ViewGene
Locus Name:
GeneID:
Location:

GeneID:679
TrivialName: PA14_60600
AnnotatorUID:
Modification Date/Time:2006-04-06 13:01:23
LocusName:PA14_60600
PAO1 Ortholog Locus:PA4581
Sequence Length:1596
Protein Length:531
Start: 5403235
Stop: 5401640
Strand: -
Type:
ChromosomeID:2
Status: ACTIVE
Frame Discrepancy: FALSE
Missense Discrepancy:FALSE
Comments:
Homology: gb|AAG07969.1|AE004871_9 (AE004871) transcriptional regulator RtcR [Pseudomonas aeruginosa PAO1]
Identities = 529/531 (99%), Positives = 530/531 (99%)
Sequence:
ATGAAACGCACGGTCGCCATCGGCTTCATCGGCGCCACCCTCGACCGTCTCGGCAAGGGCGCGGCGCGCTGG
CAAAAGTGGCGGCCGAGCATCGGCCTGTGCCAGCAGCCGGACCTGCTGATCGACCGCCTCGAACTGATCCAC
GGCAACGACGCCCGCGACCTCGGCCTGGCCGAGCGGATTCGCGCCGACATCGCCGCGGTGTCGCCGCATACC
GAGGTCCGCCTGCAGCAGATGGAACTGCGCAACCCCTGGGACTTCGAGGAGGTCTATGGCGCCCTGCACGAT
TTCGTCAGCGCCTACCCCTTCGACACCGAGCGCGAGGACTACCTGGTGCATATCACCACCGGGACCCATGTC
GCGCAGATCTGCTGGTTCCTCCTTACCGAGGCGCGCTACCTGCCGGCCCGGCTGGTGCAGACCTCGCCGTCG
CGGCGCAAGGACGAGGCGCGCCATCCCGAGGGCTCGGCGACGCTGATCGACCTCGACCTGTCCCGCTACGAC
CGCATCGCCTCGCGGTTCCGCCGCGAACAGGAGGAAAGCCTGGCTTTTCTCAAGTCGGGAATCGCCACGCGC
AATGCCGCTTTCAACCGCTCCATCGAGCAGATCGAGCGGGTCGCCGTGCGTTCGCGGGCACCCATGCTGCTG
GTGGGGCCGACCGGTGCCGGCAAATCGTTCCTCGCCCGGCGCATCTATGAACTCAAGCGCAGCCGGCACCAG
CTCGACGGGCGTTTCGTCGAGGTCAACTGCGCCACCTTGCGCGGCGACGGCGCGATGTCGGCACTGTTCGGC
CACGTCAAGGGCGCCTTCACCGGCGCGCAGAATGCGCGCGAAGGCCTGCTGCGCGCAGCCGACGGTGGCATG
CTGTTCCTCGACGAGATCGGCGAGCTGGGTGCCGACGAACAGGCGATGCTGCTCAAGGCGATCGAAGAGAAG
CGCTTCTTCCCGCTGGGTTCGGACCGTGAGGTGGAGAGCGACTTCCAGCTTATCGCCGGGACCCACCGCGAC
TTGCGCGGACGAGTGGCCGAAGGCCTGTTCCGCGAGGACCTGTTCGCCCGCATCAACCTGTGGACCTTCGAG
CTGCCGGGCCTGGCTGGACGCCGCGAGGACATCGAGCCGAACATCGACTTCGAACTGGAGCGGCACGCCCGC
GAGCAAGGGCGGCAGGTGCGTTTCAACCTGGAGGCCAAGCGTCGCTACCTGGCCTTCGCCGGTTCCAGCGAA
GCGCGCTGGGCCGGCAACTTCCGCGAGCTGTCGGCTTCCATCACACGGATGGCGACCCTGGCCGACAGCGGG
CGGATCGACGAGGCGCTGGTCGAGGAGGAGATCCTTCGCCTGCGCCAGGCCTGGGGGCTCGATGCGGGCCGG
GAGCCACTGGCTGATCTGCTGGGGCAGCGGGTGGAGGCCCTGGATCTGTTCGACCGCCTGCAACTGCAGTCG
GTGCTGGAGGTGTGCCGCGGGGCTAAGACCCTTTCCGAGGCGGGACGCCGGCTGTTCGCCGTTTCGCGCCAG
GACAAGCGCAACCCCAACGACGCCGACCGGCTGCGCAAGTACCTGGCGCGTTTCGGCCTGGACTGGGCGCAG
ATACGCGCCTGA
Translation:
MKRTVAIGFIGATLDRLGKGAARWQKWRPSIGLCQQPDLLIDRLELIHGNDARDLGLAERIRADIAAVSPHT
EVRLQQMELRNPWDFEEVYGALHDFVSAYPFDTEREDYLVHITTGTHVAQICWFLLTEARYLPARLVQTSPS
RRKDEARHPEGSATLIDLDLSRYDRIASRFRREQEESLAFLKSGIATRNAAFNRSIEQIERVAVRSRAPMLL
VGPTGAGKSFLARRIYELKRSRHQLDGRFVEVNCATLRGDGAMSALFGHVKGAFTGAQNAREGLLRAADGGM
LFLDEIGELGADEQAMLLKAIEEKRFFPLGSDREVESDFQLIAGTHRDLRGRVAEGLFREDLFARINLWTFE
LPGLAGRREDIEPNIDFELERHAREQGRQVRFNLEAKRRYLAFAGSSEARWAGNFRELSASITRMATLADSG
RIDEALVEEEILRLRQAWGLDAGREPLADLLGQRVEALDLFDRLQLQSVLEVCRGAKTLSEAGRRLFAVSRQ
DKRNPNDADRLRKYLARFGLDWAQIRA*
AnnotationID:688GeneID:679
AnnotatorUID: diggins
Modification Date/Time: 2005-05-05 10:10:28
Gene Name:rtcR
Confidence Code:2
GeneProduct:transcriptional regulatory protein RtcR
Cell Localization:()
Synonyms:
Cell Localization Confidence Code:5
MolecularFunction:
Functional Category:(25) Transcriptional regulators
Alternate Gene Product Name:
Functional Category Confidence Code:5
COGs:COG4650,pfam06956,pfam00158
Secondary Functional Category(ies):
EC Number:
Status:ACTIVE
Pathway:






