ViewGene
Locus Name:
GeneID:
Location:

GeneID:3892
TrivialName: PA14_10120
AnnotatorUID:
Modification Date/Time:2006-04-06 13:01:23
LocusName:PA14_10120
PAO1 Ortholog Locus:
Sequence Length:930
Protein Length:309
Start: 869571
Stop: 868642
Strand: -
Type:
ChromosomeID:2
Status: ACTIVE
Frame Discrepancy: FALSE
Missense Discrepancy:FALSE
Comments:
Homology: gb|AAO55138.1| (AE016861) transcriptional regulator, LysR family [Pseudomonas syringae pv. tomato str. DC3000]
Identities = 163/296 (55%), Positives = 223/296 (75%), Gaps = 1/296 (0%)
Sequence:
GTGTTTTCCTCAGAACGTCTGAAAGGCATAGACGTCTTCGTCTGCGTCGCCGAAGCCGGCAGCTTCAGCGCG
GCGGCGGAGCGACTGCACCTGACCGCCTCGGCGGTGAGCaAGGCCATTGCCCGGCTGGAAGACCGCCTCGGC
cTGCGCCTGTTCGAGAGGACCACTCGTCGACTGGCGCTGACCGACGCCGGCACGACGTTCTACCGCACCTGT
TCGCGAGTGCTCGGCGACCTCGAAGAGTCCGAGCTGGCGCTGCACGCCGAGCACCACCAGACAGGCGGACGC
ATCCGTCTCGACCTGCCTGCTTCCTACGGGCGCCTGCACGTGCTACCGGTGGTGCTCGACTTCGCCAGGCGC
CACGCGCTGCTCGTGCCACATATCTCCTTCAGCGACGACTTCATCGACCCCGTCAGCCAGGGCATCGATATC
CTGGTGCGCATAGGCGGTCCGGATATCTGGCCGGAAACCCTCGGTCACCGCTACCTCGGCGCACAGCGCCTG
GTGTTCTGTGCCGCGCCGGCCTACCTCGCCGCACACGGCGAGCCCCGCGATGTGGAAGAGCTGGCCGCTCAC
GACTGCGTGCTGTACGGCCAGGGCGATGGCCTGACCACCCCCTGGAACTTCCCGGGACACCAGCCAGGCGAG
CTGGAACGACGGGTGATGCCGACGCGGATCGCGATAGGCGATGGCGAGGGCGTGGTGCAGGCACTGCTTGCC
AGCCACGGCATCGGCCAATTGCCGACCTGGCTGGTCAGCCGGCATCTGGAGAGCGGGCGCCTGCGCGAGGTC
CTGCCACAACTGGCCAGCGACGGCCTGTCGATCAACCTGGCCTGGCAGAAGCGACGTGAAAACCTGCCCAAG
GTCGGCGCCCTGCTCGACGTGCTTGGCCGCAGCCTCATCCCCTCCGGCCACATCTTGGGCAATTAA
Translation:
MFSSERLKGIDVFVCVAEAGSFSAAAERLHLTASAVSKAIARLEDRLGLRLFERTTRRLALTDAGTTFYRTC
SRVLGDLEESELALHAEHHQTGGRIRLDLPASYGRLHVLPVVLDFARRHALLVPHISFSDDFIDPVSQGIDI
LVRIGGPDIWPETLGHRYLGAQRLVFCAAPAYLAAHGEPRDVEELAAHDCVLYGQGDGLTTPWNFPGHQPGE
LERRVMPTRIAIGDGEGVVQALLASHGIGQLPTWLVSRHLESGRLREVLPQLASDGLSINLAWQKRRENLPK
VGALLDVLGRSLIPSGHILGN*
AnnotationID:3899GeneID:3892
AnnotatorUID: danlee
Modification Date/Time: 2005-10-19 16:04:51
Gene Name:
Confidence Code:3
GeneProduct:possible LysR family transcription regulator
Cell Localization:()
Synonyms:
Cell Localization Confidence Code:5
MolecularFunction:
Functional Category:(25) Transcriptional regulators
Alternate Gene Product Name:
Functional Category Confidence Code:5
COGs:COG0583
Secondary Functional Category(ies):
EC Number:
Status:ACTIVE
Pathway:






 
Homology:
gi|50119864|ref|YP_049031.1|  LysR-family transcriptional regulator [Erwinia carotovora subsp. atroseptica SCRI1043]
     Length=310
     Score =  399 bits (1024),  Expect = 9e-110
     Identities = 183/304 (60%), Positives = 244/304 (80%), Gaps = 0/304 (0%)

gi|66044803|ref|YP_234644.1|  regulatory protein, LysR:LysR, substrate-binding [Pseudomonas syringae pv. syringae B728a]
     Length=309
     Score =  396 bits (1017),  Expect = 6e-109
     Identities = 188/306 (61%), Positives = 238/306 (77%), Gaps = 0/306 (0%)

gi|70730132|ref|YP_259871.1|  transcriptional regulator, LysR family [Pseudomonas fluorescens Pf-5]
     Length=302
     Score =  365 bits (936),  Expect = 1e-99
     Identities = 184/300 (61%), Positives = 222/300 (74%), Gaps = 0/300 (0%)

gi|71734272|ref|YP_273747.1|  transcriptional regulator, LysR family [Pseudomonas syringae pv. phaseolicola 1448A]
     Length=302
     Score =  342 bits (877),  Expect = 1e-92
     Identities = 164/300 (54%), Positives = 224/300 (74%), Gaps = 1/300 (0%)

gi|28868824|ref|NP_791443.1|  transcriptional regulator, LysR family [Pseudomonas syringae pv. tomato str. DC3000]
     Length=302
     Score =  340 bits (871),  Expect = 5e-92
     Identities = 163/296 (55%), Positives = 223/296 (75%), Gaps = 1/296 (0%)






