ViewGene

Locus Name:
GeneID:
Location:

GeneID:5215
TrivialName: PA14_30200
AnnotatorUID:
Modification Date/Time:2006-04-06 13:01:23
LocusName:PA14_30200
PAO1 Ortholog Locus:PA2622
Sequence Length:273
Protein Length:90
Start: 2616710
Stop: 2616438
Strand: -
Type:
ChromosomeID:2
Status: ACTIVE
Frame Discrepancy: FALSE
Missense Discrepancy:FALSE
Comments:
Homology: gb|AAG06010.1|AE004691_1 (AE004691) cold-shock protein CspD [Pseudomonas aeruginosa PAO1]
Identities = 90/90 (100%), Positives = 90/90 (100%)
Sequence:
ATGCTCAGCGGTAAGGTCAAGTGGTTCAACAACGCCAAGGGCTACGGGTTCATCCTGGCCGAGGGCCGAGAT
GAGGACCTGTTCGCCCATTACTCGGCCATTCAGATGGACGGTTACAAGACACTCAAGGCGGGCCAGCCGGTC
AATTTCGAGATCATCCAGGGACCGAAGGGACTGCATGCCATCAACATCAGCCCCGCCACCGCGACAACCGCC
GCACCCTCCGCCCCCGCCCCGCAGGAAGAGCCGCAGGCGACGCCCATCGAAGCCTGA
Translation:
MLSGKVKWFNNAKGYGFILAEGRDEDLFAHYSAIQMDGYKTLKAGQPVNFEIIQGPKGLHAINISPATATTA
APSAPAPQEEPQATPIEA*
AnnotationID:5220GeneID:5215
AnnotatorUID: diggins
Modification Date/Time: 2005-03-07 13:01:57
Gene Name:cspD
Confidence Code:2
GeneProduct: cold-shock protein CspD
Cell Localization:()
Synonyms:
Cell Localization Confidence Code:5
MolecularFunction:
Functional Category:(25) Transcriptional regulators
Alternate Gene Product Name:
Functional Category Confidence Code:5
COGs:pfam00313,COG1278
Secondary Functional Category(ies):adaptation, protection
EC Number:
Status:ACTIVE
Pathway:
Homology:
>gb|AAO56833.1| (AE016868) cold shock domain family protein [Pseudomonas syringae
          pv. tomato str. DC3000]
          Length = 89

 Score =  127 bits (319), Expect = 1e-29
 Identities = 62/85 (72%), Positives = 68/85 (80%), Gaps = 1/85 (1%)

>gb|AAN69604.1|AE016594_1 (AE016788) cold-shock protein CspD [Pseudomonas putida KT2440]
          Length = 88

 Score =  119 bits (299), Expect = 3e-27
 Identities = 61/90 (67%), Positives = 67/90 (74%), Gaps = 2/90 (2%)

>gb|AAN55657.1|AE015704_8 (AE015704) stress response protein CspD [Shewanella oneidensis
          MR-1]
          Length = 68

 Score =  102 bits (254), Expect = 5e-22
 Identities = 46/66 (69%), Positives = 54/66 (81%)

Structural Features:
pfam00313, CSD, 'Cold-shock' DNA-binding domain.
CD-Length = 67 residues,  98.5% aligned
Score =  103 bits (258), Expect = 4e-24
Identities = 35/66 (53%), Positives = 47/66 (71%)

COG1278, CspC, Cold shock proteins [Transcription]
CD-Length = 67 residues, 100.0% aligned
Score =  100 bits (250), Expect = 4e-23
Identities = 34/67 (50%), Positives = 43/67 (64%)
Genomic Context:
Comment:
ReferenceID:10430
Author/Investigator(s): GenNotator
Title:
PubMed:
MedLine:
Source:
Reference Type:BLASTP
Data:
URL:
ReferenceID:27575
Author/Investigator(s): GenNotator
Title: CDD Search
PubMed:
MedLine:
Source:
Reference Type:RPSBLAST
Data:
URL:
ReferenceID:33184
Author/Investigator(s):
Title: CDD Search
PubMed:
MedLine:
Source:
Reference Type:Misc (text/plain)
Data:5215_cdd.html
URL:
ReferenceID:34559
Author/Investigator(s): Wouters JA, Sanders JW, Kok J, de Vos WM, Kuipers OP, Abee T.
Title: Clustered organization and transcriptional analysis of a family of five csp genes of Lactococcus lactis MG1363.
PubMed: 9802030
MedLine:
Source:
Microbiology. 1998 Oct;144 ( Pt 10):2885-93.
Reference Type:Journal
Data:
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=9802030
ReferenceID:34560
Author/Investigator(s): Lang EA, Marques MV.
Title: Identification and transcriptional control of Caulobacter crescentus genes encoding proteins containing a cold shock domain.
PubMed: 15317764
MedLine:
Source:
J Bacteriol. 2004 Sep;186(17):5603-13.
Reference Type:Journal
Data:
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15317764
Homologs By Global Alignment
Gene ID:5215

Identity:

0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
HomologID Accession Description Length PctIdentity PctSimilarity Gaps Score
7626 PA2622_tr translation of PA2622 90 99.99 99.99 0 471.0
195106 gb|AAG06010.1|AE004691_1 (AE004691) cold-shock protein CspD [Pseudomonas aeruginosa PAO1] 90 99.99 99.99 0 471.0
195107 gb|AAO56833.1| (AE016868) cold shock domain family protein [Pseudomonas syringae pv. tomato str. DC3000] 91 68.13 74.72 3 316.0
195108 gb|AAN69604.1|AE016594_1 (AE016788) cold-shock protein CspD [Pseudomonas putida KT2440] 90 67.77 74.44 2 301.0
195113 emb|CAC90195.1| (AJ414148) cold shock-like protein [Yersinia pestis CO92] 91 53.84 63.73 5 242.0
GC ORFID: 48217How Found: BLASTX
GC_TrimmedSeqID: 69Blast Result ID
Subject Sequence Name: t_PA2622Glimmer Score:
Start: 2337216Stop: 2337488
Length: 273
Start Codon: ATGTruncated Start:
Stop Codon: TGATruncated Stop:
Homolog: t_PA2622 translation of PA2622Homolog Bit Score 186.0
Other Homologs: psyr_15may02_Scaffold17_revised_gene2752 (ORF: BLASTX 104.0), t_PA2622 (ORF: GLIMMER)
GC ORF Sequence
ATGCTCAGCGGTAAGGTCAAGTGGTTCAACAACGCCAAGGGCTACGGGTTCATCCTGGCCGAGGGCCGAGAT
GAGGACCTGTTCGCCCATTACTCGGCCATTCAGATGGACGGTTACAAGACACTCAAGGCGGGCCAGCCGGTC
AATTTCGAGATCATCCAGGGACCGAAGGGACTGCATGCCATCAACATCAGCCCCGCCACCGCGACAACCGCC
GCACCCTCCGCCCCCGCCCCGCAGGAAGAGCCGCAGGCGACGCCCATCGAAGCCTGA