 
Homology:
>emb|CAD13750.1| (AL646058) PROBABLE SIGMA-54 INTERACTING TRANSCRIPTION REGULATOR
           PROTEIN [Ralstonia solanacearum]
          Length = 535

 Score =  762 bits (1967), Expect = 0.0
 Identities = 389/533 (72%), Positives = 440/533 (82%), Gaps = 6/533 (1%)

>dbj|BAB37688.1| (AP002565) putative 2-component regulator [Escherichia coli
           O157:H7]
          Length = 532

 Score =  712 bits (1837), Expect = 0.0
 Identities = 360/530 (67%), Positives = 424/530 (80%), Gaps = 4/530 (0%)






 
Structural Features:
COG4650, RtcR, Sigma54-dependent transcription regulator containing 
an AAA-type ATPase domain and a DNA-binding domain 
[Transcription / Signal transduction mechanisms]
CD-Length = 531 residues,  99.2% aligned
Score =  891 bits (2304), Expect = 0.0
Identities = 377/531 (70%), Positives = 431/531 (81%), Gaps = 4/531 (0%)

pfam06956, RtcR, Regulator of RNA terminal phosphate cyclase. 
CD-Length = 185 residues, 100.0% aligned
Score =  328 bits (842), Expect = 2e-90
Identities = 155/188 (82%), Positives = 166/188 (88%), Gaps = 3/188 (1%)

pfam00158, Sigma54_activat, Sigma-54 interaction domain.
CD-Length = 222 residues, 100.0% aligned
Score =  222 bits (567), Expect = 2e-58
Identities = 104/232 (44%), Positives = 133/232 (57%), Gaps = 11/232 (4%)






   
Genomic Context:






   
Comment:


















    ReferenceID:1361




  
Author/Investigator(s):
        GenNotator





  
Title:
        




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:BLASTP 







    
Data:


    		




 
URL:

















    ReferenceID:18503




  
Author/Investigator(s):
        GenNotator





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:RPSBLAST 







    
Data:


    		




 
URL:

















    ReferenceID:31637




  
Author/Investigator(s):
        





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:Misc (text/plain)







    
Data:679_cdd.html


    		




 
URL:

















    ReferenceID:33116




  
Author/Investigator(s):
        Genschik P, Drabikowski K, Filipowicz W.





  
Title:
        Characterization of the Escherichia coli RNA 3'-terminal phosphate cyclase and its sigma54-regulated operon.




  
PubMed:
        9738023


MedLine:
        




    
Source:
J Biol Chem. 1998 Sep 25;273(39):25516-26.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=9738023









           
Homologs By Global Alignment 

           

       



     
Gene ID:679
           
Identity:

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

                           

     
HomologID
                           Accession
                           Description
                           Length
                           PctIdentity
                           PctSimilarity
                           Gaps
                           Score
     

     
     
1142
                           PA4581_tr
                           translation of PA4581
                           531
                           99.62
                           99.81
                           0
                           2701.0
     

     
     
42460
                           gb|AAG07969.1|AE004871_9
                           (AE004871) transcriptional regulator RtcR [Pseudomonas aeruginosa PAO1]
                           531
                           99.62
                           99.81
                           0
                           2701.0
     

     
     
42461
                           emb|CAD13750.1|
                           (AL646058) PROBABLE SIGMA-54 INTERACTING TRANSCRIPTION REGULATOR PROTEIN [Ralstonia solanacearum]
                           538
                           72.30
                           81.78
                           10
                           1974.0
     

