ViewGene
Locus Name:
GeneID:
Location:

GeneID:4954
TrivialName: PA14_51840
AnnotatorUID:
Modification Date/Time:2006-04-06 13:01:23
LocusName:PA14_51840
PAO1 Ortholog Locus:
Sequence Length:615
Protein Length:204
Start: 4604200
Stop: 4604814
Strand: +
Type:
ChromosomeID:2
Status: ACTIVE
Frame Discrepancy: FALSE
Missense Discrepancy:FALSE
Comments:
Homology: gb|AAN66833.1|AE016312_4 (AE016778) cold-shock domain family protein [Pseudomonas putida KT2440]
Identities = 64/74 (86%), Positives = 71/74 (95%)
Sequence:
ATGTTGAAAATCGTCCTTCTGGTCACGGGCGTCGCCGCCCTATTGCTGTCCTTCATTCCCAGCCTAAGAACC
GAAGCCACACCCTTCCTGCAACATCCCGATGCCATCTACCTGGCCATTCTGGGCCTGATCAACCTGCTCTTC
GCTCCCGTACTGCAATCGTCACATCCAACCCGCCCGCTGCAGGCCGGCGCAGCCGCCCTGCTGGTCCTGGGC
GTCGTCCTGCAGGCACTGATCCTGCTGGCGCCGCTGCCGACCATCGCCGACCAGCCGGCGATCGTCCTGCCC
CTGCTAAGCCTGGTGCTGGCCACGGCCCTGCAACTGGCGGGCAGCCTGAAGCCCGGCAAACCGGTCTCGCGC
AGCGCCAGCGCCCCGACGGCCCTCGGCGGCAGCCAGGACAGCGGCAACCGGGAGACCGGTACCGTGAAGTGG
TTCAACACCTCAAAAGGTTTCGGCTTCATTTCCCGCGATTCGGGCGAGGACATCTTCGTCCACTTCCGAGCG
ATTCGCGGCGAAGGCCACCGCATCCTCATCGAAGGCCAGCGCGTGGAGTTCTCGGTGGTACAACGGGACAAG
GGCCTGCAGGCGGAAGACGTAATCGCCTCCCGCCGCTGA
Translation:
MLKIVLLVTGVAALLLSFIPSLRTEATPFLQHPDAIYLAILGLINLLFAPVLQSSHPTRPLQAGAAALLVLG
VVLQALILLAPLPTIADQPAIVLPLLSLVLATALQLAGSLKPGKPVSRSASAPTALGGSQDSGNRETGTVKW
FNTSKGFGFISRDSGEDIFVHFRAIRGEGHRILIEGQRVEFSVVQRDKGLQAEDVIASRR*
AnnotationID:4959GeneID:4954
AnnotatorUID: danlee
Modification Date/Time: 2006-03-17 13:01:10
Gene Name:
Confidence Code:3
GeneProduct:probable cold-shock protein
Cell Localization:(1) Cytoplasmic
Synonyms:
Cell Localization Confidence Code:5
MolecularFunction:
Functional Category:(25) Transcriptional regulators
Alternate Gene Product Name:
Functional Category Confidence Code:5
COGs:
Secondary Functional Category(ies):
EC Number:
Status:ACTIVE
Pathway:






 
Homology:
gi|84316572|ref|ZP_00965045.1|  COG1278: Cold shock proteins [Pseudomonas aeruginosa C3719]
Length=204

 Score =  387 bits (994),  Expect = 1e-106
 Identities = 203/204 (99%), Positives = 203/204 (99%), Gaps = 0/204 (0%)

gi|84322547|ref|ZP_00970632.1|  COG1278: Cold shock proteins [Pseudomonas aeruginosa 2192]
Length=170

 Score =  303 bits (777),  Expect = 2e-81
 Identities = 157/159 (98%), Positives = 158/159 (99%), Gaps = 0/159 (0%)

gi|77384639|gb|ABA76152.1|  Cold-shock DNA-binding protein [Pseudomonas fluorescens PfO-1]
 gi|77460636|ref|YP_350143.1|  Cold-shock DNA-binding protein [Pseudomonas fluorescens PfO-1]
Length=200

 Score =  241 bits (616),  Expect = 9e-63
 Identities = 130/204 (63%), Positives = 155/204 (75%), Gaps = 10/204 (4%)

gi|9946868|gb|AAG04350.1|  probable cold-shock protein [Pseudomonas aeruginosa PAO1]
 gi|15596158|ref|NP_249652.1|  probable cold-shock protein [Pseudomonas aeruginosa PAO1]
Length=63

 Score =  127 bits (320),  Expect = 2e-28
 Identities = 62/63 (98%), Positives = 63/63 (100%), Gaps = 0/63 (0%)






