ViewGene
Locus Name:
GeneID:
Location:

GeneID:716
TrivialName: PA14_29620
AnnotatorUID:
Modification Date/Time:2006-04-06 13:01:23
LocusName:PA14_29620
PAO1 Ortholog Locus:PA2665
Sequence Length:1554
Protein Length:517
Start: 2567978
Stop: 2566425
Strand: -
Type:
ChromosomeID:2
Status: ACTIVE
Frame Discrepancy: FALSE
Missense Discrepancy:FALSE
Comments:
Homology: gb|AAG06053.1|AE004695_6 (AE004695) probable transcriptional regulator [Pseudomonas aeruginosa PAO1]
Identities = 516/517 (99%), Positives = 516/517 (99%)
Sequence:
ATGACCACCAATCCCTTGCTTGCCACCCTGATCCCGCTGGTTGCCGACCTGTCCCGCGACCTGCCGGAAGAC
GAACGCTACCGCCGCCTGCTCCAGGCCCTGCGCGACCTGCTGCCCTGCGACGCCACCGCGCTGCTGCGCCTG
GACGGCGAATACCTGATCCCGCTGGCGGTGGACGGCCTCAGCCCGGACACCCTCGGCCGGCGCTTCCGGGTC
GGCGAACATCCGCGCCTCGAGGCTCTCCTGGAGCGCCGCGGGCCGACCCGCTTCCCCGCCGACTGCGGCCTG
CCCGATCCCTACGACGGTCTGGTGGAAGGCCTCCACGGCCACCTGGAAATCCATGATTGCCTGGGCTGTCCG
CTGTACCTCGACGACCAGCCCTGGGGCTTGCTGACCCTGGATACCCTCGATCCGTCGCGCTTCGCCAGCGCC
GACCTGGATACCCTGGAGGCCTTCGCCAGCCTCGCCGCCGCCACGGTCAAGGCCAGCGAGCGGATGCGCGAC
CTGACCCGCCGCGCCGAGGACGAGCACCAGCGCGCCGAGGCCTATCTCGAAGCCGCTGGCGAGCGGCCACGG
GAAATGATCGGCCAGAGCGCCGCGCACAAGGCGCTGCTGGAAGAAATCCGCCTGGTCGCCAACAGCGACCTG
AGCGTACTGATCACCGGCGAGACCGGGGTCGGCAAGGAACTGGTGGCGCAATCCATCCACCGGCATTCCATG
CGCAGCGGCAAGCCGATGATCAGTCTCAACTGCGCCGCGCTGCCCGAGACCCTGGTGGAAAGCGAATTGTTC
GGCCATGTGCGCGGCGCCTTCTCCGGCGCGGTCAACGAACGGCGCGGCAAGTTCGAACTGGCCGACGGCGGC
AGCCTGTTCCTCGACGAGGTCGGCGAGTTGCCGCTGGCGGTGCAGGCCAAGCTGCTCCGCGTGCTGCAGAGC
GGGCAGTTGCAGCGGGTCGGCTCCGATCGCGAGCACCGCGTCGACGTACGCCTGATCGCAGCCACCAACCGC
GACCTGGCCGAGGAAGTACGTGCCGGGCGCTTCCGCGCCGATCTCTACCATCGCCTCAGCGTCTATCCCTTG
CGCGTGCCGCCGCTGCGCGAGCGCGGCCGCGATATCCTCCTGCTGGCCGGCTACTTCCTCGAGGAAAACCGA
CCGCGCCTGGGACTGCGCAGCCTGCGCCTGGACCACGAGGCCCAGGCCGCGCTCCTCGACTATCGCTGGCCG
GGCAACGTGCGCGAACTCGAGCACCTGGTCGGCCGCGCCTCGCTCAAGGCCCTCGGCCACAATCCGGAGCGG
TCGCGGATCGTCACCCTGCATCGGCAGGATCTCGACCTGCCCGCGGAAACCCCCGCGCCACCTCGCAGCGTG
GTCGAGCCCGCGCCCGCCGCGCCAACGACCGGTCACTCGTTGCGCGCGGCCACCGACGCCTACCAACGCCAC
CTGATCCAGGACTGCCTGGCCCGTCACCAGGGAAGCTGGGCCTCGGCTGCACGCGAGCTGGGCCTGGATCGC
GCCAACCTGGCGCGCCTGGCGCGCCGCCTGCAACTCAGGTGA
Translation:
MTTNPLLATLIPLVADLSRDLPEDERYRRLLQALRDLLPCDATALLRLDGEYLIPLAVDGLSPDTLGRRFRV
GEHPRLEALLERRGPTRFPADCGLPDPYDGLVEGLHGHLEIHDCLGCPLYLDDQPWGLLTLDTLDPSRFASA
DLDTLEAFASLAAATVKASERMRDLTRRAEDEHQRAEAYLEAAGERPREMIGQSAAHKALLEEIRLVANSDL
SVLITGETGVGKELVAQSIHRHSMRSGKPMISLNCAALPETLVESELFGHVRGAFSGAVNERRGKFELADGG
SLFLDEVGELPLAVQAKLLRVLQSGQLQRVGSDREHRVDVRLIAATNRDLAEEVRAGRFRADLYHRLSVYPL
RVPPLRERGRDILLLAGYFLEENRPRLGLRSLRLDHEAQAALLDYRWPGNVRELEHLVGRASLKALGHNPER
SRIVTLHRQDLDLPAETPAPPRSVVEPAPAAPTTGHSLRAATDAYQRHLIQDCLARHQGSWASAARELGLDR
ANLARLARRLQLR*
AnnotationID:725GeneID:716
AnnotatorUID: diggins
Modification Date/Time: 2005-03-07 17:05:52
Gene Name:
Confidence Code:3
GeneProduct:putative transcriptional regulator
Cell Localization:()
Synonyms:norR
Cell Localization Confidence Code:5
MolecularFunction:
Functional Category:(25) Transcriptional regulators
Alternate Gene Product Name:putative sigma-54 dependent transcriptional regulator
Functional Category Confidence Code:5
COGs:COG3604,pfam00158,COG1221
Secondary Functional Category(ies):
EC Number:
Status:ACTIVE
Pathway:






 
Homology:
>gb|AAN66432.1|AE016273_1 (AE016777) sigma-54 dependent transcriptional regulator
           [Pseudomonas putida KT2440]
          Length = 518

 Score =  743 bits (1919), Expect = 0.0
 Identities = 378/519 (72%), Positives = 429/519 (82%), Gaps = 3/519 (0%)

>gb|AAP85995.1| (AY305378) sigma 54 dependent transcriptional activator [Ralstonia
           eutropha]
          Length = 514

 Score =  507 bits (1305), Expect = e-143
 Identities = 284/510 (55%), Positives = 345/510 (67%), Gaps = 14/510 (2%)

>emb|CAD18110.1| (AL646082) PROBABLE SIGMA-54 INTERACTING TRANSCRIPTION REGULATOR
           PROTEIN [Ralstonia solanacearum]
          Length = 510

 Score =  504 bits (1298), Expect = e-142
 Identities = 286/511 (55%), Positives = 342/511 (66%), Gaps = 12/511 (2%)






 
Structural Features:
COG3604, FhlA, Transcriptional regulator containing GAF, AAA-type ATPase, 
and DNA binding domains 
[Transcription / Signal transduction mechanisms]
CD-Length = 550 residues,  94.2% aligned
Score =  595 bits (1535), Expect = 5e-171
Identities = 268/521 (51%), Positives = 329/521 (63%), Gaps = 13/521 (2%)

pfam00158, Sigma54_activat, Sigma-54 interaction domain.
CD-Length = 222 residues, 100.0% aligned
Score =  302 bits (776), Expect = 5e-83
Identities = 132/222 (59%), Positives = 171/222 (77%)

COG1221, PspF, Transcriptional regulators containing an AAA-type ATPase 
domain and a DNA-binding domain 
[Transcription / Signal transduction mechanisms]
CD-Length = 403 residues,  86.6% aligned
Score =  264 bits (676), Expect = 2e-71
Identities = 150/358 (41%), Positives = 197/358 (55%), Gaps = 11/358 (3%)






   
Genomic Context:






   
Comment:
other possible gene name: ygaA


















    ReferenceID:1435




  
Author/Investigator(s):
        GenNotator





  
Title:
        




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:BLASTP 







    
Data:


    		




 
URL:

















    ReferenceID:18577




  
Author/Investigator(s):
        GenNotator





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:RPSBLAST 







    
Data:


    		




 
URL:

















    ReferenceID:36358




  
Author/Investigator(s):
        





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:Misc (text/plain)







    
Data:716_cdd.html


    		




 
URL:









           
Homologs By Global Alignment 

           

       



     
Gene ID:716
           
Identity:

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

                           

     
HomologID
                           Accession
                           Description
                           Length
                           PctIdentity
                           PctSimilarity
                           Gaps
                           Score
     

     
     
1228
                           PA2665_tr
                           translation of PA2665
                           517
                           99.80
                           99.80
                           0
                           2634.0
     

     
     
46780
                           gb|AAG06053.1|AE004695_6
                           (AE004695) probable transcriptional regulator [Pseudomonas aeruginosa PAO1]
                           517
                           99.80
                           99.80
                           0
                           2634.0
     

     
     
46781
                           gb|AAN66432.1|AE016273_1
                           (AE016777) sigma-54 dependent transcriptional regulator [Pseudomonas putida KT2440]
                           525
                           72.76
                           82.66
                           15
                           1931.0
     

     
     
46782
                           dbj|BAC16772.1|
                           (AB035325) NtrC/NifA family homolog regulator [Burkholderia sp. TH2]
                           533
                           67.35
                           78.23
                           17
                           1810.0
     

     
     
46784
                           emb|CAD18110.1|
                           (AL646082) PROBABLE SIGMA-54 INTERACTING TRANSCRIPTION REGULATOR PROTEIN [Ralstonia solanacearum]
                           533
                           54.22
                           64.91
                           39
                           1310.0
     

     






