ViewGene
Locus Name:
GeneID:
Location:

GeneID:2463
TrivialName: PA14_09910
AnnotatorUID:
Modification Date/Time:2006-04-06 13:01:23
LocusName:PA14_09910
PAO1 Ortholog Locus:PA4174
Sequence Length:924
Protein Length:307
Start: 852836
Stop: 851913
Strand: -
Type:
ChromosomeID:2
Status: ACTIVE
Frame Discrepancy: FALSE
Missense Discrepancy:FALSE
Comments:
Homology: gb|AAG07561.1|AE004834_1 (AE004834) probable transcriptional regulator [Pseudomonas aeruginosa PAO1]
Identities = 303/307 (98%), Positives = 305/307 (99%)
Sequence:
ATGGACCGTTTCGATGCGATGCAGGCCTTTGCCCGTGTGGTGGAGACCGGCAGCTTCACCAAGGCGGCGGAG
ACGCTGCACATGAGCCGCACCAGCGTCACCCAGTTGGTCCAGCAACTGGAAGCGCGGCTGCGGGTACGCCTG
CTCAACCGCACCACGCGCAAGCTCAACCTGACCGCCGACGGCGCCGCCTACTACGAGCGGGTGGTACGCCTG
CTGGCGGAACTGGACGATGCCGAGACCAGCCTCTCCAGCGCCGCCCTGGCGCCCCGCGGGCGTCTCCGGATC
GACGTGCCGAGCCCGCTGGCGCGGCTGCTGCTGATCCCGGCGTTGCCCGAGTTCCATGCGCGCTATCCGGAT
ATCCAGATCGACCTGGGCGTGAGCGATCGGCTCGTCGACCTGATCGACGAGAACGTCGATTGCGTCATCCGC
GGCGGCGAACTGCGCGACCAGTCGCTGATGGCGCGGCGGGTCGGCGACCTGCAACTGGGGGTCTACGCGGCA
CCGGCCTACTTGCAGCGCGCCGGCGTGCCGAGCCACCCGCGCGAACTGGAGGACAGCCACCAGCGCATCGTC
GGCTTCCTCTGGGCGCGCACCGGCAAGGCCCTGCCCTACGCCATGCACAGAGGCGAGGAAAGCCTGCGGGTG
GCGGGCCGCCATGTGCTGGCGGTGGACGACGGCAACGCCTACCTGGCGGCCGGGCTGGCCGGCCTGGGCATC
CTCTGGCTGCCGCACTACATGGCGCGTGAGCCCCTCGCCCGCGGCGAGCTGCTGCCGCTGTTCGAGGACTGG
AGCCTGGAGCCGATGCCGCTGTACCTGGCGTTCCCGCCGAACCGCCACGTCAGCGGCAAGCTGCGGGTGTTC
ATCGAGTGGGTCGCCGAACTGATCGCGCGGCATGCGCCGCCGTTGCATCCGCCGCTCTGA
Translation:
MDRFDAMQAFARVVETGSFTKAAETLHMSRTSVTQLVQQLEARLRVRLLNRTTRKLNLTADGAAYYERVVRL
LAELDDAETSLSSAALAPRGRLRIDVPSPLARLLLIPALPEFHARYPDIQIDLGVSDRLVDLIDENVDCVIR
GGELRDQSLMARRVGDLQLGVYAAPAYLQRAGVPSHPRELEDSHQRIVGFLWARTGKALPYAMHRGEESLRV
AGRHVLAVDDGNAYLAAGLAGLGILWLPHYMAREPLARGELLPLFEDWSLEPMPLYLAFPPNRHVSGKLRVF
IEWVAELIARHAPPLHPPL*
AnnotationID:2471GeneID:2463
AnnotatorUID: diggins
Modification Date/Time: 2005-03-31 07:07:33
Gene Name:
Confidence Code:3
GeneProduct:putative transcriptional regulator
Cell Localization:()
Synonyms:lysR
Cell Localization Confidence Code:5
MolecularFunction:
Functional Category:(25) Transcriptional regulators
Alternate Gene Product Name:
Functional Category Confidence Code:5
COGs:COG0583,pfam00126,pfam03466
Secondary Functional Category(ies):
EC Number:
Status:ACTIVE
Pathway:






 
Homology:
>emb|CAD44482.1| (AJ297529) LysR protein [Pseudomonas stutzeri]
          Length = 307

 Score =  508 bits (1308), Expect = e-143
 Identities = 247/301 (82%), Positives = 276/301 (91%)

>gb|AAM38604.1| (AE012025) transcriptional regulator [Xanthomonas axonopodis pv.
           citri str. 306]
          Length = 308

 Score =  456 bits (1172), Expect = e-127
 Identities = 223/305 (73%), Positives = 259/305 (84%)

>emb|CAE44764.1| (BX640412) probable LysR-family transcriptional regulator
           [Bordetella pertussis]
          Length = 328

 Score =  445 bits (1144), Expect = e-124
 Identities = 218/306 (71%), Positives = 254/306 (83%)








