ViewGene
Locus Name:
GeneID:
Location:

GeneID:1754
TrivialName: PA14_34210
AnnotatorUID:
Modification Date/Time:2006-04-06 13:01:23
LocusName:PA14_34210
PAO1 Ortholog Locus:PA2354
Sequence Length:1131
Protein Length:376
Start: 3042252
Stop: 3043382
Strand: +
Type:
ChromosomeID:2
Status: ACTIVE
Frame Discrepancy: FALSE
Missense Discrepancy:FALSE
Comments:
Homology: gb|AAG05742.1|AE004661_9 (AE004661) probable transcriptional regulator [Pseudomonas aeruginosa PAO1]
Identities = 373/376 (99%), Positives = 374/376 (99%)
Sequence:
ATGAACGCTTCTACCCATACTCCCGACCGGCTGCTGACGCTGCCACGTTCGCCGAGCCTGGCGACCTCGATC
CGCGCCACCGCCCAGGTCTTCGAGGACCCGAAGTCCCAGGCCCTGCTCGAACACCTGCGCCAGGTGGCGCCG
AGCGAGGCCAGCGTGCTGGTGATCGGCGAGACCGGCACCGGCAAGGAACTGGTGGCGCGGCATATCCACAAC
CTCAGCGCGCGGCGCAACGGCCCGTTCGTGGCGGTCAACTGCGGGGCCTTCTCCGAGTCACTGGTGGAAGCC
GAGCTGTTCGGCCACGAGAAGGGCGCCTTTACGGGCGCCCTGGCGGCCAAGGCCGGCTGGTTCGAGGAAGCC
AACGGCGGCACCCTGTTCCTCGACGAGATCGGCGACCTGCCGATGCCGATCCAGGTCAAGCTGCTGCGTGTG
TTGCAGGAGCGCGAGGTGGTGCGCCTGGGTTCGCGCAAGAGCATCCCCATCGACGTGCGCGTGCTGGCGGCG
ACCAACGTGCAACTGGAGCGGGCGATCAATGCCGGGCACTTCCGCGAGGACCTGTACTACCGGCTCAATGTC
GTCAGCCTGGAGCTGTCGCCGTTGCGCGAGCGACCCGGCGACATCCTGCCGCTGACCCGCCACTTCATCGCC
GAGTACAGCCGTCGCCTGGGCTACGGCCAGAGCCAGTTGAGCCCGGAGGCGGCGCAGAAGTTGCGCGCCTAT
TCCTGGCCGGGGAACATCCGCGAGCTGGAGAACGTCATCCACCATACCTTGCTGATCTGCCGCGACGGGCTG
ATCCGCGCCGATGACCTGCACCTGTCCAACCTGCGCCTGGAGCGTGGCGAGGAGCTGGCGCGCGGGGTCCCG
GCGAGCGGCGCCGCCGAGCACTTGTTGCAGCAGGCTTTCCAGCGGCTGTTCGAAGAGCAGGGCGAGAACCTC
CATGGGCGGGTCGAGGATGCCCTGCTGCGCGCGGCGTACCGTTTCTGCCATGGCAACCAGGTGCATACCGCC
AACCTGCTGGGACTCAGCCGCAACGTCACGCGCACGCGGCTGATCGCCATCGGCGAGCTGGTGGTGAACAAG
CGCGGTGGCCAGCGGATCGATGGCGAGCGGGCGGTGCGGTTGTCGATCTGA
Translation:
MNASTHTPDRLLTLPRSPSLATSIRATAQVFEDPKSQALLEHLRQVAPSEASVLVIGETGTGKELVARHIHN
LSARRNGPFVAVNCGAFSESLVEAELFGHEKGAFTGALAAKAGWFEEANGGTLFLDEIGDLPMPIQVKLLRV
LQEREVVRLGSRKSIPIDVRVLAATNVQLERAINAGHFREDLYYRLNVVSLELSPLRERPGDILPLTRHFIA
EYSRRLGYGQSQLSPEAAQKLRAYSWPGNIRELENVIHHTLLICRDGLIRADDLHLSNLRLERGEELARGVP
ASGAAEHLLQQAFQRLFEEQGENLHGRVEDALLRAAYRFCHGNQVHTANLLGLSRNVTRTRLIAIGELVVNK
RGGQRIDGERAVRLSI*
AnnotationID:1763GeneID:1754
AnnotatorUID: diggins
Modification Date/Time: 2005-03-04 16:04:55
Gene Name:
Confidence Code:3
GeneProduct:putative transcriptional regulator
Cell Localization:()
Synonyms:sfnR
Cell Localization Confidence Code:5
MolecularFunction:putative sigma54-dependent transcriptional regulator
Functional Category:(25) Transcriptional regulators
Alternate Gene Product Name:
Functional Category Confidence Code:5
COGs:COG1221,pfam00158
Secondary Functional Category(ies):
EC Number:
Status:ACTIVE
Pathway:






 
Homology:
>dbj|BAC66053.1| (AB091764) sigma54-dependent transcriptional regulator [Pseudomonas
           putida]
          Length = 366

 Score =  575 bits (1482), Expect = e-163
 Identities = 298/369 (80%), Positives = 325/369 (88%), Gaps = 6/369 (1%)

>gb|AAM35733.1| (AE011716) transcriptional regulator [Xanthomonas axonopodis pv.
           citri str. 306]
          Length = 375

 Score =  484 bits (1246), Expect = e-136
 Identities = 256/357 (71%), Positives = 289/357 (80%), Gaps = 7/357 (1%)

>gb|AAO58643.1| (AE016875) sigma-54-binding protein [Pseudomonas syringae pv.
           tomato str. DC3000]
          Length = 316

 Score =  277 bits (709), Expect = 7e-74
 Identities = 149/298 (50%), Positives = 205/298 (68%), Gaps = 5/298 (1%)








 
Structural Features:
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 =  341 bits (875), Expect = 1e-94
Identities = 162/361 (44%), Positives = 198/361 (54%), Gaps = 13/361 (3%)

pfam00158, Sigma54_activat, Sigma-54 interaction domain.
CD-Length = 222 residues,  98.6% aligned
Score =  298 bits (764), Expect = 9e-82
Identities = 130/219 (59%), Positives = 161/219 (73%)






   
Genomic Context:






   
Comment:


















    ReferenceID:3511




  
Author/Investigator(s):
        GenNotator





  
Title:
        




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:BLASTP 







    
Data:


    		




 
URL:

















    ReferenceID:20658




  
Author/Investigator(s):
        GenNotator





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:RPSBLAST 







    
Data:


    		




 
URL:

















    ReferenceID:32902




  
Author/Investigator(s):
        





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:Misc (text/plain)







    
Data:1754_cdd.html


    		




 
URL:









           
Homologs By Global Alignment 

           

       



     
Gene ID:1754
           
Identity:

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

                           

     
HomologID
                           Accession
                           Description
                           Length
                           PctIdentity
                           PctSimilarity
                           Gaps
                           Score
     

     
     
3092
                           PA2354_tr
                           translation of PA2354
                           376
                           99.20
                           99.46
                           0
                           1886.0
     

     
     
95472
                           gb|AAG05742.1|AE004661_9
                           (AE004661) probable transcriptional regulator [Pseudomonas aeruginosa PAO1]
                           376
                           99.20
                           99.46
                           0
                           1886.0
     

     
     
95473
                           dbj|BAC66053.1|
                           (AB091764) sigma54-dependent transcriptional regulator [Pseudomonas putida]
                           378
                           78.83
                           85.97
                           14
                           1485.0
     

     
     
95475
                           gb|AAN68379.1|AE016470_8
                           (AE016784) sigma-54 dependent transcriptional regulator [Pseudomonas putida KT2440]
                           377
                           77.71
                           86.73
                           11
                           1458.0
     

     
     
95474
                           gb|AAO56942.1|
                           (AE016868) sigma-54 dependent transcriptional regulator, putative [Pseudomonas syringae pv. tomato str. DC3000]
                           377
                           75.86
                           86.47
                           10
                           1461.0
     

