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