Difference between revisions of "RibU"
(New page: * '''Description:''' write here <br/><br/> {| align="right" border="1" cellpadding="2" |- |style="background:#ABCDEF;" align="center"|'''Gene name''' |''ypaA'' |- |style="background:#ABC...) |
|||
(58 intermediate revisions by 7 users not shown) | |||
Line 1: | Line 1: | ||
− | * '''Description:''' | + | * '''Description:''' riboflavin [[ECF transporter]], S protein <br/><br/> |
{| align="right" border="1" cellpadding="2" | {| align="right" border="1" cellpadding="2" | ||
|- | |- | ||
|style="background:#ABCDEF;" align="center"|'''Gene name''' | |style="background:#ABCDEF;" align="center"|'''Gene name''' | ||
− | |'' | + | |''ribU '' |
|- | |- | ||
− | |style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' '' | + | |style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ypaA'' |
|- | |- | ||
− | |style="background:#ABCDEF;" align="center"| '''Essential''' || | + | |style="background:#ABCDEF;" align="center"| '''Essential''' || no |
|- | |- | ||
− | |style="background:#ABCDEF;" align="center"| '''Product''' || | + | |style="background:#ABCDEF;" align="center"| '''Product''' || S protein of riboflavin [[ECF transporter]] |
|- | |- | ||
− | |style="background:#ABCDEF;" align="center"|'''Function''' || | + | |style="background:#ABCDEF;" align="center"|'''Function''' || riboflavin uptake |
+ | |- | ||
+ | |colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU23050 ribU] | ||
+ | |- | ||
+ | |colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=RibU RibU] | ||
+ | |- | ||
+ | |colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=ribU ribU]''' | ||
|- | |- | ||
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 20 kDa, 10.12 | |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 20 kDa, 10.12 | ||
Line 18: | Line 24: | ||
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 570 bp, 190 aa | |style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 570 bp, 190 aa | ||
|- | |- | ||
− | |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || | + | |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[fer]]'', ''[[ypzE]]'' |
|- | |- | ||
− | |style="background:#FAF8CC;" align="center"|'''[http:// | + | |style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU23050 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU23050 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU23050 DNA_with_flanks] |
− | |||
|- | |- | ||
|colspan="2" | '''Genetic context''' <br/> [[Image:ypaA_context.gif]] | |colspan="2" | '''Genetic context''' <br/> [[Image:ypaA_context.gif]] | ||
+ | <div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div> | ||
+ | |- | ||
+ | |colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=fmnP_2410017_2410589_-1 Expression at a glance]'''   {{PubMed|22383849}}<br/>[[Image:ribU_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU23050]] | ||
|- | |- | ||
|} | |} | ||
__TOC__ | __TOC__ | ||
+ | <br/><br/><br/><br/> | ||
+ | <br/><br/><br/><br/> | ||
+ | <br/><br/><br/><br/> | ||
+ | <br/><br/> | ||
− | + | = [[Categories]] containing this gene/protein = | |
+ | {{SubtiWiki category|[[ECF transporter]]}}, | ||
+ | {{SubtiWiki category|[[biosynthesis of cofactors]]}}, | ||
+ | {{SubtiWiki category|[[membrane proteins]]}} | ||
+ | |||
+ | = This gene is a member of the following [[regulons]] = | ||
+ | {{SubtiWiki regulon|[[FMN-box]]}} | ||
=The gene= | =The gene= | ||
Line 35: | Line 53: | ||
=== Basic information === | === Basic information === | ||
− | * ''' | + | * '''Locus tag:''' BSU23050 |
===Phenotypes of a mutant === | ===Phenotypes of a mutant === | ||
=== Database entries === | === Database entries === | ||
+ | * '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU23050&redirect=T BSU23050] | ||
− | * '''DBTBS entry:''' | + | * '''DBTBS entry:''' no entry |
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11428] | * '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11428] | ||
=== Additional information=== | === Additional information=== | ||
− | |||
=The protein= | =The protein= | ||
Line 62: | Line 80: | ||
* '''Kinetic information:''' | * '''Kinetic information:''' | ||
