ViewGene
Locus Name:
GeneID:
Location:

GeneID:5396
TrivialName: PA14_21760
AnnotatorUID:
Modification Date/Time:2006-04-06 13:01:23
LocusName:PA14_21760
PAO1 Ortholog Locus:PA3266
Sequence Length:210
Protein Length:69
Start: 1893556
Stop: 1893347
Strand: -
Type:
ChromosomeID:2
Status: ACTIVE
Frame Discrepancy: FALSE
Missense Discrepancy:FALSE
Comments:
Homology: gb|AAG06654.1|AE004749_3 (AE004749) cold acclimation protein B [Pseudomonas aeruginosa PAO1]
Identities = 68/69 (98%), Positives = 69/69 (100%)
Sequence:
ATGTCGAATCGTCAGAACGGCACCGTAAAATGGTTCAACGACGCCAAAGGCTTCGGCTTCATCACCCCGGAA
AGCGGTAACGACCTGTTCGTTCACTTCCGTTCCATCCAGGGCACCGGCTTCAAGAGCCTGCAGGAAGGCCAG
AAGGTTTCCTTCGTGGTCGTCAACGGCCAGAAAGGCCTGCAAGCCGACGAAGTACAAGTTATCTAA
Translation:
MSNRQNGTVKWFNDAKGFGFITPESGNDLFVHFRSIQGTGFKSLQEGQKVSFVVVNGQKGLQADEVQVI*
AnnotationID:5401GeneID:5396
AnnotatorUID: diggins
Modification Date/Time: 2005-04-14 17:05:53
Gene Name:capB
Confidence Code:2
GeneProduct: cold acclimation protein B
Cell Localization:()
Synonyms:cspA
Cell Localization Confidence Code:5
MolecularFunction:
Functional Category:(1) Adaptation, protection
Alternate Gene Product Name:major cold shock protein
Functional Category Confidence Code:5
COGs:smart00357,pfam00313,COG1278
Secondary Functional Category(ies):transcriptional regulator
EC Number:
Status:ACTIVE
Pathway:






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

 Score =  127 bits (318), Expect = 2e-29
 Identities = 59/69 (85%), Positives = 64/69 (92%)

>gb|AAO54799.1| (AE016860) cold shock domain family protein [Pseudomonas syringae
          pv. tomato str. DC3000]
          Length = 70

 Score =  117 bits (293), Expect = 1e-26
 Identities = 54/66 (81%), Positives = 60/66 (90%)

>dbj|BAC60152.1| (AP005079) cold shock transcriptional regulator CspA [Vibrio
          parahaemolyticus]
          Length = 70

 Score =  100 bits (248), Expect = 2e-21
 Identities = 48/70 (68%), Positives = 58/70 (82%), Gaps = 1/70 (1%)






 
Structural Features:
smart00357, CSP, Cold shock protein domain
CD-Length = 62 residues, 100.0% aligned
Score = 57.1 bits (138), Expect = 4e-10
Identities = 33/66 (50%), Positives = 42/66 (63%), Gaps = 7/66 (10%)

pfam00313, CSD, 'Cold-shock' DNA-binding domain.
CD-Length = 67 residues, 100.0% aligned
Score = 88.7 bits (220), Expect = 1e-19
Identities = 42/67 (62%), Positives = 50/67 (74%), Gaps = 1/67 (1%)

COG1278, CspC, Cold shock proteins [Transcription]
CD-Length = 67 residues, 100.0% aligned
Score = 94.1 bits (234), Expect = 2e-21
Identities = 38/67 (56%), Positives = 46/67 (68%), Gaps = 1/67 (1%)






   
Genomic Context:






   
Comment:


















    ReferenceID:10790




  
Author/Investigator(s):
        GenNotator





  
Title:
        




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:BLASTP 







    
Data:


    		




 
URL:

















    ReferenceID:27939




  
Author/Investigator(s):
        GenNotator





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:RPSBLAST 







    
Data:


    		




 
URL:

















    ReferenceID:32277




  
Author/Investigator(s):
        





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:Misc (text/plain)







    
Data:5396_cdd.html


    		




 
URL:

















    ReferenceID:34006




  
Author/Investigator(s):
        Makino S, Uchida I, Terakado N, Sasakawa C, Yoshikawa M.





  
Title:
        Molecular characterization and protein analysis of the cap region, which is essential for encapsulation in Bacillus anthracis.




  
PubMed:
        2536679


MedLine:
        




    
Source:
J Bacteriol. 1989 Feb;171(2):722-30.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=2536679

















    ReferenceID:34007




  
Author/Investigator(s):
        Jones PG, Inouye M.





  
Title:
        The cold-shock response--a hot topic.