     






      

          
GC ORFID: 44756How Found: BLASTX

          
GC_TrimmedSeqID: 69Blast Result ID

          
Subject Sequence Name: t_PA2354Glimmer Score: 

          
Start: 1911664Stop: 1910534

          
Length: 1131


          
Start Codon: ATGTruncated Start:

          
Stop Codon: TGATruncated Stop: 

          
Homolog: t_PA2354 translation of PA2354Homolog Bit Score 731.0

          
Other Homologs:  psyr_15may02_Scaffold1_revised_gene1290 (ORF: BLASTX 568.0), t_PA2359 (ORF: BLASTX 450.0), t_PA1099 (ORF: BLASTX 264.0), psyr_15may02_Scaffold8_revised_gene7916 (ORF: BLASTX 254.0), t_PA1097 (ORF: BLASTX 249.0), psyr_15may02_Scaffold8_revised_gene7914 (ORF: BLASTX 246.0), t_PA5511 (ORF: BLASTX 227.0), t_PA2005 (ORF: BLASTX 214.0), t_PA1196 (ORF: BLASTX 207.0), psyr_15may02_Scaffold2_revised_gene4053 (ORF: BLASTX 202.0), t_PA2354 (ORF: GLIMMER)

          
GC ORF Sequence

           
ATGAACGCTTCTACCCATACTCCCGACCGGCTGCTGACGCTGCCACGTTCGCCGAGCCTGGCGACCTCGATC 
CGCGCCACCGCCCAGGTCTTCGAGGACCCGAAGTCCCAGGCCCTGCTCGAACACCTGCGCCAGGTGGCGCCG 
AGCGAGGCCAGCGTGCTGGTGATCGGCGAGACCGGCACCGGCAAGGAACTGGTGGCGCGGCATATCCACAAC 
CTCAGCGCGCGGCGCAACGGCCCGTTCGTGGCGGTCAACTGCGGGGCCTTCTCCGAGTCACTGGTGGAAGCC 
GAGCTGTTCGGCCACGAGAAGGGCGCCTTTACGGGCGCCCTGGCGGCCAAGGCCGGCTGGTTCGAGGAAGCC 
AACGGCGGCACCCTGTTCCTCGACGAGATCGGCGACCTGCCGATGCCGATCCAGGTCAAGCTGCTGCGTGTG 
TTGCAGGAGCGCGAGGTGGTGCGCCTGGGTTCGCGCAAGAGCATCCCCATCGACGTGCGCGTGCTGGCGGCG 
ACCAACGTGCAACTGGAGCGGGCGATCAATGCCGGGCACTTCCGCGAGGACCTGTACTACCGGCTCAATGTC 
GTCAGCCTGGAGCTGTCGCCGTTGCGCGAGCGACCCGGCGACATCCTGCCGCTGACCCGCCACTTCATCGCC 
GAGTACAGCCGTCGCCTGGGCTACGGCCAGAGCCAGTTGAGCCCGGAGGCGGCGCAGAAGTTGCGCGCCTAT 
TCCTGGCCGGGGAACATCCGCGAGCTGGAGAACGTCATCCACCATACCTTGCTGATCTGCCGCGACGGGCTG 
ATCCGCGCCGATGACCTGCACCTGTCCAACCTGCGCCTGGAGCGTGGCGAGGAGCTGGCGCGCGGGGTCCCG 
GCGAGCGGCGCCGCCGAGCACTTGTTGCAGCAGGCTTTCCAGCGGCTGTTCGAAGAGCAGGGCGAGAACCTC 
CATGGGCGGGTCGAGGATGCCCTGCTGCGCGCGGCGTACCGTTTCTGCCATGGCAACCAGGTGCATACCGCC 
AACCTGCTGGGACTCAGCCGCAACGTCACGCGCACGCGGCTGATCGCCATCGGCGAGCTGGTGGTGAACAAG 
CGCGGTGGCCAGCGGATCGATGGCGAGCGGGCGGTGCGGTTGTCGATCTGA