ViewGene

Locus Name:
GeneID:
Location:

GeneID:4427
TrivialName: PA14_17420
AnnotatorUID:
Modification Date/Time:2006-04-06 13:01:23
LocusName:PA14_17420
PAO1 Ortholog Locus:PA3627
Sequence Length:474
Protein Length:157
Start: 1495111
Stop: 1495584
Strand: +
Type:
ChromosomeID:2
Status: ACTIVE
Frame Discrepancy: FALSE
Missense Discrepancy:FALSE
Comments:
Homology: gb|AAG07015.1|AE004782_13 (AE004782) 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase [Pseudomonas aeruginosa PAO1]
Identities = 156/157 (99%), Positives = 156/157 (99%)
Sequence:
ATGCGAATTGGCCATGGCTACGACGTGCATCGCTTCGGCGAGGGCGACTTCATCACCCTCGGCGGCGTGCGC
ATTCCCCACAAACATGGGCTGGTCGCCCACTCCGACGGCGACGTGCTGCTGCACGCCTTGTCCGATGCGCTG
CTCGGCGCGGCGGCGCTGGGCGACATCGGCAAGCACTTCCCGGACACCGACCCGCGGTTCAAGGGCGCCGAC
AGTCGCGCGCTGCTGCGACACGTGGTCGCCATCGTCGCCGAGAAGGGCTGGAAGGTCGGCAACGTCGACGCC
ACCATCGTCGCCCAGGCACCGAAGATGGCGCCGCACATCGAAACCATGCGCGGGTCGATCGCCGAGGACCTC
GGCGTCGCGGTCGACCAGGTCAACGTCAAGGCCACCACTACCGAGCGGCTAGGTTTCACCGGACGCGAAGAG
GGCATTGCTGTACATGCGGTCGCTTTGCTGATGGCCCGATGA
Translation:
MRIGHGYDVHRFGEGDFITLGGVRIPHKHGLVAHSDGDVLLHALSDALLGAAALGDIGKHFPDTDPRFKGAD
SRALLRHVVAIVAEKGWKVGNVDATIVAQAPKMAPHIETMRGSIAEDLGVAVDQVNVKATTTERLGFTGREE
GIAVHAVALLMAR*
AnnotationID:4433GeneID:4427
AnnotatorUID: diggins
Modification Date/Time: 2005-06-24 19:07:40
Gene Name:ispF
Confidence Code:2
GeneProduct:2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
Cell Localization:()
Synonyms:ygbB
Cell Localization Confidence Code:5
MolecularFunction:
Functional Category:(4) Biosynthesis of cofactors, prosthetic groups and carriers
Alternate Gene Product Name:
Functional Category Confidence Code:5
COGs:COG0245,pfam02542
Secondary Functional Category(ies):fatty acid and phospholipid metabolism
EC Number:4.6.1.12
Status:ACTIVE
Pathway:
Isoprenoid biosynthesis; 
Isopentenyl-PP biosynthesis via DXP pathway; 
Isopentenyl-PP from 1-deoxy-D-xylulose 5-phosphate: step 4.
Homology:
>gb|AAN67239.1|AE016351_1 (AE016780) YgbB/YacN family protein [Pseudomonas putida KT2440]
          Length = 157

 Score =  281 bits (719), Expect = 9e-76
 Identities = 139/155 (89%), Positives = 147/155 (94%)

>gb|AAL21809.1| (AE008833) 2C-methyl-d-erythritol-2,4-cyclodiphosphate synthase
           [Salmonella typhimurium LT2]
          Length = 159

 Score =  219 bits (558), Expect = 4e-57
 Identities = 112/155 (72%), Positives = 125/155 (80%)

>gb|AAN81762.1|AE016765_164 (AE016765) 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
           [Escherichia coli CFT073]
          Length = 159

 Score =  217 bits (552), Expect = 2e-56
 Identities = 111/155 (71%), Positives = 124/155 (80%)
Structural Features:
COG0245, IspF, 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase 
[Lipid metabolism]
CD-Length = 159 residues,  97.5% aligned
Score =  240 bits (614), Expect = 1e-64
Identities = 109/155 (70%), Positives = 130/155 (83%)

