revised_gene2542 (ORF: BLASTX 664.0), t_PA4538 (ORF: GLIMMER)

          
GC ORF Sequence

           
ATGTCCCATCGCATCGTGATCGTCGGCGGCGGCGCCGGCGGGCTGGAGCTCGCCACCCGTCTCGGCCGCACC 
CTGGGTAAACGCGGCAAGGCCCAGGTCACCCTGGTCGACGCCAACCTCACCCACATCTGGAAACCCCTGCTG 
CACGAAGTCGCTGCCGGCTCGCTCAACTCCTCCGAGGACGAGCTGAACTACGTCGCCCAGGCGAAATGGAAC 
CACTTCGAATTCCAGCTCGGCCGCATGCAGGGCCTGGATCGCGCCGGCAAGCGGGTCCGCCTGGCCGCACTG 
GTGGACGAGAATGGCGTTGAGCTGGTTCCCGAGCGCGACATCGCCTACGACACCCTGGTGATCGCCGTCGGC 
AGCACCACCAACGACTTCGGCACCGAGGGCGCTGCGGAACACTGCATTTTCCTCGATACCCGCGCCCAGGCC 
GAACGCTTCCACCGCCAGCTGCTCGGCCAGTACCTGCGTGCGCATACCGGGCACGACGCGAACAACAACGCA 
GTGAGTATCGCCATCATCGGCGCCGGCGCCACCGGCGTCGAACTGGCTGCGGAACTGCACCACGCCGCGCAG 
ATGCTGGCCGCCTACGGGCTCGACCGGATCCGCCCGGAAGACCTGCACATCAGCCTGGTCGAAGCCGGCCCA 
CGGGTGCTGCCGGCGCTGCCCGAACGTATCAGCCAGCCGGTGCACCAGACCCTGAGCAAGCTCGGCGTACGG 
GTGATGACCGGCTCGGCGGTGAGCAAGGTAGATGCGGACGGCCTCTGGACCGGCGACGGCGAGTTCGTCCCG 
GCGACGCTCAAGGTCTGGGCGGCGGGCATCCGGGCTCCGGCCTTCCTCAAGGAACTCGACGGCCTGGAAAGC 
AACCGTATCAACCAACTGGTGGTCCGCCCGACCCTGCAGACCACCCGCGACGATGACATCTTCGCCTTCGGC 
GACTGCGCCGCCTGTCCCCAGCCGGCGCAACCGGGAGAGCAACCGCGCAACGTGCCGCCACGCGCCCAGGCC 
GCGCACCAGCAGGCCTCGCTGCTGGTGAAATCGCTGCGTGCCCGTCTCGAAGGCAAGCCGCTGGGCGAATAT 
CACTACCGCGACTACGGTTCGTTGATCTCGCTGTCGCGCTTCAGCGCAGTCGGCAATCTGATGGGCAATCTG 
ATGGGTAGCGTCATGCTCGAAGGCTGGCTAGCGCGGATGTTCTACGTATCGCTATACCGCATGCACCAGATG 
GCGTTGTACGGTCCGCTGCGCACCGCGATGCTGATGCTCAGCGGCCGCCTGCGCAGCACCGAGCCACGCCTC 
AAGCTGCACTGA