Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
twitter

Escherichia coli K-12 substr. MG1655 Polypeptide: predicted chloramphenicol resistance permease



Gene: rarD Accession Numbers: EG11466 (EcoCyc), b3819, ECK3813

Synonyms: yigH

Regulation Summary Diagram: ?

Summary:
RarD is an inner membrane protein with nine predicted transmembrane domains. The C terminus is located in the cytoplasm [Daley05].
ArcA appears to activate rarD gene expression under anaerobiosis. A putative ArcA binding site was identified 560 bp upstream of this gene [Salmon05]; but no promoter upstream of it has been identified.

Locations: inner membrane

Map Position: [4,001,311 <- 4,002,201] (86.24 centisomes)
Length: 891 bp / 296 aa

Molecular Weight of Polypeptide: 33.283 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0012472 , EchoBASE:EB1434 , EcoGene:EG11466 , EcoliWiki:b3819 , OU-Microarray:b3819 , PortEco:rarD , PR:PRO_000023679 , Protein Model Portal:P27844 , RefSeq:YP_026262 , RegulonDB:EG11466 , String:511145.b3819 , UniProt:P27844

Relationship Links: InterPro:IN-FAMILY:IPR000620 , InterPro:IN-FAMILY:IPR004626 , Pfam:IN-FAMILY:PF00892

GO Terms:

Biological Process: GO:0006810 - transport Inferred by computational analysis [UniProtGOA11a, GOA01a]
Molecular Function: GO:0005215 - transporter activity Inferred by computational analysis [GOA01a]
Cellular Component: GO:0005886 - plasma membrane Inferred from experiment Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, DiazMejia09, Daley05]
GO:0016021 - integral component of membrane Inferred from experiment Inferred by computational analysis [UniProtGOA11a, Daley05]
GO:0005887 - integral component of plasma membrane Inferred by computational analysis [GOA01a]
GO:0016020 - membrane Inferred by computational analysis [UniProtGOA11a, GOA01a]

MultiFun Terms: transport Putative uncharacterized transport protein

Essentiality data for rarD 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]

Credits:
Last-Curated ? 12-Oct-2006 by Keseler I , SRI International


Sequence Features

Feature Class Location Citations Comment
Transmembrane-Region 12 -> 34
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Conserved-Region 18 -> 145
[UniProt09]
UniProt: DUF6;
Transmembrane-Region 38 -> 60
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 73 -> 95
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 100 -> 122
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Sequence-Conflict 102
[Daniels92, UniProt10]
Alternate sequence: A → R; UniProt: (in Ref. 2; AAA67615);
Sequence-Conflict 123 -> 124
[Daniels92, UniProt10]
Alternate sequence: ER → DG; UniProt: (in Ref. 2; AAA67615);
Transmembrane-Region 129 -> 146
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 150 -> 167
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 180 -> 197
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 212 -> 234
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 239 -> 261
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 271 -> 290
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
Suzanne Paley on Thu Oct 21, 2004:
Position updated based on U00096.2 release of genome
10/20/97 Gene b3819 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11466; confirmed by SwissProt match.


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

Daley05: Daley DO, Rapp M, Granseth E, Melen K, Drew D, von Heijne G (2005). "Global topology analysis of the Escherichia coli inner membrane proteome." Science 308(5726);1321-3. PMID: 15919996

Daniels92: Daniels DL, Plunkett G, Burland V, Blattner FR (1992). "Analysis of the Escherichia coli genome: DNA sequence of the region from 84.5 to 86.5 minutes." Science 1992;257(5071);771-8. PMID: 1379743

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

Salmon05: Salmon KA, Hung SP, Steffen NR, Krupp R, Baldi P, Hatfield GW, Gunsalus RP (2005). "Global gene expression profiling in Escherichia coli K12: effects of oxygen availability and ArcA." J Biol Chem 280(15);15084-96. PMID: 15699038

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

UniProt10: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

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


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 Fri Nov 28, 2014, biocyc11.