From midori at ebi.ac.uk Fri Jul 10 04:00:34 2009 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Fri, 10 Jul 2009 11:00:34 UT Subject: [Annotation] SourceForge Annotation Tracker Update Message-ID: <200907101100.n6AB0Ym9014444@pigeon.ebi.ac.uk> An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available URL: From FMcCarthy at cvm.msstate.edu Wed Jul 22 08:50:12 2009 From: FMcCarthy at cvm.msstate.edu (Fiona McCarthy) Date: Wed, 22 Jul 2009 10:50:12 -0500 Subject: [Annotation] GO:0004802 transketolase activity: modification Message-ID: Hi all, regarding: GO:0004802 transketolase activity Current definition: Catalysis of the reaction: sedoheptulose 7-phosphate + D-glyceraldehyde 3-phosphate = D-ribose 5-phosphate + D-xylulose 5-phosphate. In photosynthesis transketolase also catalyzes the transfer of a 2-carbon fragment from a 6-carbon ketose(Frutose-6-P) to aldose (glyceraldhyde-3-P) to to form a 4 carbon (erythrose 4-P) and 5 carbon ketose(xylulose 5-P). I think the definition should be changed to: the reversible transfer of a 2-carbon ketol group (CH2OH-CO-) from a ketose phosphate donor to an aldose phosphate acceptor to form tetrose and pentose phosphates (from Lehninger). Also, current synonyms are: exact glycolaldehydetransferase activity exact glycoaldehyde transferase activity exact sedoheptulose-7-phosphate:D-glyceraldehyde-3-phosphate glycolaldehydetransferase activity I would also add: exact fructose 6-phosphate + D-glyceraldehyde 3-phosphate = D-erythrose 4- phosphate + D-xylulose 5-phosphate glycolaldehydetransferase activity Anyone with more biochemistry (or photosynthesis) expertise want to comment? Fiona The AgBase Databases Department of Basic Sciences Box 6100 MS 39762-6100 Mississippi State University USA Tel: (+ 1) 662 325 5859 Fax: (+ 1) 662 325 1031 http://www.agbase.msstate.edu/ From vpetri at mcw.edu Wed Jul 22 09:24:47 2009 From: vpetri at mcw.edu (Petri, Victoria) Date: Wed, 22 Jul 2009 11:24:47 -0500 Subject: [Annotation] GO:0004802 transketolase activity: modification In-Reply-To: References: Message-ID: <1448A38A42714048B9C53E473E13CCF0022C3D2E@davis.hmgc.mcw.edu> Hello, Fiona is right. Actually, the second instance mentioned which occurs in photosynthesis, is also the second reaction carried out by a transketolase in the pentose phosphate pathway (the second, non-oxidative phase, last step); here in the opposite direction to produce the second fructose-6-phosphate and glyceraldehyde-3-phosphate. Victoria Victoria Petri, Ph.D. Research Scientist Rat Genome Database http://rgd.mcw.edu Medical College of Wisconsin 8701 Watertown Plank Road Milwaukee, WI 53226 (414) 456-7507 vpetri at mcw.edu -----Original Message----- From: annotation-bounces at genome.stanford.edu [mailto:annotation-bounces at genome.stanford.edu] On Behalf Of Fiona McCarthy Sent: Wednesday, July 22, 2009 10:50 AM To: annotation at genome.stanford.edu Cc: so35 at pss.msstate.edu Subject: [Annotation] GO:0004802 transketolase activity: modification Hi all, regarding: GO:0004802 transketolase activity Current definition: Catalysis of the reaction: sedoheptulose 7-phosphate + D-glyceraldehyde 3-phosphate = D-ribose 5-phosphate + D-xylulose 5-phosphate. In photosynthesis transketolase also catalyzes the transfer of a 2-carbon fragment from a 6-carbon ketose(Frutose-6-P) to aldose (glyceraldhyde-3-P) to to form a 4 carbon (erythrose 4-P) and 5 carbon ketose(xylulose 5-P). I think the definition should be changed to: the reversible transfer of a 2-carbon ketol group (CH2OH-CO-) from a ketose phosphate donor to an aldose phosphate acceptor to form tetrose and pentose phosphates (from Lehninger). Also, current synonyms are: exact glycolaldehydetransferase activity exact glycoaldehyde transferase activity exact sedoheptulose-7-phosphate:D-glyceraldehyde-3-phosphate glycolaldehydetransferase activity I would also add: exact fructose 6-phosphate + D-glyceraldehyde 3-phosphate = D-erythrose 4- phosphate + D-xylulose 5-phosphate glycolaldehydetransferase activity Anyone with more biochemistry (or photosynthesis) expertise want to comment? Fiona The AgBase Databases Department of Basic Sciences Box 6100 MS 39762-6100 Mississippi State University USA Tel: (+ 1) 662 325 5859 Fax: (+ 1) 662 325 1031 http://www.agbase.msstate.edu/ _______________________________________________ Annotation mailing list Annotation at geneontology.org http://fafner.stanford.edu/mailman/listinfo/annotation From kchris at genome.stanford.edu Wed Jul 22 