potential Interpro mappings

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potential mappings

Hsp70 protein binding ISS with Pfam:PF00226 DNA J domain (IPR003095/IPR001623)

glycine catabolism ISS with Pfam:PF01571 Glycine cleavage T protein (aminomethyl transferase (IPR006222)

phosphoinositide binding ISS with Pfam:PF00787 PX domain (IPR001683)

nucleus ISS with Pfam:PF04921 XAP5 protein (IPR007005)

microtubule-based movement ISS with PF00225 Kinesin motor domain (IPR001752) (and also microtubule-motor activity)

alcohol dehydrogenase activity, iron-dependent ISS with PF00465 (IPR001670)

ubiquitin cycle ISS with PF00225 PF00240 (IPR000626)

SNAP receptor activity Pfam:PF00957 synaptobrevin(IPR001388)

PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) is an RNA binding motif, but occasionally binds ss DNA so cant have this mapping (suggested mapping nucleic acid binding?)

PF00013 KH domain (I have also mapped this to RNA binding, when it is involved in for example 'U2-type catalytic spliceosome formation for first transesterification step' but this mapping to RNA binding may be globally valid for this domain?)

Reported by: ValWood

Original Ticket: "geneontology/annotation-issues/79":https://sourceforge.net/p/geneontology/annotation-issues/79

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not so sure about this one, but the parent ' heat shock protein binding' might be OK?

Hsp70 protein binding ISS with Pfam:PF00226 DNA J domain (IPR003095/IPR001623)

Original comment by: ValWood

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• milestone: --> InterPro
• assigned_to: nobody --> orchard

Original comment by: mah11

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Hsp70 protein binding ISS with Pfam:PF00226 DNA J domain (IPR003095/IPR001623) I've limited this to 'heat shock protein binding' as in your e-mail

glycine catabolism ISS with Pfam:PF01571 Glycine cleavage T protein (aminomethyl transferase (IPR006222)

Agreed - and added

phosphoinositide binding ISS with Pfam:PF00787 PX domain (IPR001683)

Cannot do this one on the basis of existing SP annotation

nucleus ISS with Pfam:PF04921 XAP5 protein (IPR007005) Agreed

microtubule-based movement ISS with PF00225 Kinesin motor domain (IPR001752) (and also microtubule-motor activity) Agreed

alcohol dehydrogenase activity, iron-dependent ISS with PF00465 (IPR001670) Cannot do this one - patterns also hit proteins annotated to other EC nos.

ubiquitin cycle ISS with PF00225 PF00240 (IPR000626) Pattern also hits NEDD8 and a couple of other "ubiquitin-like" molecules so will leave IP2GO at "protein modification"

SNAP receptor activity Pfam:PF00957 synaptobrevin(IPR001388) Played safe with this one, since SNAP is only mentioned in 2/49 entries and added "integral to membrane" and "vesicle-mediated transport "

PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) is an RNA binding motif, but occasionally binds ss DNA so cant have this mapping (suggested mapping nucleic acid binding?) Corrected

PF00013 KH domain (I have also mapped this to RNA binding, when it is involved in for example 'U2-type catalytic spliceosome formation for first transesterification step' but this mapping to RNA binding may be globally valid for this domain?) This was already mapped to "nucleis Acid binding" so have left it at that.

Original comment by: orchard

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• status: open --> closed

Original comment by: orchard

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Hi Sandra,

only a couple of comments:

would it be worth changing the name of the iron-only dehydrogenase family to somthing more generic?

also SNAP receptor activity Pfam:PF00957 synaptobrevin(IPR001388) Played safe with this one, since SNAP is only mentioned in 2/49 entries and added "integral to membrane" and "vesicle-mediated transport "

possibly this one would be OK the logic being synaptobrevin, T-SNARES and V-SNAREs are all types of SNAP receptor. We don't have 'synaptobevin as a term or synonym as far as I can tell because this is the name of a family' of SNARES rather than an activity, but SNARE is a synonym of SNAP receptor so i think this is probably OK. certainly all of the pombe and cerevisiae synaptobrevins are SNARES/SNAP receptors, although you may have additional reasons for leaving this off.

I think there should also probably be a term SNARE core complex synonym SNAP receptor which is made of a combination of 4 of synaptobrevin/Syntaxin/SNAP which would also be appropriate for this domain. i'll make a SF entry for the new term anyway...I'll use it and it can always be added with later

val

Original comment by: ValWood

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Original comment by: ValWood

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Forgot to close this one. Sandra

Original comment by: orchard

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Original comment by: orchard