pfam02542, YgbB, YgbB family. The ygbB protein is a 
putative enzyme of deoxy-xylulose pathway 
(terpenoid biosynthesis).
CD-Length = 157 residues,  98.7% aligned
Score =  209 bits (534), Expect = 2e-55
Identities = 95/155 (61%), Positives = 117/155 (75%)
Genomic Context:
Comment:
ReferenceID:8855
Author/Investigator(s): GenNotator
Title:
PubMed:
MedLine:
Source:
Reference Type:BLASTP
Data:
URL:
ReferenceID:25998
Author/Investigator(s): GenNotator
Title: CDD Search
PubMed:
MedLine:
Source:
Reference Type:RPSBLAST
Data:
URL:
ReferenceID:31915
Author/Investigator(s):
Title: CDD Search
PubMed:
MedLine:
Source:
Reference Type:Misc (text/plain)
Data:4427_cdd.html
URL:
ReferenceID:34182
Author/Investigator(s): Rohdich F, Wungsintaweekul J, Fellermeier M, Sagner S, Herz S, Kis K, Eisenreich W, Bacher A, Zenk MH.
Title: Cytidine 5'-triphosphate-dependent biosynthesis of isoprenoids: YgbP protein of Escherichia coli catalyzes the formation of 4-diphosphocytidyl-2-C-methylerythritol.
PubMed: 10518523
MedLine:
Source:
Proc Natl Acad Sci U S A. 1999 Oct 12;96(21):11758-63.
Reference Type:Journal
Data:
URL:http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=10518523
ReferenceID:34183
Author/Investigator(s): Campos N, Rodriguez-Concepcion M, Sauret-Gueto S, Gallego F, Lois LM, Boronat A.
Title: Escherichia coli engineered to synthesize isopentenyl diphosphate and dimethylallyl diphosphate from mevalonate: a novel system for the genetic analysis of the 2-C-methyl-d-erythritol 4-phosphate pathway for isoprenoid biosynthesis.
PubMed: 11115399
MedLine:
Source:
Biochem J. 2001 Jan 1;353(Pt 1):59-67.
Reference Type:Journal
Data:
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11115399
Homologs By Global Alignment
Gene ID:4427

Identity:

0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
HomologID Accession Description Length PctIdentity PctSimilarity Gaps Score
6768 PA3627_tr translation of PA3627 157 99.36 99.36 0 801.0
181239 gb|AAG07015.1|AE004782_13 (AE004782) 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase [Pseudomonas aeruginosa PAO1] 157 99.36 99.36 0 801.0
181240 gb|AAN67239.1|AE016351_1 (AE016780) YgbB/YacN family protein [Pseudomonas putida KT2440] 157 88.53 93.63 0 717.0
181241 gb|AAO55080.1| (AE016861) 2C-methyl-D-erythritol 2,4-cyclodiphosphate [Pseudomonas syringae pv. tomato str. DC3000] 157 84.71 89.80 0 682.0
181244 emb|CAD06035.1| (AL627276) 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase [Salmonella enterica subsp. enterica serovar Typhi] 159 70.44 77.98 2 554.0
GC ORFID: 47429How Found: BLASTX
GC_TrimmedSeqID: 69Blast Result ID
Subject Sequence Name: t_PA3627Glimmer Score:
Start: 3458826Stop: 3458353
Length: 474
Start Codon: ATGTruncated Start:
Stop Codon: TGATruncated Stop:
Homolog: t_PA3627 translation of PA3627Homolog Bit Score 313.0
Other Homologs: psyr_15may02_Scaffold3_revised_gene4646 (ORF: BLASTX 270.0), t_PA3627 (ORF: GLIMMER)
GC ORF Sequence
ATGCGAATTGGCCATGGCTACGACGTGCATCGCTTCGGCGAGGGCGACTTCATCACCCTCGGCGGCGTGCGC
ATTCCCCACAAACATGGGCTGGTCGCCCACTCCGACGGCGACGTGCTGCTGCACGCCTTGTCCGATGCGCTG
CTCGGCGCGGCGGCGCTGGGCGACATCGGCAAGCACTTCCCGGACACCGACCCGCGGTTCAAGGGCGCCGAC
AGTCGCGCGCTGCTGCGACACGTGGTCGCCATCGTCGCCGAGAAGGGCTGGAAGGTCGGCAACGTCGACGCC
ACCATCGTCGCCCAGGCACCGAAGATGGCGCCGCACATCGAAACCATGCGCGGGTCGATCGCCGAGGACCTC
GGCGTCGCGGTCGACCAGGTCAACGTCAAGGCCACCACTACCGAGCGGCTAGGTTTCACCGGACGCGAAGAG
GGCATTGCTGTACATGCGGTCGCTTTGCTGATGGCCCGATGA