SubtiWiki - User contributions [en]

XylB

2011-05-10T11:47:31Z

Evdannies: /* Biological materials */

* '''Description:''' xylulokinase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''xylB''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yncA ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || xylulokinase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || utilization of xylan and xylose
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbohydrate_metabolic_pathways.html Sugar catabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 55 kDa, 6.459
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1497 bp, 499 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[xylA]]'', ''[[yncB]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB13645]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:xylB_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[utilization of specific carbon sources]]}}

= This gene is a member of the following [[regulons]] =
{{SubtiWiki regulon|[[CcpA regulon]]}},
{{SubtiWiki regulon|[[XylR regulon]]}}

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU17610

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/xylAB.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10807]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' ATP + D-xylulose = ADP + D-xylulose 5-phosphate (according to Swiss-Prot)

* '''Protein family:''' FGGY kinase family (according to Swiss-Prot)

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=2NLX 2NLX] (from ''E. coli'', 35% identity, 52% similarity) {{PubMed|17123542}}

* '''UniProt:''' [http://www.uniprot.org/uniprot/P39211 P39211]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU17610]

* '''E.C. number:''' [http://www.expasy.org/enzyme/2.7.1.17 2.7.1.17]

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[xylA]]-[[xylB]]'' {{PubMed|1921970}}

* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|2454911}}

* '''Regulation:'''
** carbon catabolite repression ([[CcpA]]) {{PubMed|8132469}}
** induction by xylose ([[XylR]]) {{PubMed|2454911}}

* '''Regulatory mechanism:'''
** [[CcpA]]: transcription repression {{PubMed|8132469}}
** [[XylR]]: transcription repression {{PubMed|2454911}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP1151 (del aphA3) available in [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:'''

* '''Antibody:'''

=Labs working on this gene/protein=

[[Wolfgang Hillen]], Erlangen University, Germany [http://www.biologie.uni-erlangen.de/mibi/index2.html Homepage]

=Your additional remarks=

=References=
<pubmed>17123542 1921970 2454911 8132469</pubmed>
[[Category:Protein-coding genes]]

XylA

2011-05-10T11:46:00Z

Evdannies: /* Biological materials */

* '''Description:''' xylose isomerase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''xylA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || xylose isomerase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || utilization of xylan and xylose
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbohydrate_metabolic_pathways.html Sugar catabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 50 kDa, 5.635
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1335 bp, 445 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[xylR]]'', ''[[xylB]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB13644]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:xylA_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[utilization of specific carbon sources]]}}

= This gene is a member of the following [[regulons]] =
{{SubtiWiki regulon|[[CcpA regulon]]}},
{{SubtiWiki regulon|[[XylR regulon]]}}

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU17600

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/xylAB.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10806]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' D-xylose = D-xylulose (according to Swiss-Prot)

* '''Protein family:''' xylose isomerase family (according to Swiss-Prot)

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''

* '''Interactions:'''

* '''Localization:''' cytoplasm (according to Swiss-Prot)

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1A0D 1A0D] (Geobacillus stearothermophilus)

* '''UniProt:''' [http://www.uniprot.org/uniprot/P04788 P04788]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU17600]

* '''E.C. number:''' [http://www.expasy.org/enzyme/5.3.1.5 5.3.1.5]

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[xylA]]-[[xylB]]'' {{PubMed|1921970}}

* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|2454911}}

* '''Regulation:'''
** carbon catabolite repression ([[CcpA]]) {{PubMed|8132469}}
** induction by xylose ([[XylR]]) {{PubMed|2454911}}

* '''Regulatory mechanism:'''
** [[CcpA]]: transcription repression {{PubMed|8132469}}
** [[XylR]]: transcription repression {{PubMed|2454911}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP1151 (del aphA3) available in [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:'''

* '''Antibody:'''

=Labs working on this gene/protein=

[[Wolfgang Hillen]], Erlangen University, Germany [http://www.biologie.uni-erlangen.de/mibi/index2.html Homepage]

=Your additional remarks=

=References=

<pubmed>7966270,,1921970 8132469 2454911 1588910, </pubmed>

[[Category:Protein-coding genes]]