 
Structural Features:
COG0583, LysR, Transcriptional regulator [Transcription].
             CD-Length = 297 residues,  97.6% aligned
             Score =  133 bits (335), Expect = 3e-32

pfam03466, LysR_substrate, LysR substrate binding domain. The structure of this domain is known and is 
similar to the periplasmic binding proteins..
             CD-Length = 209 residues,  98.6% aligned
             Score = 89.3 bits (221), Expect = 5e-19

pfam00126, HTH_1, Bacterial regulatory helix-turn-helix protein, lysR family..
             CD-Length = 60 residues,  98.3% aligned
             Score = 75.5 bits (186), Expect = 7e-15






   
Genomic Context:






   
Comment:


















    ReferenceID:14955




  
Author/Investigator(s):
        GenNotator





  
Title:
        




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:BLASTP 







    
Data:


    		




 
URL:

















    ReferenceID:17074




  
Author/Investigator(s):
        





  
Title:
        CDD search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:Misc (text/plain)







    
Data:3892_CDD.html


    		




 
URL:

















    ReferenceID:24929




  
Author/Investigator(s):
        GenNotator





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:RPSBLAST 







    
Data:


    		




 
URL:









           
Homologs By Global Alignment 

           

       



     
Gene ID:3892
           
Identity:

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

                           

     
HomologID
                           Accession
                           Description
                           Length
                           PctIdentity
                           PctSimilarity
                           Gaps
                           Score
     

     
     
170361
                           gb|AAO55138.1|
                           (AE016861) transcriptional regulator, LysR family [Pseudomonas syringae pv. tomato str. DC3000]
                           309
                           52.75
                           72.49
                           7
                           864.0
     

     
     
170362
                           gb|AAL27377.1|AF426171_8
                           (AF426171) putative transcriptional regulator [Yersinia pestis]
                           323
                           39.93
                           58.82
                           34
                           595.0
     

     
     
170364
                           emb|CAC47029.1|
                           (AL591790) PUTATIVE TRANSCRIPTION REGULATOR PROTEIN [Sinorhizobium meliloti]
                           318
                           38.36
                           54.08
                           28
                           537.0
     

     
     
170363
                           dbj|BAB49674.1|
                           (AP003000) probable transcriptional regulator [Mesorhizobium loti]
                           314
                           37.89
                           53.82
                           15
                           530.0
     

     






      

          
GC ORFID: 46894How Found: BLASTX

          
GC_TrimmedSeqID: 69Blast Result ID

          
Subject Sequence Name: psyr_15may02_Scaffold10_revised_gene1731Glimmer Score: 

          
Start: 4084366Stop: 4085295

          
Length: 930


          
Start Codon: GTGTruncated Start:

          
Stop Codon: TAATruncated Stop: 

          
Homolog: psyr_15may02_Scaffold10_revised_gene1731 related to: gi|16611834|gb|AAL27377.1|AF426171_8 (AF426171) putative transcriptional regulator [Yersinia pestis]Homolog Bit Score 394.0

          
Other Homologs:  psyr_15may02_Scaffold10_revised_gene1731 (ORF: GLIMMER)

          
GC ORF Sequence

           
GTGTTTTCCTCAGAACGTCTGAAAGGCATAGACGTCTTCGTCTGCGTCGCCGAAGCCGGCAGCTTCAGCGCG 
GCGGCGGAGCGACTGCACCTGACCGCCTCGGCGGTGAGCaAGGCCATTGCCCGGCTGGAAGACCGCCTCGGC 
cTGCGCCTGTTCGAGAGGACCACTCGTCGACTGGCGCTGACCGACGCCGGCACGACGTTCTACCGCACCTGT 
TCGCGAGTGCTCGGCGACCTCGAAGAGTCCGAGCTGGCGCTGCACGCCGAGCACCACCAGACAGGCGGACGC 
ATCCGTCTCGACCTGCCTGCTTCCTACGGGCGCCTGCACGTGCTACCGGTGGTGCTCGACTTCGCCAGGCGC 
CACGCGCTGCTCGTGCCACATATCTCCTTCAGCGACGACTTCATCGACCCCGTCAGCCAGGGCATCGATATC 
CTGGTGCGCATAGGCGGTCCGGATATCTGGCCGGAAACCCTCGGTCACCGCTACCTCGGCGCACAGCGCCTG 
GTGTTCTGTGCCGCGCCGGCCTACCTCGCCGCACACGGCGAGCCCCGCGATGTGGAAGAGCTGGCCGCTCAC 
GACTGCGTGCTGTACGGCCAGGGCGATGGCCTGACCACCCCCTGGAACTTCCCGGGACACCAGCCAGGCGAG 
CTGGAACGACGGGTGATGCCGACGCGGATCGCGATAGGCGATGGCGAGGGCGTGGTGCAGGCACTGCTTGCC 
AGCCACGGCATCGGCCAATTGCCGACCTGGCTGGTCAGCCGGCATCTGGAGAGCGGGCGCCTGCGCGAGGTC 
CTGCCACAACTGGCCAGCGACGGCCTGTCGATCAACCTGGCCTGGCAGAAGCGACGTGAAAACCTGCCCAAG 
GTCGGCGCCCTGCTCGACGTGCTTGGCCGCAGCCTCATCCCCTCCGGCCACATCTTGGGCAATTAA