ViewGene
Locus Name:
GeneID:
Location:

GeneID:5392
TrivialName: PA14_05960
AnnotatorUID:
Modification Date/Time:2006-04-06 13:01:23
LocusName:PA14_05960
PAO1 Ortholog Locus:PA0456
Sequence Length:210
Protein Length:69
Start: 528054
Stop: 528263
Strand: +
Type:
ChromosomeID:2
Status: ACTIVE
Frame Discrepancy: FALSE
Missense Discrepancy:FALSE
Comments:
Homology: gb|AAG03845.1|AE004483_3 (AE004483) probable cold-shock protein [Pseudomonas aeruginosa PAO1]
Identities = 69/69 (100%), Positives = 69/69 (100%)
Sequence:
ATGTCCCGTCAGAACGGCACCGTTAAGTGGTTCAACGAAACCAAAGGCTACGGCTTCATTACCCCGGAAAGC
GGCCCGGACGTTTTCGTTCACTTCCGTGCCATCGAAGGTAACGGCTTCAAGACCCTGGCCGAAGGCCAGAAG
GTCAGCTTCGAAGTCGTACAAGGCCAGAAAGGCATGCAGGCCGAGCGCGTTCAGGTGATCAACTAA
Translation:
MSRQNGTVKWFNETKGYGFITPESGPDVFVHFRAIEGNGFKTLAEGQKVSFEVVQGQKGMQAERVQVIN*
AnnotationID:5397GeneID:5392
AnnotatorUID: diggins
Modification Date/Time: 2005-03-25 14:02:49
Gene Name:
Confidence Code:3
GeneProduct:putative major cold shock protein
Cell Localization:()
Synonyms:cspB
Cell Localization Confidence Code:5
MolecularFunction:
Functional Category:(25) Transcriptional regulators
Alternate Gene Product Name:putative cold acclimation protein B
Functional Category Confidence Code:5
COGs:pfam00313,smart00357
Secondary Functional Category(ies):adaptation, protection
EC Number:
Status:ACTIVE
Pathway:






 
Homology:
>gb|AAN66610.1|AE016288_9 (AE016777) cold-shock domain family protein [Pseudomonas putida
           KT2440]
          Length = 165

 Score =  118 bits (296), Expect = 7e-27
 Identities = 53/66 (80%), Positives = 61/66 (92%)

>gb|AAM41566.1| (AE012336) major cold shock protein [Xanthomonas campestris pv.
          campestris str. ATCC 33913]
          Length = 69

 Score =  114 bits (286), Expect = 1e-25
 Identities = 51/66 (77%), Positives = 59/66 (89%)

>gb|AAO29822.1| (AE012560) temperature acclimation protein B [Xylella fastidiosa
          Temecula1]
          Length = 73

 Score =  109 bits (272), Expect = 4e-24
 Identities = 49/66 (74%), Positives = 59/66 (89%)








 
Structural Features:
pfam00313, CSD, 'Cold-shock' DNA-binding domain.
CD-Length = 67 residues, 100.0% aligned
Score = 90.6 bits (225), Expect = 3e-20
Identities = 42/67 (62%), Positives = 51/67 (76%), Gaps = 1/67 (1%)

smart00357, CSP, Cold shock protein domain
CD-Length = 62 residues, 100.0% aligned
Score = 58.3 bits (141), Expect = 2e-10
Identities = 32/66 (48%), Positives = 40/66 (60%), Gaps = 7/66 (10%)









   
Genomic Context:






   
Comment:
another possible gene name: capB


















    ReferenceID:10782




  
Author/Investigator(s):
        GenNotator





  
Title:
        




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:BLASTP 







    
Data:


    		




 
URL:

















    ReferenceID:27931




  
Author/Investigator(s):
        GenNotator





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:RPSBLAST 







    
Data:


    		




 
URL:

















    ReferenceID:33777




  
Author/Investigator(s):
        





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:Misc (text/plain)







    
Data:5392_cdd.html


    		




 
URL:









           
Homologs By Global Alignment 

           

       



     
Gene ID:5392
           
Identity:

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

                           

     
HomologID
                           Accession
                           Description
                           Length
                           PctIdentity
                           PctSimilarity
                           Gaps
                           Score
     

     
     
7786
                           PA0456_tr
                           translation of PA0456
                           69
                           99.99
                           99.99
                           0
                           362.0
     

     
     
196375
                           gb|AAG03845.1|AE004483_3
                           (AE004483) probable cold-shock protein [Pseudomonas aeruginosa PAO1]
                           69
                           99.99
                           99.99
                           0
                           362.0
     

     
     
196377
                           gb|AAM41566.1|
                           (AE012336) major cold shock protein [Xanthomonas campestris pv. campestris str. ATCC 33913]
                           70
                           72.85
                           84.28
                           2
                           285.0
     

     
     
196391
                           gb|AAN55809.1|AE015718_1
                           (AE015718) cold shock domain family protein [Shewanella oneidensis MR-1]
                           69
                           72.46
                           76.81
                           0
                           255.0
     

     
     
7787
                           PA3266_tr
                           translation of PA3266
                           70
                           71.42
                           85.71
                           2
                           278.0
     

     






      

          
GC ORFID: 48394How Found: BLASTX

          
GC_TrimmedSeqID: 69Blast Result ID

          
Subject Sequence Name: t_PA0456Glimmer Score: 

          
Start: 6329396Stop: 6329605

          
Length: 210


          
Start Codon: ATGTruncated Start:

          
Stop Codon: TAATruncated Stop: 

          
Homolog: t_PA0456 translation of PA0456Homolog Bit Score 144.0

          
Other Homologs:  psyr_15may02_Scaffold3_revised_gene4968 (ORF: BLASTX 114.0), t_PA3266 (ORF: BLASTX 112.0), psyr_15may02_Scaffold5_revised_gene6109 (ORF: BLASTX 104.0), t_PA0456 (ORF: GLIMMER)

          
GC ORF Sequence

           
ATGTCCCGTCAGAACGGCACCGTTAAGTGGTTCAACGAAACCAAAGGCTACGGCTTCATTACCCCGGAAAGC 
GGCCCGGACGTTTTCGTTCACTTCCGTGCCATCGAAGGTAACGGCTTCAAGACCCTGGCCGAAGGCCAGAAG 
GTCAGCTTCGAAGTCGTACAAGGCCAGAAAGGCATGCAGGCCGAGCGCGTTCAGGTGATCAACTAA