− | * '''Domains:''' | + | * '''[[Domains]]:''' |
* '''Modification:''' | * '''Modification:''' | ||
− | * ''' | + | * '''[[Cofactors]]:''' |
* '''Effectors of protein activity:''' | * '''Effectors of protein activity:''' | ||
− | * '''Interactions:''' | + | * '''[[SubtInteract|Interactions]]:''' |
+ | ** [[YbaF]]-[[RibU]] {{PubMed|20497229}} | ||
− | * '''Localization:''' | + | * '''[[Localization]]:''' membrane |
=== Database entries === | === Database entries === | ||
+ | * '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU23050&redirect=T BSU23050] | ||
− | * '''Structure:''' | + | * '''Structure:''' [http://www.pdb.org/pdb/explore/explore.do?structureId=3P5N 3P5N] (RibU from ''Staphylococcus aureus'') |
− | * ''' | + | * '''UniProt:''' [http://www.uniprot.org/uniprot/P50726 P50726] |
− | * '''KEGG entry:''' | + | * '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU23050] |
* '''E.C. number:''' | * '''E.C. number:''' | ||
Line 88: | Line 108: | ||
=Expression and regulation= | =Expression and regulation= | ||
− | * '''Operon:''' | + | * '''Operon:''' ''[[ribU]]'' {{PubMed|21815947}} |
+ | ** there is a promoter directly in front of ''[[ribU]]'' {{PubMed|17693491}} | ||
+ | |||
+ | * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=fmnP_2410017_2410589_-1 ribU] {{PubMed|22383849}} | ||
− | * '''Sigma factor:''' | + | * '''[[Sigma factor]]:''' |
− | * '''Regulation:''' | + | * '''Regulation:''' expressed in the absence of FMN ([[FMN-box]]) {{PubMed|17693491}} |
− | * '''Regulatory mechanism:''' | + | * '''Regulatory mechanism:''' [[FMN-box]]: [[riboswitch]], controls access of the ribosome to the Shine-Dalgarno sequence {{PubMed|12456892}} |
− | * '''Additional information:''' | + | * '''Additional information:''' |
+ | ** the mRNA is substantially stabilized upon depletion of [[Rny|RNase Y]] {{PubMed|21815947}} | ||
=Biological materials = | =Biological materials = | ||
− | * '''Mutant:''' | + | * '''Mutant:''' |
* '''Expression vector:''' | * '''Expression vector:''' | ||
Line 117: | Line 141: | ||
=References= | =References= | ||
+ | ==Reviews== | ||
+ | <pubmed> 20497229 22574898 24362466 </pubmed> | ||
+ | ==Original publications== | ||
+ | <pubmed>12456892, 20972419,17693491,21815947 24356467 24755604 25438558 </pubmed> | ||
− | + | [[Category:Protein-coding genes]] |
Latest revision as of 18:10, 5 December 2014
- Description: riboflavin ECF transporter, S protein
Gene name | ribU |
Synonyms | ypaA |
Essential | no |
Product | S protein of riboflavin ECF transporter |
Function | riboflavin uptake |
Gene expression levels in SubtiExpress: ribU | |
Interactions involving this protein in SubtInteract: RibU | |
Metabolic function and regulation of this protein in SubtiPathways: ribU | |
MW, pI | 20 kDa, 10.12 |
Gene length, protein length | 570 bp, 190 aa |
Immediate neighbours | fer, ypzE |
Sequences | Protein DNA DNA_with_flanks |
Genetic context This image was kindly provided by SubtiList
| |
Expression at a glance PubMed 500px |
Contents
Categories containing this gene/protein
ECF transporter, biosynthesis of cofactors, membrane proteins
This gene is a member of the following regulons
The gene
Basic information
- Locus tag: BSU23050
Phenotypes of a mutant
Database entries
- BsubCyc: BSU23050
- DBTBS entry: no entry
- SubtiList entry: [1]
Additional information
The protein
Basic information/ Evolution
- Catalyzed reaction/ biological activity:
- Protein family:
- Paralogous protein(s):
Extended information on the protein
- Kinetic information:
- Modification:
- Effectors of protein activity:
- Localization: membrane
Database entries
- BsubCyc: BSU23050
- Structure: 3P5N (RibU from Staphylococcus aureus)
- UniProt: P50726
- KEGG entry: [2]
- E.C. number:
Additional information
Expression and regulation
- Regulatory mechanism: FMN-box: riboswitch, controls access of the ribosome to the Shine-Dalgarno sequence PubMed
Biological materials
- Mutant:
- Expression vector:
- lacZ fusion:
- GFP fusion:
- two-hybrid system:
- Antibody:
Labs working on this gene/protein
Your additional remarks
References
Reviews
Original publications