11:44:59 2009 From: kchris at genome.stanford.edu (Karen Christie) Date: Wed, 22 Jul 2009 11:44:59 -0700 (PDT) Subject: [Annotation] GO:0004802 transketolase activity: modification In-Reply-To: <1448A38A42714048B9C53E473E13CCF0022C3D2E@davis.hmgc.mcw.edu> References: <1448A38A42714048B9C53E473E13CCF0022C3D2E@davis.hmgc.mcw.edu> Message-ID: Hi Fiona, For changes to the ontology itself, it's best to post an item on the SourceForge tracker for ontology changes: https://sourceforge.net/tracker/?group_id=36855&atid=440764 If you haven't used SourceForge before, you'll probably need to register, but then you can post this item there. Basically, the GO editorial office likes for all requests for new terms or changes to existing ones to be posted here, both to make it generally accessible and for record keeping. -Karen On Wed, 22 Jul 2009, Petri, Victoria wrote: > Hello, > > Fiona is right. Actually, the second instance mentioned which occurs in > photosynthesis, is also the second reaction carried out by a > transketolase in the pentose phosphate pathway (the second, > non-oxidative phase, last step); here in the opposite direction to > produce the second fructose-6-phosphate and glyceraldehyde-3-phosphate. > > Victoria > > Victoria Petri, Ph.D. > Research Scientist > Rat Genome Database > http://rgd.mcw.edu > Medical College of Wisconsin > 8701 Watertown Plank Road > Milwaukee, WI 53226 > (414) 456-7507 > vpetri at mcw.edu > > -----Original Message----- > From: annotation-bounces at genome.stanford.edu > [mailto:annotation-bounces at genome.stanford.edu] On Behalf Of Fiona > McCarthy > Sent: Wednesday, July 22, 2009 10:50 AM > To: annotation at genome.stanford.edu > Cc: so35 at pss.msstate.edu > Subject: [Annotation] GO:0004802 transketolase activity: modification > > Hi all, > > regarding: > > GO:0004802 transketolase activity > Current definition: > Catalysis of the reaction: sedoheptulose 7-phosphate + D-glyceraldehyde > 3-phosphate = D-ribose 5-phosphate + D-xylulose 5-phosphate. > > In photosynthesis transketolase also catalyzes the transfer of a > 2-carbon > fragment from a 6-carbon ketose(Frutose-6-P) to aldose > (glyceraldhyde-3-P) > to to form a 4 carbon (erythrose 4-P) and 5 carbon ketose(xylulose 5-P). > > I think the definition should be changed to: > the reversible transfer of a 2-carbon ketol group (CH2OH-CO-) from a > ketose phosphate donor to an aldose phosphate acceptor to form tetrose > and pentose phosphates > (from Lehninger). > > Also, current synonyms are: > exact glycolaldehydetransferase activity > exact glycoaldehyde transferase activity > exact sedoheptulose-7-phosphate:D-glyceraldehyde-3-phosphate > glycolaldehydetransferase activity > > I would also add: > exact fructose 6-phosphate + D-glyceraldehyde 3-phosphate = > D-erythrose > 4- phosphate + D-xylulose 5-phosphate glycolaldehydetransferase activity > > > Anyone with more biochemistry (or photosynthesis) expertise want to > comment? > Fiona > > > The AgBase Databases > Department of Basic Sciences > Box 6100 > MS 39762-6100 > Mississippi State University > USA > Tel: (+ 1) 662 325 5859 > Fax: (+ 1) 662 325 1031 > > http://www.agbase.msstate.edu/ > > _______________________________________________ > Annotation mailing list > Annotation at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/annotation > > _______________________________________________ > Annotation mailing list > Annotation at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/annotation > From midori at ebi.ac.uk Mon Jul 27 04:00:33 2009 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Mon, 27 Jul 2009 11:00:33 UT Subject: [Annotation] SourceForge Annotation Tracker Update Message-ID: <200907271100.n6RB0Xk4010308@pigeon.ebi.ac.uk> An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available URL: From huntley at ebi.ac.uk Fri Jul 31 02:50:10 2009 From: huntley at ebi.ac.uk (Rachael Huntley) Date: Fri, 31 Jul 2009 10:50:10 +0100 Subject: [Annotation] GPI-anchored proteins Message-ID: <4A72BE52.1080609@ebi.ac.uk> Hi all, I'm after some advice. I'm a little confused about these two terms, with respect to GPI-anchored proteins; GO:0031224 intrinsic to membrane - Located in a membrane such that some covalently attached portion of the gene product, for example part of a peptide sequence or some other covalently attached moiety such as a GPI anchor, spans or is embedded in one or both leaflets of the membrane. Note that proteins intrinsic to membranes cannot be removed without