ViewGene
Locus Name:
GeneID:
Location:

GeneID:4901
TrivialName: PA14_38570
AnnotatorUID:
Modification Date/Time:2006-04-06 13:01:23
LocusName:PA14_38570
PAO1 Ortholog Locus:PA2005
Sequence Length:1371
Protein Length:456
Start: 3440271
Stop: 3441641
Strand: +
Type:
ChromosomeID:2
Status: ACTIVE
Frame Discrepancy: FALSE
Missense Discrepancy:FALSE
Comments:
Homology: gb|AAG05393.1|AE004627_1 (AE004627) probable transcriptional regulator [Pseudomonas aeruginosa PAO1]
Identities = 450/456 (98%), Positives = 452/456 (99%)
Sequence:
CTGTTCGAGATCGTCGAAGGCTCCAGCGAAGGCACGGTGATCGTCGACCGCGAGGCCCGCATCGTCTGGATC
AACCAGCGCTACGCCCAGCGTTTCGGCCTCGCCGACCCGGCGCAGGCCATCGGCCGGCCCTGCGAAAGCGTG
ATCCCCGGTAGCCTGCTGCGCGAGGTGGTACGCAGCGGCAAGCCGATCCTGCTGGACATGATGGACAGCGCG
AAGGACCCGCTGGTGGTGATGCGCCTGCCGATCCACGACGACGCCGGCGAGGTGATCGGCGCCATCGGCTTC
GCCCTGCTCGACGAACTGCGTTCGCTGTCGCCGCTGGTGACCCGCTACCTGAGCATGCAGCGCGAACTGGCC
TCGACCCGCTCGCAATTGCAGGCGCGCCAGGCCAAGTACAGCTTCAGCCACTTCGTCGGTACCAGTCCGGCC
AGCCTGGAAGTCAAGCGCCGCGCCCGCCGTGGCGCGGCCAGCGAAGCGCCGGTGCTGTTGCTCGGCGAGACC
GGTACCGGCAAGGAACTGCTCGCCCACGCCATCCACAGCGCTTCGCCGCGGGCGCACAAGGCCTTCGTCAGC
GTGAACGCCGCGGCGATCCCGGAAAGCCTGCTGGAGGCCGAATTCTTCGGTACCGCCCCGGGGGCCTTCACC
GGTGCCGAGCGCAAGGGCCGGCCAGGCAAGTTGCAGGTGGCCCAGGGCGGCACGTTGTTCCTCGACGAGATC
GGCGACATGCCGCTGGCCTTGCAAGGCAAGCTGTTGCGCGTGCTACAGGAGAAAGAGTTCGAAGCGGTGGGT
TCCAACGAAGTGATCCGCAGCGACATCCGCCTGGTCGCCGCCACTTCCATCGACCTGCAGCAGGCGATGCGC
GAAGGCCGTTTCCGCGCTGACCTCTACTACCGGCTGAACGTCCTGCCGATCGAGATCCCACCGTTGCGCCAG
CGCCTGGACGACCTCCCGGCGCTCTGCGAGTCGATCCTCGACAGCCTCGACCACGGCCGTCTCCACGAACTC
GGCGGCGACGCCCTGGCGCTGCTCGCCCGGCATGCCTGGCCGGGCAATGTTCGCGAACTGCGCAACGTGCTG
GAACGCGCGCTGCTGCTGGCCGACCAACCGTTGCTGGACGCCGCCGCCCTCGGCGCGGCGCTCGGCCCCCTG
CAACCGCTGCCGGAGCTGCCTCGAGCGGCGGACGACAGGCCGGTCGGGGATTTCCAACAGGCCCGCGAAGCC
TTCGAGCGCGACCTGATCGGACGGGCCCTGGCGCAGAGTGCCGGCAATGTGGTGGAAGCGGCGAAACGCCTG
GGCCTGGGTCGCTCGACCCTGTACAAGAAGATCGTGGCGCTGGGCATGCGTCTCGATAACGGGACCCATCTC
TAA
Translation:
MFEIVEGSSEGTVIVDREARIVWINQRYAQRFGLADPAQAIGRPCESVIPGSLLREVVRSGKPILLDMMDSA
KDPLVVMRLPIHDDAGEVIGAIGFALLDELRSLSPLVTRYLSMQRELASTRSQLQARQAKYSFSHFVGTSPA
SLEVKRRARRGAASEAPVLLLGETGTGKELLAHAIHSASPRAHKAFVSVNAAAIPESLLEAEFFGTAPGAFT
GAERKGRPGKLQVAQGGTLFLDEIGDMPLALQGKLLRVLQEKEFEAVGSNEVIRSDIRLVAATSIDLQQAMR
EGRFRADLYYRLNVLPIEIPPLRQRLDDLPALCESILDSLDHGRLHELGGDALALLARHAWPGNVRELRNVL
ERALLLADQPLLDAAALGAALGPLQPLPELPRAADDRPVGDFQQAREAFERDLIGRALAQSAGNVVEAAKRL
GLGRSTLYKKIVALGMRLDNGTHL*
AnnotationID:4906GeneID:4901
AnnotatorUID: diggins
Modification Date/Time: 2005-03-02 18:06:49
Gene Name:
Confidence Code:3
GeneProduct:putative sigma-54 dependent transcriptional regulator
Cell Localization:()
Synonyms:PA2005
Cell Localization Confidence Code:5
MolecularFunction:
Functional Category:(25) Transcriptional regulators
Alternate Gene Product Name:
Functional Category Confidence Code:5
COGs:COG2204,COG3604,pfam00158
Secondary Functional Category(ies):
EC Number:
Status:ACTIVE
Pathway:






 
Homology:
>gb|AAN68683.1|AE016497_8 (AE016785) sigma-54 dependent transcriptional regulator
           [Pseudomonas putida KT2440]
          Length = 481

 Score =  647 bits (1668), Expect = 0.0
 Identities = 333/448 (74%), Positives = 384/448 (85%), Gaps = 8/448 (1%)

>dbj|BAC46155.1| (AP005938) transcriptional regulatory protein [Bradyrhizobium
           japonicum USDA 110]
          Length = 480

 Score =  435 bits (1118), Expect = e-121
 Identities = 229/455 (50%), Positives = 307/455 (67%), Gaps = 10/455 (2%)








 
Structural Features:
COG2204, AtoC, Response regulator containing CheY-like receiver, AAA-type ATPase, 
and DNA-binding domains [Signal transduction mechanisms]
CD-Length = 464 residues,  85.6% aligned
Score =  344 bits (883), Expect = 2e-95
Identities = 174/400 (43%), Positives = 239/400 (59%), Gaps = 13/400 (3%)

COG3604, FhlA, Transcriptional regulator containing GAF, AAA-type ATPase, and 
DNA binding domains [Transcription / Signal transduction mechanisms]
CD-Length = 550 residues,  82.2% aligned
Score =  319 bits (820), Expect = 3e-88
Identities = 179/455 (39%), Positives = 249/455 (54%), Gaps = 51/455 (11%)

pfam00158, Sigma54_activat, Sigma-54 interaction domain.
CD-Length = 222 residues,  99.5% aligned
Score =  274 bits (702), Expect = 2e-74
Identities = 128/222 (57%), Positives = 159/222 (71%), Gaps = 4/222 (1%)






   
Genomic Context:






   
Comment:


















    ReferenceID:15208




  
Author/Investigator(s):
        GenNotator





  
Title:
        




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:BLASTP 







    
Data:


    		




 
URL:

















    ReferenceID:26943




  
Author/Investigator(s):
        GenNotator





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:RPSBLAST 







    
Data:


    		




 
URL:

















    ReferenceID:32679




  
Author/Investigator(s):
        





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:Misc (text/plain)







    
Data:4901_cdd.html


    		




 
URL:









           
Homologs By Global Alignment 

           

       



     
Gene ID:4901
           
Identity:

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

                           

     
HomologID
                           Accession
                           Description
                           Length
                           PctIdentity
                           PctSimilarity
                           Gaps
                           Score
     

     
     
7282
                           PA2005_tr
                           translation of PA2005
                           481
                           93.76
                           93.97
                           25
                           2239.0
     

     
     
189575
                           gb|AAG05393.1|AE004627_1
                           (AE004627) probable transcriptional regulator [Pseudomonas aeruginosa PAO1]
                           481
                           93.76
                           93.97
                           25
                           2239.0
     

     
     
189576
                           gb|AAN68683.1|AE016497_8
                           (AE016785) sigma-54 dependent transcriptional regulator [Pseudomonas putida KT2440]
                           497
                           67.20
                           77.26
                           57
                           1677.0
     

     
     
189577
                           dbj|BAC46155.1|
                           (AP005938) transcriptional regulatory protein [Bradyrhizobium japonicum USDA 110]
                           494
                           47.36
                           62.95
                           52
                           1134.0
     

     
     
189598
                           dbj|BAA84117.1|
                           (AB031996) regulator protein [Ralstonia sp. KN1]
                           498
                           37.75
                           49.59
                           94
                           661.0
     

     






      

          
GC ORFID: 47903How Found: BLASTX

          
GC_TrimmedSeqID: 69Blast Result ID

          
Subject Sequence Name: t_PA1945Glimmer Score: 

