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discounted EARLY registration ends Dec 31, 2014
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Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites MAYBE down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites MAYBE down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites MAYBE down
12/28 - 12/31
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Escherichia coli K-12 substr. MG1655 Polypeptide: putative sulfatase



Gene: ydeN Accession Numbers: G6788 (EcoCyc), b1498, ECK1492

Regulation Summary Diagram: ?

Summary:
No information about this protein was found by a literature search conducted on May 25, 2005.

Gene Citations: [Stringer14]

Locations: periplasmic space

Map Position: [1,578,866 <- 1,580,548] (34.03 centisomes)
Length: 1683 bp / 560 aa

Molecular Weight of Polypeptide: 62.802 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0004988 , DIP:DIP-11682N , EchoBASE:EB3557 , EcoGene:EG13796 , EcoliWiki:b1498 , ModBase:P77318 , OU-Microarray:b1498 , PortEco:ydeN , Pride:P77318 , Protein Model Portal:P77318 , RefSeq:NP_416015 , RegulonDB:G6788 , SMR:P77318 , String:511145.b1498 , UniProt:P77318

Relationship Links: InterPro:IN-FAMILY:IPR000917 , InterPro:IN-FAMILY:IPR017849 , InterPro:IN-FAMILY:IPR017850 , InterPro:IN-FAMILY:IPR024607 , Pfam:IN-FAMILY:PF00884 , Prosite:IN-FAMILY:PS00149 , Prosite:IN-FAMILY:PS00523

In Paralogous Gene Group: 299 (3 members)

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0008152 - metabolic process Inferred by computational analysis [GOA01a]
Molecular Function: GO:0003824 - catalytic activity Inferred by computational analysis [GOA01a]
GO:0008484 - sulfuric ester hydrolase activity Inferred by computational analysis [GOA01a]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11a]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0030288 - outer membrane-bounded periplasmic space Inferred from experiment Inferred by computational analysis [DiazMejia09, LopezCampistrou05]

MultiFun Terms: metabolism metabolism of other compounds sulfur metabolism

Essentiality data for ydeN knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]

Sequence Features

Feature Class Location Citations Comment
Signal-Sequence 1 -> 29
[UniProt10]
UniProt: Non-Experimental Qualifier: potential;
Chain 30 -> 560
[UniProt09]
UniProt: Uncharacterized sulfatase ydeN;
Metal-Binding-Site 66
[UniProt10]
UniProt: Calcium; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 67
[UniProt10]
UniProt: Calcium; Non-Experimental Qualifier: by similarity;
3-oxoalanine-Modification 132
[UniProt11a]
UniProt: 3-oxoalanine (Ser); Non-Experimental Qualifier: by similarity.
Metal-Binding-Site 132
[UniProt10]
UniProt: Calcium; via 3-oxoalanine; Non-Experimental Qualifier: by similarity;
Active-Site 185
[UniProt10]
UniProt: Non-Experimental Qualifier: potential;
Metal-Binding-Site 345
[UniProt10]
UniProt: Calcium; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 346
[UniProt10]
UniProt: Calcium; Non-Experimental Qualifier: by similarity;


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
Peter D. Karp on Wed Jan 18, 2006:
Gene right-end position adjusted based on analysis performed in the 2005 E. coli annotation update [Riley06 ].
Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


References

Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

LopezCampistrou05: Lopez-Campistrous A, Semchuk P, Burke L, Palmer-Stone T, Brokx SJ, Broderick G, Bottorff D, Bolch S, Weiner JH, Ellison MJ (2005). "Localization, annotation, and comparison of the Escherichia coli K-12 proteome under two states of growth." Mol Cell Proteomics 4(8);1205-9. PMID: 15911532

Riley06: Riley M, Abe T, Arnaud MB, Berlyn MK, Blattner FR, Chaudhuri RR, Glasner JD, Horiuchi T, Keseler IM, Kosuge T, Mori H, Perna NT, Plunkett G, Rudd KE, Serres MH, Thomas GH, Thomson NR, Wishart D, Wanner BL (2006). "Escherichia coli K-12: a cooperatively developed annotation snapshot--2005." Nucleic Acids Res 34(1);1-9. PMID: 16397293

Stringer14: Stringer AM, Currenti S, Bonocora RP, Baranowski C, Petrone BL, Palumbo MJ, Reilly AA, Zhang Z, Erill I, Wade JT (2014). "Genome-scale analyses of Escherichia coli and Salmonella enterica AraC reveal noncanonical targets and an expanded core regulon." J Bacteriol 196(3);660-71. PMID: 24272778

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt11a: UniProt Consortium (2011). "UniProt version 2011-11 released on 2011-11-22 00:00:00." Database.

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

Other References Related to Gene Regulation

Huerta03: Huerta AM, Collado-Vides J (2003). "Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals." J Mol Biol 333(2);261-78. PMID: 14529615

Oberto10: Oberto J (2010). "FITBAR: a web tool for the robust prediction of prokaryotic regulons." BMC Bioinformatics 11;554. PMID: 21070640


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 18.5 on Thu Dec 25, 2014, BIOCYC14A.