 
Structural Features:
pfam00313, CSD, 'Cold-shock' DNA-binding domain..
             CD-Length = 67 residues, 100.0% aligned
             Score = 97.6 bits (243), Expect = 9e-22

smart00357, CSP, Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone
in bacteria and is involved in regulating translation in eukaryotes. Contains sub-family of RNA-binding
domains in the Rho transcription termination factor. .
             CD-Length = 62 residues,  96.8% aligned
             Score = 59.5 bits (144), Expect = 3e-10






   
Genomic Context:






   
Comment:
C-terminal 63 amino acids (142-204) are 62/63=98% identical to PAO1 PA0961 
(additional 141 amino acid N-termius).
NOTE that PAO1 does contain a predicted ORF with an earlier start site that would 
correspond to the entire length of 4954 (PA14_51840).


















    ReferenceID:9908




  
Author/Investigator(s):
        GenNotator





  
Title:
        




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:BLASTP 







    
Data:


    		




 
URL:

















    ReferenceID:27049




  
Author/Investigator(s):
        GenNotator





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:RPSBLAST 







    
Data:


    		




 
URL:









           
Homologs By Global Alignment 

           

       



     
Gene ID:4954
           
Identity:

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

                           

     
HomologID
                           Accession
                           Description
                           Length
                           PctIdentity
                           PctSimilarity
                           Gaps
                           Score
     

     
     
191094
                           gb|AAN66833.1|AE016312_4
                           (AE016778) cold-shock domain family protein [Pseudomonas putida KT2440]
                           208
                           32.21
                           36.53
                           121
                           341.0
     

     
     
7359
                           PA0961_tr
                           translation of PA0961
                           204
                           30.88
                           30.88
                           141
                           323.0
     

     
     
191095
                           gb|AAO57443.1|
                           (AE016870) cold shock domain family protein [Pseudomonas syringae pv. tomato str. DC3000]
                           206
                           30.58
                           33.49
                           135
                           330.0
     

     
     
191096
                           gb|AAG04350.1|AE004530_3
                           (AE004530) probable cold-shock protein [Pseudomonas aeruginosa PAO1]
                           204
                           30.39
                           30.88
                           141
                           320.0
     

     
     
7360
                           PA1159_tr
                           translation of PA1159
                           204
                           24.01
                           27.94
                           135
                           267.0
     

     






      

          
GC ORFID: 47956How Found: BLASTX

          
GC_TrimmedSeqID: 69Blast Result ID

          
Subject Sequence Name: psyr_15may02_Scaffold3_revised_gene4760Glimmer Score: 

          
Start: 349707Stop: 349093

          
Length: 615


          
Start Codon: ATGTruncated Start:

          
Stop Codon: TGATruncated Stop: 

          
Homolog: psyr_15may02_Scaffold3_revised_gene4760 related to: gi|15596158|ref|NP_249652.1| (NC_002516) probable cold-shock protein [Pseudomonas aeruginosa] pir||C83524 probable cold-shock protein PA0961 [imported] - Pseudomonas aeruginosa (strain PAO1) gb|AAG04350.Homolog Bit Score 233.0

          
Other Homologs:  t_PA0961 (ORF: BLASTX 129.0), t_PA1159 (ORF: BLASTX 109.0), psyr_15may02_Scaffold3_revised_gene4760 (ORF: GLIMMER)

          
GC ORF Sequence

           
ATGTTGAAAATCGTCCTTCTGGTCACGGGCGTCGCCGCCCTATTGCTGTCCTTCATTCCCAGCCTAAGAACC 
GAAGCCACACCCTTCCTGCAACATCCCGATGCCATCTACCTGGCCATTCTGGGCCTGATCAACCTGCTCTTC 
GCTCCCGTACTGCAATCGTCACATCCAACCCGCCCGCTGCAGGCCGGCGCAGCCGCCCTGCTGGTCCTGGGC 
GTCGTCCTGCAGGCACTGATCCTGCTGGCGCCGCTGCCGACCATCGCCGACCAGCCGGCGATCGTCCTGCCC 
CTGCTAAGCCTGGTGCTGGCCACGGCCCTGCAACTGGCGGGCAGCCTGAAGCCCGGCAAACCGGTCTCGCGC 
AGCGCCAGCGCCCCGACGGCCCTCGGCGGCAGCCAGGACAGCGGCAACCGGGAGACCGGTACCGTGAAGTGG 
TTCAACACCTCAAAAGGTTTCGGCTTCATTTCCCGCGATTCGGGCGAGGACATCTTCGTCCACTTCCGAGCG 
ATTCGCGGCGAAGGCCACCGCATCCTCATCGAAGGCCAGCGCGTGGAGTTCTCGGTGGTACAACGGGACAAG 
GGCCTGCAGGCGGAAGACGTAATCGCCTCCCGCCGCTGA