          
Start: 1513640Stop: 1512270

          
Length: 1371


          
Start Codon: CTGTruncated Start:

          
Stop Codon: TAATruncated Stop: 

          
Homolog: t_PA1945 translation of PA1945Homolog Bit Score 241.0

          
Other Homologs:  psyr_15may02_Scaffold8_revised_gene7914 (ORF: BLASTX 236.0), t_PA1097 (ORF: BLASTX 233.0), t_PA1099 (ORF: BLASTX 229.0), t_PA4547 (ORF: BLASTX 229.0), t_PA1663 (ORF: BLASTX 225.0), psyr_15may02_Scaffold2_revised_gene3179 (ORF: BLASTX 224.0), psyr_15may02_Scaffold3_revised_gene4961 (ORF: BLASTX 221.0), t_PA2354 (ORF: BLASTX 213.0), psyr_15may02_Scaffold8_revised_gene7916 (ORF: BLASTX 211.0), t_PA2359 (ORF: BLASTX 204.0), psyr_15may02_Scaffold3_revised_gene4480 (ORF: BLASTX 178.0), psyr_15may02_Scaffold3_revised_gene4481 (ORF: BLASTX 178.0), t_PA3932 (ORF: BLASTX 170.0), t_PA2005 (ORF: GLIMMER)

          
GC ORF Sequence

           
CTGTTCGAGATCGTCGAAGGCTCCAGCGAAGGCACGGTGATCGTCGACCGCGAGGCCCGCATCGTCTGGATC 
AACCAGCGCTACGCCCAGCGTTTCGGCCTCGCCGACCCGGCGCAGGCCATCGGCCGGCCCTGCGAAAGCGTG 
ATCCCCGGTAGCCTGCTGCGCGAGGTGGTACGCAGCGGCAAGCCGATCCTGCTGGACATGATGGACAGCGCG 
AAGGACCCGCTGGTGGTGATGCGCCTGCCGATCCACGACGACGCCGGCGAGGTGATCGGCGCCATCGGCTTC 
GCCCTGCTCGACGAACTGCGTTCGCTGTCGCCGCTGGTGACCCGCTACCTGAGCATGCAGCGCGAACTGGCC 
TCGACCCGCTCGCAATTGCAGGCGCGCCAGGCCAAGTACAGCTTCAGCCACTTCGTCGGTACCAGTCCGGCC 
AGCCTGGAAGTCAAGCGCCGCGCCCGCCGTGGCGCGGCCAGCGAAGCGCCGGTGCTGTTGCTCGGCGAGACC 
GGTACCGGCAAGGAACTGCTCGCCCACGCCATCCACAGCGCTTCGCCGCGGGCGCACAAGGCCTTCGTCAGC 
GTGAACGCCGCGGCGATCCCGGAAAGCCTGCTGGAGGCCGAATTCTTCGGTACCGCCCCGGGGGCCTTCACC 
GGTGCCGAGCGCAAGGGCCGGCCAGGCAAGTTGCAGGTGGCCCAGGGCGGCACGTTGTTCCTCGACGAGATC 
GGCGACATGCCGCTGGCCTTGCAAGGCAAGCTGTTGCGCGTGCTACAGGAGAAAGAGTTCGAAGCGGTGGGT 
TCCAACGAAGTGATCCGCAGCGACATCCGCCTGGTCGCCGCCACTTCCATCGACCTGCAGCAGGCGATGCGC 
GAAGGCCGTTTCCGCGCTGACCTCTACTACCGGCTGAACGTCCTGCCGATCGAGATCCCACCGTTGCGCCAG 
CGCCTGGACGACCTCCCGGCGCTCTGCGAGTCGATCCTCGACAGCCTCGACCACGGCCGTCTCCACGAACTC 
GGCGGCGACGCCCTGGCGCTGCTCGCCCGGCATGCCTGGCCGGGCAATGTTCGCGAACTGCGCAACGTGCTG 
GAACGCGCGCTGCTGCTGGCCGACCAACCGTTGCTGGACGCCGCCGCCCTCGGCGCGGCGCTCGGCCCCCTG 
CAACCGCTGCCGGAGCTGCCTCGAGCGGCGGACGACAGGCCGGTCGGGGATTTCCAACAGGCCCGCGAAGCC 
TTCGAGCGCGACCTGATCGGACGGGCCCTGGCGCAGAGTGCCGGCAATGTGGTGGAAGCGGCGAAACGCCTG 
GGCCTGGGTCGCTCGACCCTGTACAAGAAGATCGTGGCGCTGGGCATGCGTCTCGATAACGGGACCCATCTC 
TAA