disrupting the membrane, e.g. by detergent. GO:0019898 extrinsic to membrane - Loosely bound to one surface of a membrane, but not integrated into the hydrophobic region. Note that proteins extrinsic to membranes can be removed by treatments that do not disrupt the membrane, such as salt solutions. This term can be used instead of these obsolete terms: GO:0015025 GPI-anchored membrane-bound receptor (consider GO:0019898) Both mention GPI anchor, the first (intrinsic to membrane) in the definition and the second as a suggestion to use extrinsic to membrane instead of the obsolete GO:0015025 GPI-anchored membrane-bound receptor I don't know much about GPI-anchored proteins, but from what I can gather they can be extracted by detergent-solubilizing a membrane (PMID:19374451) which would suggest use of the term GO:0031224 intrinsic to membrane. However, the GPI-anchor can be disrupted by phospholipase C, thus releasing the associated protein, which would suggest use of the term GO:0019898 extrinsic to membrane. Additionally, GO:0031224 intrinsic to membrane has the child GO:0031225 anchored to membrane (Def: Tethered to a membrane by a covalently attached anchor, such as a lipid moiety, that is embedded in the membrane. When used to describe a protein, indicates that none of the peptide sequence is embedded in the membrane.) which would be a term I would use for GPI-anchored proteins. Can anyone suggest whether GPI-anchored proteins should be annotated to extrinsic or intrinsic to membrane. Either way, it looks as though the ontology could be refined in this area. Thanks for your help. Rachael. -- GOA and IntAct Curator European Bioinformatics Institute Welcome Trust Genome Campus Hinxton Cambridge, CB10 1SD UK Tel: 01223 492515 Fax: 01223 494468 Email: huntley at ebi.ac.uk GOA: http://www.ebi.ac.uk/GOA IntAct: http://www.ebi.ac.uk/intact From midori at ebi.ac.uk Fri Jul 31 02:58:32 2009 From: midori at ebi.ac.uk (Midori Harris) Date: Fri, 31 Jul 2009 10:58:32 +0100 (BST) Subject: [Annotation] GPI-anchored proteins In-Reply-To: <4A72BE52.1080609@ebi.ac.uk> References: <4A72BE52.1080609@ebi.ac.uk> Message-ID: GPI-anchored proteins should be annotated to GO:0031225. The 'consider' tag for GO:0015025 should be changed; I can take care of that today. m On Fri, 31 Jul 2009, Rachael Huntley wrote: > Hi all, > > I'm after some advice. I'm a little confused about these two terms, with > respect to GPI-anchored proteins; > > GO:0031224 intrinsic to membrane - Located in a membrane such that some > covalently attached portion of the gene product, for example part of a > peptide sequence or some other covalently attached moiety such as a GPI > anchor, spans or is embedded in one or both leaflets of the membrane. Note > that proteins intrinsic to membranes cannot be removed without disrupting the > membrane, e.g. by detergent. > > GO:0019898 extrinsic to membrane - Loosely bound to one surface of a > membrane, but not integrated into the hydrophobic region. Note that proteins > extrinsic to membranes can be removed by treatments that do not disrupt the > membrane, such as salt solutions. > This term can be used instead of these obsolete terms: GO:0015025 > GPI-anchored membrane-bound receptor (consider GO:0019898) > > Both mention GPI anchor, the first (intrinsic to membrane) in the definition > and the second as a suggestion to use extrinsic to membrane instead of the > obsolete GO:0015025 GPI-anchored membrane-bound receptor > > I don't know much about GPI-anchored proteins, but from what I can gather > they can be extracted by detergent-solubilizing a membrane (PMID:19374451) > which would suggest use of the term GO:0031224 intrinsic to membrane. > However, the GPI-anchor can be disrupted by phospholipase C, thus releasing > the associated protein, which would suggest use of the term GO:0019898 > extrinsic to membrane. > > Additionally, GO:0031224 intrinsic to membrane has the child GO:0031225 > anchored to membrane (Def: Tethered to a membrane by a covalently attached > anchor, such as a lipid moiety, that is embedded in the membrane. When used > to describe a protein, indicates that none of the peptide sequence is > embedded in the membrane.) which would be a term I would use for GPI-anchored > proteins. > > Can anyone suggest whether GPI-anchored proteins should be annotated to > extrinsic or intrinsic to membrane. Either way, it looks as though the > ontology could be refined in this area. > > Thanks for your help. > > Rachael. > >