Biosynthesis of cofactors

2011-03-07T08:57:12Z

Jdindas: /* Biosynthesis of lipoic acid */

{{CategoryTree
|Parents=
* 2. [[Metabolism]]
** 2.6. [[Additional metabolic pathways]]
|Neighbours=
* 2.6.1. [[Biosynthesis of cell wall components]]
* 2.6.2. [[Biosynthesis of cofactors]]
* 2.6.3. [[Phosphate metabolism]]
* 2.6.4. [[Sulfur metabolism]]
* 2.6.5. [[Iron metabolism]]
* 2.6.6. [[Miscellaneous metabolic pathways]]
|Related=
none
|}}

== Genes in this functional category ==

=== Biosynthesis/ acquisition of biotin ===
* [[bioA]]
* [[bioB]]
* [[bioD]]
* [[bioF]]
* [[bioI]]
* [[bioW]]
* [[birA]]
* [[yhfU]]

=== Biosynthesis/ acquisition of riboflavin/ fad ===
* [[ribA]]
* [[ribC]]
* [[ribD]]
* [[ribE]]
* [[ribH]]
* [[ribT]]
* [[ribU]]

=== Biosynthesis/ acquisition of thiamine ===
* [[dxs]]
* [[nifZ]]
* [[tenA]]
* [[tenI]]
* [[thiC]]
* [[thiD]]
* [[thiE]]
* [[thiF]]
* [[thiG]]
* [[thiL]]
* [[thiM]]
* [[thiO]]
* [[thiS]]
* [[thiT]]
* [[thiU]]
* [[thiV]]
* [[thiW]]
* [[thiX]]
* [[ylmB]]
* [[yloS]]

=== Biosynthesis/ acquisition of thiamine/ based on similarity ===
* [[ytbJ]]

=== Biosynthesis of coenzyme a ===
* [[coaA]]
* [[coaX]]
* [[panB]]
* [[panC]]
* [[panD]]
* [[ylbQ]]
* [[yloI]]
* [[ytaG]]

=== Biosynthesis of folate ===
* [[dfrA]]
* [[folB]]
* [[folC]]
* [[folE]]
* [[folE2]]
* [[folK]]
* [[pabA]]
* [[pabB]]
* [[pabC]]
* [[sul]]

=== Biosynthesis of heme/ siroheme ===
* [[ctaA]]
* [[ctaB]]
* [[ctaO]]
* [[gsaB]]
* [[hemA]]
* [[hemB]]
* [[hemC]]
* [[hemD]]
* [[hemE]]
* [[hemH]]
* [[hemL]]
* [[hemN]]
* [[hemQ]]
* [[hemX]]
* [[hemY]]
* [[hemZ]]
* [[ylnD]]
* [[ylnE]]
* [[ylnF]]

=== Biosynthesis of lipoic acid ===
* [[lipA]]
* [[lipM]]
* [[lplJ]]
* [[lipL]]

=== Biosynthesis of menaquinone ===
* [[hepS]]
* [[hepT]]
* [[menA]]
* [[menB]]
* [[menC]]
* [[menD]]
* [[menE]]
* [[menF]]
* [[menH]]

=== Biosynthesis of menaquinone/ based on similarity ===
* [[ytxM]]

=== Biosynthesis of molybdopterin ===
* [[moaA]]
* [[moaB]]
* [[moaD]]
* [[moaE]]
* [[mobA]]
* [[mobB]]
* [[moeA]]
* [[moeB]]

=== Biosynthesis of nad(p) ===
* [[nadA]]
* [[nadB]]
* [[nadC]]
* [[nadD]]
* [[nadE]]
* [[nadF]]
* [[nadR]]
* [[nifS]]
* [[ytdI]]

=== Biosynthesis of pyridoxal phosphate ===
* [[pdxK]]
* [[pdxS]]
* [[pdxT]]

== Metabolism of cofactors in [http://subtiwiki.uni-goettingen.de/subtipathways.html ''Subti''Pathways]==

* [http://subtiwiki.uni-goettingen.de/pathways/CoA_synthesis.html CoA synthesis]

* [http://subtiwiki.uni-goettingen.de/pathways/folate_biosynthesis.html Folate biosynthesis]

* [http://subtiwiki.uni-goettingen.de/pathways/menaquinone.html Menaquinone]

* [http://subtiwiki.uni-goettingen.de/pathways/riboflavin.html Riboflavin and FAD synthesis]

* [http://subtiwiki.uni-goettingen.de/pathways/thiamin.html Thiamin synthesis]

* [http://subtiwiki.uni-goettingen.de/pathways/biotin/index.html Biotin synthesis]

==Important reviews==
<pubmed> 19348578 18314013 14675553 10382260 11153271
</pubmed>

YhfK

2011-03-07T08:53:00Z

Jdindas:

* '''Description:''' unknown <br/><br/>

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yhfK''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 22 kDa, 5.178
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 642 bp, 214 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[lplJ]]'', ''[[lcfB]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB12866]+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:yhfK_context.gif]]
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
|-
|}

__TOC__

<br/><br/>

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[phosphoproteins]]}},
{{SubtiWiki category|[[proteins of unknown function]]}}

= This gene is a member of the following [[regulons]] =

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU10260

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' no entry

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13056]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:'''

* '''Protein family:''' sugar epimerase family (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:''' phosphorylated on ser/ thr/ tyr [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed]

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

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

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O07609 O07609]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU10260]

* '''E.C. number:'''

=== Additional information===

=Expression and regulation=

* '''Operon:'''

* '''[[[[Sigma factor]]]]:'''

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>16493705, </pubmed>

[[Category:Protein-coding genes]]

YhfI

2011-03-07T08:51:29Z

Jdindas:

* '''Description:''' unknown <br/><br/>

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yhfI''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 26 kDa, 5.606
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 732 bp, 244 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yhfH]]'', ''[[lplJ]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB12864]+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:yhfI_context.gif]]
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
|-
|}

__TOC__

<br/><br/>

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[proteins of unknown function]]}}

= This gene is a member of the following [[regulons]] =

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU10240

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' no entry

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13054]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:'''

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O07607 O07607]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU10240]

* '''E.C. number:'''

=== Additional information===

=Expression and regulation=

* '''Operon:'''

* '''[[[[Sigma factor]]]]:'''

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

[[Category:Protein-coding genes]]

LplJ

2011-03-07T08:49:45Z

Jdindas: moved YhfJ to LplJ: 21338420

* '''Description:''' similar to lipoate-protein ligase <br/><br/>

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yhfJ''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 37 kDa, 5.835
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 993 bp, 331 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yhfI]]'', ''[[yhfK]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB12865]+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:yhfJ_context.gif]]
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
|-
|}

__TOC__

<br/><br/>

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[poorly characterized/ putative enzymes]]}}

= This gene is a member of the following [[regulons]] =

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU10250

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' no entry

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13055]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:'''

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O07608 O07608]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU10250]

* '''E.C. number:'''

=== Additional information===

=Expression and regulation=

* '''Operon:'''

* '''[[Sigma factor]]:'''

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

[[Category:Protein-coding genes]]

YhfJ

2011-03-07T08:49:45Z

Jdindas: moved YhfJ to LplJ: 21338420