 
Structural Features:
COG0583, LysR, Transcriptional regulator [Transcription]
CD-Length = 297 residues,  99.7% aligned
Score =  142 bits (358), Expect = 5e-35
Identities = 108/306 (35%), Positives = 152/306 (49%), Gaps = 14/306 (4%)

pfam03466, LysR_substrate, LysR substrate binding domain.
CD-Length = 209 residues,  99.0% aligned
Score = 98.9 bits (246), Expect = 7e-22
Identities = 72/212 (33%), Positives = 97/212 (45%), Gaps = 8/212 (3%)

pfam00126, HTH_1, Bacterial regulatory helix-turn-helix protein, lysR family.
CD-Length = 60 residues,  98.3% aligned
Score = 62.4 bits (152), Expect = 7e-11
Identities = 26/59 (44%), Positives = 37/59 (62%)






   
Genomic Context:






   
Comment:


















    ReferenceID:4929




  
Author/Investigator(s):
        GenNotator





  
Title:
        




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:BLASTP 







    
Data:


    		




 
URL:

















    ReferenceID:22075




  
Author/Investigator(s):
        GenNotator





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:RPSBLAST 







    
Data:


    		




 
URL:

















    ReferenceID:36902




  
Author/Investigator(s):
        





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:Misc (text/plain)







    
Data:2463_cdd.html


    		




 
URL:









           
Homologs By Global Alignment 

           

       



     
Gene ID:2463
           
Identity:

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

                           

     
HomologID
                           Accession
                           Description
                           Length
                           PctIdentity
                           PctSimilarity
                           Gaps
                           Score
     

     
     
4131
                           PA4174_tr
                           translation of PA4174
                           307
                           98.69
                           99.34
                           0
                           1552.0
     

     
     
123135
                           gb|AAG07561.1|AE004834_1
                           (AE004834) probable transcriptional regulator [Pseudomonas aeruginosa PAO1]
                           307
                           98.69
                           99.34
                           0
                           1552.0
     

     
     
123136
                           emb|CAD44482.1|
                           (AJ297529) LysR protein [Pseudomonas stutzeri]
                           309
                           80.25
                           89.96
                           4
                           1303.0
     

     
     
123137
                           gb|AAM38604.1|
                           (AE012025) transcriptional regulator [Xanthomonas axonopodis pv. citri str. 306]
                           308
                           72.40
                           84.09
                           1
                           1168.0
     

     
     
123138
                           gb|AAM42977.1|
                           (AE012493) transcriptional regulator [Xanthomonas campestris pv. campestris str. ATCC 33913]
                           310
                           70.96
                           83.22
                           3
                           1154.0
     

     






      

          
GC ORFID: 45465How Found: BLASTX

          
GC_TrimmedSeqID: 69Blast Result ID

          
Subject Sequence Name: t_PA4174Glimmer Score: 

          
Start: 4101101Stop: 4102024

          
Length: 924


          
Start Codon: ATGTruncated Start:

          
Stop Codon: TGATruncated Stop: 

          
Homolog: t_PA4174 translation of PA4174Homolog Bit Score 602.0

          
Other Homologs:  t_PA2877 (ORF: BLASTX 256.0), t_PA2534 (ORF: BLASTX 253.0), psyr_15may02_Scaffold9_revised_gene8132 (ORF: BLASTX 246.0), t_PA4174 (ORF: GLIMMER)

          
GC ORF Sequence

           
ATGGACCGTTTCGATGCGATGCAGGCCTTTGCCCGTGTGGTGGAGACCGGCAGCTTCACCAAGGCGGCGGAG 
ACGCTGCACATGAGCCGCACCAGCGTCACCCAGTTGGTCCAGCAACTGGAAGCGCGGCTGCGGGTACGCCTG 
CTCAACCGCACCACGCGCAAGCTCAACCTGACCGCCGACGGCGCCGCCTACTACGAGCGGGTGGTACGCCTG 
CTGGCGGAACTGGACGATGCCGAGACCAGCCTCTCCAGCGCCGCCCTGGCGCCCCGCGGGCGTCTCCGGATC 
GACGTGCCGAGCCCGCTGGCGCGGCTGCTGCTGATCCCGGCGTTGCCCGAGTTCCATGCGCGCTATCCGGAT 
ATCCAGATCGACCTGGGCGTGAGCGATCGGCTCGTCGACCTGATCGACGAGAACGTCGATTGCGTCATCCGC 
GGCGGCGAACTGCGCGACCAGTCGCTGATGGCGCGGCGGGTCGGCGACCTGCAACTGGGGGTCTACGCGGCA 
CCGGCCTACTTGCAGCGCGCCGGCGTGCCGAGCCACCCGCGCGAACTGGAGGACAGCCACCAGCGCATCGTC 
GGCTTCCTCTGGGCGCGCACCGGCAAGGCCCTGCCCTACGCCATGCACAGAGGCGAGGAAAGCCTGCGGGTG 
GCGGGCCGCCATGTGCTGGCGGTGGACGACGGCAACGCCTACCTGGCGGCCGGGCTGGCCGGCCTGGGCATC 
CTCTGGCTGCCGCACTACATGGCGCGTGAGCCCCTCGCCCGCGGCGAGCTGCTGCCGCTGTTCGAGGACTGG 
AGCCTGGAGCCGATGCCGCTGTACCTGGCGTTCCCGCCGAACCGCCACGTCAGCGGCAAGCTGCGGGTGTTC 
ATCGAGTGGGTCGCCGAACTGATCGCGCGGCATGCGCCGCCGTTGCATCCGCCGCTCTGA