     
     
42462
                           gb|AAL22383.1|
                           (AE008862) sigma N (sigma 54)-dependent regulator of rtcBA expression [Salmonella typhimurium LT2]
                           531
                           69.11
                           80.41
                           4
                           1861.0
     

     
     
42465
                           gb|AAQ58711.1|
                           (AE016913) transcriptional regulatory protein rtcr [Chromobacterium violaceum ATCC 12472]
                           543
                           67.77
                           77.34
                           20
                           1850.0
     

     






      

          
GC ORFID: 43681How Found: BLASTX

          
GC_TrimmedSeqID: 69Blast Result ID

          
Subject Sequence Name: t_PA4581Glimmer Score: 

          
Start: 4666915Stop: 4665320

          
Length: 1596


          
Start Codon: ATGTruncated Start:

          
Stop Codon: TGATruncated Stop: 

          
Homolog: t_PA4581 translation of PA4581Homolog Bit Score 1045.0

          
Other Homologs:  t_PA2359 (ORF: BLASTX 154.0), t_PA4581 (ORF: GLIMMER)

          
GC ORF Sequence

           
ATGAAACGCACGGTCGCCATCGGCTTCATCGGCGCCACCCTCGACCGTCTCGGCAAGGGCGCGGCGCGCTGG 
CAAAAGTGGCGGCCGAGCATCGGCCTGTGCCAGCAGCCGGACCTGCTGATCGACCGCCTCGAACTGATCCAC 
GGCAACGACGCCCGCGACCTCGGCCTGGCCGAGCGGATTCGCGCCGACATCGCCGCGGTGTCGCCGCATACC 
GAGGTCCGCCTGCAGCAGATGGAACTGCGCAACCCCTGGGACTTCGAGGAGGTCTATGGCGCCCTGCACGAT 
TTCGTCAGCGCCTACCCCTTCGACACCGAGCGCGAGGACTACCTGGTGCATATCACCACCGGGACCCATGTC 
GCGCAGATCTGCTGGTTCCTCCTTACCGAGGCGCGCTACCTGCCGGCCCGGCTGGTGCAGACCTCGCCGTCG 
CGGCGCAAGGACGAGGCGCGCCATCCCGAGGGCTCGGCGACGCTGATCGACCTCGACCTGTCCCGCTACGAC 
CGCATCGCCTCGCGGTTCCGCCGCGAACAGGAGGAAAGCCTGGCTTTTCTCAAGTCGGGAATCGCCACGCGC 
AATGCCGCTTTCAACCGCTCCATCGAGCAGATCGAGCGGGTCGCCGTGCGTTCGCGGGCACCCATGCTGCTG 
GTGGGGCCGACCGGTGCCGGCAAATCGTTCCTCGCCCGGCGCATCTATGAACTCAAGCGCAGCCGGCACCAG 
CTCGACGGGCGTTTCGTCGAGGTCAACTGCGCCACCTTGCGCGGCGACGGCGCGATGTCGGCACTGTTCGGC 
CACGTCAAGGGCGCCTTCACCGGCGCGCAGAATGCGCGCGAAGGCCTGCTGCGCGCAGCCGACGGTGGCATG 
CTGTTCCTCGACGAGATCGGCGAGCTGGGTGCCGACGAACAGGCGATGCTGCTCAAGGCGATCGAAGAGAAG 
CGCTTCTTCCCGCTGGGTTCGGACCGTGAGGTGGAGAGCGACTTCCAGCTTATCGCCGGGACCCACCGCGAC 
TTGCGCGGACGAGTGGCCGAAGGCCTGTTCCGCGAGGACCTGTTCGCCCGCATCAACCTGTGGACCTTCGAG 
CTGCCGGGCCTGGCTGGACGCCGCGAGGACATCGAGCCGAACATCGACTTCGAACTGGAGCGGCACGCCCGC 
GAGCAAGGGCGGCAGGTGCGTTTCAACCTGGAGGCCAAGCGTCGCTACCTGGCCTTCGCCGGTTCCAGCGAA 
GCGCGCTGGGCCGGCAACTTCCGCGAGCTGTCGGCTTCCATCACACGGATGGCGACCCTGGCCGACAGCGGG 
CGGATCGACGAGGCGCTGGTCGAGGAGGAGATCCTTCGCCTGCGCCAGGCCTGGGGGCTCGATGCGGGCCGG 
GAGCCACTGGCTGATCTGCTGGGGCAGCGGGTGGAGGCCCTGGATCTGTTCGACCGCCTGCAACTGCAGTCG 
GTGCTGGAGGTGTGCCGCGGGGCTAAGACCCTTTCCGAGGCGGGACGCCGGCTGTTCGCCGTTTCGCGCCAG 
GACAAGCGCAACCCCAACGACGCCGACCGGCTGCGCAAGTACCTGGCGCGTTTCGGCCTGGACTGGGCGCAG 
ATACGCGCCTGA