  
PubMed:
        8022259


MedLine:
        




    
Source:
Mol Microbiol. 1994 Mar;11(5):811-8.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=8022259

















    ReferenceID:34008




  
Author/Investigator(s):
        Schroder K, Zuber P, Willimsky G, Wagner B, Marahiel MA.





  
Title:
        Mapping of the Bacillus subtilis cspB gene and cloning of its homologs in thermophilic, mesophilic and psychrotrophic bacilli.




  
PubMed:
        8294017


MedLine:
        




    
Source:
Gene. 1993 Dec 22;136(1-2):277-80.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=8294017

















    ReferenceID:34009




  
Author/Investigator(s):
        Peyret JL, Bayan N, Joliff G, Gulik-Krzywicki T, Mathieu L, Schechter E, Leblon G.





  
Title:
        Characterization of the cspB gene encoding PS2, an ordered surface-layer protein in Corynebacterium glutamicum.




  
PubMed:
        8412676


MedLine:
        




    
Source:
Mol Microbiol. 1993 Jul;9(1):97-109.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=8412676

















    ReferenceID:34010




  
Author/Investigator(s):
        Willimsky G, Bang H, Fischer G, Marahiel MA.





  
Title:
        Characterization of cspB, a Bacillus subtilis inducible cold shock gene affecting cell viability at low temperatures.




  
PubMed:
        1400185


MedLine:
        




    
Source:
J Bacteriol. 1992 Oct;174(20):6326-35.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=1400185

















    ReferenceID:34011




  
Author/Investigator(s):
        Etchegaray JP, Inouye M.





  
Title:
        A sequence downstream of the initiation codon is essential for cold shock induction of cspB of Escherichia coli.




  
PubMed:
        10482531


MedLine:
        




    
Source:
J Bacteriol. 1999 Sep;181(18):5852-4.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10482531

















    ReferenceID:34012




  
Author/Investigator(s):
        Phadtare S, Inouye M.





  
Title:
        Sequence-selective interactions with RNA by CspB, CspC and CspE, members of the CspA family of Escherichia coli.




  
PubMed:
        10476034


MedLine:
        




    
Source:
Mol Microbiol. 1999 Sep;33(5):1004-14.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10476034









           
Homologs By Global Alignment 

           

       



     
Gene ID:5396
           
Identity:

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

                           

     
HomologID
                           Accession
                           Description
                           Length
                           PctIdentity
                           PctSimilarity
                           Gaps
                           Score
     

     
     
7792
                           PA3266_tr
                           translation of PA3266
                           69
                           98.55
                           99.99
                           0
                           358.0
     

     
     
196406
                           gb|AAG06654.1|AE004749_3
                           (AE004749) cold acclimation protein B [Pseudomonas aeruginosa PAO1]
                           69
                           98.55
                           99.99
                           0
                           358.0
     

     
     
196407
                           gb|AAB40922.1|
                           (U82822) major cold shock protein CspA [Pseudomonas aeruginosa]
                           69
                           98.55
                           99.99
                           0
                           358.0
     

     
     
196408
                           gb|AAM41566.1|
                           (AE012336) major cold shock protein [Xanthomonas campestris pv. campestris str. ATCC 33913]
                           69
                           85.50
                           92.75
                           0
                           318.0
     

     
     
196409
                           gb|AAM37247.1|
                           (AE011876) major cold shock protein [Xanthomonas axonopodis pv. citri str. 306]
                           69
                           84.05
                           92.75
                           0
                           314.0
     

     






      

          
GC ORFID: 48398How Found: BLASTX

          
GC_TrimmedSeqID: 69Blast Result ID

          
Subject Sequence Name: t_PA3266Glimmer Score: 

          
Start: 3060375Stop: 3060584

          
Length: 210


          
Start Codon: ATGTruncated Start:

          
Stop Codon: TAATruncated Stop: 

          
Homolog: t_PA3266 translation of PA3266Homolog Bit Score 142.0

          
Other Homologs:  psyr_15may02_Scaffold3_revised_gene4968 (ORF: BLASTX 119.0), psyr_15may02_Scaffold5_revised_gene6109 (ORF: BLASTX 117.0), t_PA0456 (ORF: BLASTX 112.0), psyr_15may02_Scaffold1_revised_gene302 (ORF: BLASTX 108.0), t_PA3266 (ORF: GLIMMER)

          
GC ORF Sequence

           
ATGTCGAATCGTCAGAACGGCACCGTAAAATGGTTCAACGACGCCAAAGGCTTCGGCTTCATCACCCCGGAA 
AGCGGTAACGACCTGTTCGTTCACTTCCGTTCCATCCAGGGCACCGGCTTCAAGAGCCTGCAGGAAGGCCAG 
AAGGTTTCCTTCGTGGTCGTCAACGGCCAGAAAGGCCTGCAAGCCGACGAAGTACAAGTTATCTAA