      

          
GC ORFID: 43718How Found: BLASTX

          
GC_TrimmedSeqID: 69Blast Result ID

          
Subject Sequence Name: t_PA2665Glimmer Score: 

          
Start: 2385948Stop: 2387501

          
Length: 1554


          
Start Codon: ATGTruncated Start:

          
Stop Codon: TGATruncated Stop: 

          
Homolog: t_PA2665 translation of PA2665Homolog Bit Score 1019.0

          
Other Homologs:  t_PA4726 (ORF: BLASTX 249.0), t_PA1099 (ORF: BLASTX 248.0), psyr_15may02_Scaffold15_revised_gene2516 (ORF: BLASTX 248.0), t_PA1945 (ORF: BLASTX 239.0), t_PA1663 (ORF: BLASTX 236.0), psyr_15may02_Scaffold8_revised_gene7916 (ORF: BLASTX 235.0), t_PA5166 (ORF: BLASTX 233.0), t_PA2359 (ORF: BLASTX 231.0), t_PA4547 (ORF: BLASTX 227.0), psyr_15may02_Scaffold1_revised_gene1290 (ORF: BLASTX 226.0), psyr_15may02_Scaffold14_revised_gene2286 (ORF: BLASTX 224.0), t_PA1196 (ORF: BLASTX 218.0), t_PA2665 (ORF: GLIMMER)

          
GC ORF Sequence

           
ATGACCACCAATCCCTTGCTTGCCACCCTGATCCCGCTGGTTGCCGACCTGTCCCGCGACCTGCCGGAAGAC 
GAACGCTACCGCCGCCTGCTCCAGGCCCTGCGCGACCTGCTGCCCTGCGACGCCACCGCGCTGCTGCGCCTG 
GACGGCGAATACCTGATCCCGCTGGCGGTGGACGGCCTCAGCCCGGACACCCTCGGCCGGCGCTTCCGGGTC 
GGCGAACATCCGCGCCTCGAGGCTCTCCTGGAGCGCCGCGGGCCGACCCGCTTCCCCGCCGACTGCGGCCTG 
CCCGATCCCTACGACGGTCTGGTGGAAGGCCTCCACGGCCACCTGGAAATCCATGATTGCCTGGGCTGTCCG 
CTGTACCTCGACGACCAGCCCTGGGGCTTGCTGACCCTGGATACCCTCGATCCGTCGCGCTTCGCCAGCGCC 
GACCTGGATACCCTGGAGGCCTTCGCCAGCCTCGCCGCCGCCACGGTCAAGGCCAGCGAGCGGATGCGCGAC 
CTGACCCGCCGCGCCGAGGACGAGCACCAGCGCGCCGAGGCCTATCTCGAAGCCGCTGGCGAGCGGCCACGG 
GAAATGATCGGCCAGAGCGCCGCGCACAAGGCGCTGCTGGAAGAAATCCGCCTGGTCGCCAACAGCGACCTG 
AGCGTACTGATCACCGGCGAGACCGGGGTCGGCAAGGAACTGGTGGCGCAATCCATCCACCGGCATTCCATG 
CGCAGCGGCAAGCCGATGATCAGTCTCAACTGCGCCGCGCTGCCCGAGACCCTGGTGGAAAGCGAATTGTTC 
GGCCATGTGCGCGGCGCCTTCTCCGGCGCGGTCAACGAACGGCGCGGCAAGTTCGAACTGGCCGACGGCGGC 
AGCCTGTTCCTCGACGAGGTCGGCGAGTTGCCGCTGGCGGTGCAGGCCAAGCTGCTCCGCGTGCTGCAGAGC 
GGGCAGTTGCAGCGGGTCGGCTCCGATCGCGAGCACCGCGTCGACGTACGCCTGATCGCAGCCACCAACCGC 
GACCTGGCCGAGGAAGTACGTGCCGGGCGCTTCCGCGCCGATCTCTACCATCGCCTCAGCGTCTATCCCTTG 
CGCGTGCCGCCGCTGCGCGAGCGCGGCCGCGATATCCTCCTGCTGGCCGGCTACTTCCTCGAGGAAAACCGA 
CCGCGCCTGGGACTGCGCAGCCTGCGCCTGGACCACGAGGCCCAGGCCGCGCTCCTCGACTATCGCTGGCCG 
GGCAACGTGCGCGAACTCGAGCACCTGGTCGGCCGCGCCTCGCTCAAGGCCCTCGGCCACAATCCGGAGCGG 
TCGCGGATCGTCACCCTGCATCGGCAGGATCTCGACCTGCCCGCGGAAACCCCCGCGCCACCTCGCAGCGTG 
GTCGAGCCCGCGCCCGCCGCGCCAACGACCGGTCACTCGTTGCGCGCGGCCACCGACGCCTACCAACGCCAC 
CTGATCCAGGACTGCCTGGCCCGTCACCAGGGAAGCTGGGCCTCGGCTGCACGCGAGCTGGGCCTGGATCGC 
GCCAACCTGGCGCGCCTGGCGCGCCGCCTGCAACTCAGGTGA