Fix EC class 7 - transporters

pgaudet commented 5 years ago

EC class 7 is a new class; we have most transporters under EC3.6.3.x (?)

[x] EC:3.6.3.8 -> EC:7.2.2.10
[x] EC:3.6.3.21 -> EC:7.4.2.1
[x] EC:3.6.3.22 -> EC:7.4.2.2
[x] EC:3.6.3.46 -> EC:7.2.2.2
[x] GO:0015624 ferric-enterobactin-transporting ATPase activity | EC:3.6.3.34 | MetaCyc ABC-10-RXN | 0 annotations -> EC 7.2.2.17
[x] GO:0015408 ferric-transporting ATPase activity EC:3.6.3.30 -> EC:7.2.2.7
[x] -GO:0015625 ferric-hydroxamate-transporting ATPase activity | EC:3.6.3.34 | MetaCyc ABC-11-RXN | 0 annotations -> EC:7.2.2.16
[x] EC:3.6.3.19 -> EC:7.5.2.1
[x] EC:3.6.3.18 -> EC:7.5.2.2
[x] EC:3.6.3.40 -> EC:7.5.2.4
[x] EC:3.6.3.44 -> EC:7.6.2.2
[x] EC:3.6.3.37 -> EC:7.6.2.6
[x] EC:3.6.3.20 -> EC:7.6.2.10
[x] EC:3.6.3.31 -> EC:7.6.2.11
[x] EC:3.6.3.23 -> EC:7.4.2.6

Additions

[x] EC:7.6.2.3 GO:0015431 ATPase-coupled glutathione S-conjugate transmembrane transporter activity
[x] EC:7.6.2.4 GO:0015607 fatty-acyl-CoA transmembrane transporter activity + change label - all annotated proteins are ABC transporters
[x] EC:7.4.2.5 GO:0015462 ATPase-coupled protein transmembrane transporter activity

Merges

[x] 'GO:0102023 ATPase-coupled vitamin B12 transmembrane transporter activity' (0 annotations; GOC:pz) into GO:0015420 ATPase-coupled cobalamin transmembrane transporter activity (15 annotations) same EC, same compound)
[x] 'GO:0015622 ferric-hydroxamate transmembrane transporter activity' (no annotations, no mappings) into 'GO:0015625 ATPase-coupled ferric-hydroxamate transmembrane transporter activity' (corresponds to EC:7.2.2.16 and MetaCyc MetaCyc:ABC-11-RXN)
[x] 'GO:0015162 teichoic acid transmembrane transporter activity' 4 ISS to ABC transporters, no mappings into 'GO:0015438 ATPase-coupled teichoic acid transmembrane transporter activity' : 0 annotations; mapping to EC

pgaudet commented 5 years ago

ECs added: Full list

[x] 7.2.2.2
[x] 7.2.2.5
[x] 7.2.2.7
[x] 7.2.2.11
[x] 7.2.2.17
[x] 7.3.2.1
[x] 7.3.2.3
[x] 7.3.2.4
[x] 7.3.2.5
[x] 7.3.2.6
[x] 7.4.2.1
[x] 7.4.2.2
[x] 7.4.2.5
[x] 7.4.2.6
[x] 7.5.2.1
[x] 7.6.2.3
[x] 7.6.2.4
[x] 7.6.2.5
[x] 7.6.2.6
[x] 7.6.2.7
[x] 7.6.2.8
[x] 7.6.2.9
[x] 7.6.2.10
[x] 7.2.2.10
[x] 7.2.2.13
[x] 7.2.2.16
[x] 7.5.2.2
[x] 7.5.2.4
[x] 7.6.2.2
[x] 7.6.2.11

pgaudet commented 5 years ago

[x] EC:3.6.3.6 -> 7.1.2.1 P-type H(+)-exporting transporter (GO:0008553)
- [x] EC:3.6.3.7 -> 7.2.2.3 GO:0008554 sodium transmembrane transporter activity, phosphorylative mechanism
- [x] Merge GO:0036442 proton-exporting ATPase activity (RHEA:20852: cross linked to EC:3.6.3.6) into GO:0008553 proton-exporting ATPase activity, phosphorylative mechanism (EC:3.6.3.6)
- [x] Add RHEA:13973 cross ref to GO:0009678 pyrophosphate hydrolysis-driven proton transmembrane transporter activity
[x] EC:3.6.3.35 -> EC:7.2.2.5 GO:0015410 manganese transmembrane transporter activity, phosphorylative mechanism
[x] EC:3.6.3.9 -> EC:7.2.2.13 GO:0005391 sodium:potassium-exchanging ATPase activity
[x] EC:7.2.2.6 -> 7.2.2.6 GO:0008556 potassium transmembrane transporter activity, phosphorylative mechanism
[x] 3.6.3.8 -> 7.2.2.10 GO:0008556 calcium transmembrane transporter activity, phosphorylative mechanism (GO:0005388)

pgaudet commented 5 years ago

Added to GO GO:0015451 decarboxylation-driven active transmembrane transporter activity:

[x] 7.2.4.1 Carboxybiotin decarboxylase
[x] 7.2.4.2 Oxaloacetate decarboxylase (Na(+) extruding)
[x] 7.2.4.3 (S)-methylmalonyl-CoA decarboxylase (sodium-transporting)
[x] 7.2.4.4 Biotin-dependent malonate decarboxylase
[x] 7.2.4.5 Glutaconyl-CoA decarboxylase

pgaudet commented 5 years ago

[x] Merge GO:0015619 thiamine pyrophosphate-transporting ATPase activity TC:3.A.1.19.1 into GO:0048502 ATPase-coupled thiamine transmembrane transporter activity RHEA:29811

pgaudet commented 5 years ago

[x] Merge 'cadaverine transmembrane transporter activity' 0 annot /0 xref into 'lysine:cadaverine antiporter activity' 3 annot

pgaudet commented 5 years ago

'proton-transporting ATPase activity, rotational mechanism' -> EC 7.1.2.2 'sodium-transporting ATP synthase activity, rotational mechanism' -> 7.2.2.1¨ see https://github.com/geneontology/go-ontology/issues/17412

pgaudet commented 5 years ago

[x] EC:1.6.5.3 -> EC:7.1.1.2 NADH dehydrogenase (ubiquinone) activity + changed RHEA x ref and definition
[x] Merge GO:0004008 copper-exporting ATPase activity into GO:0043682 copper-transporting ATPase activity - both correspond to 7.2.2.9 (P-type Cu2+ transporter)
[x] EC:3.6.3.2 -> 7.2.2.14 magnesium-importing ATPase activity
[x] EC 3.6.3.53 -> 7.2.2.15 silver transmembrane transporter activity, phosphorylative mechanism
[x] EC 3.6.3.31 -> 7.6.2.11 ATPase-coupled putrescine transmembrane transporter activity

pgaudet commented 5 years ago

[x] merge GO:0102017 ATPase-coupled alkylphosphonate transmembrane transporter activity (0 annotations) into GO:0015416 ATPase-coupled organic phosphonate transmembrane transporter activity (same EC:7.3.2.2)

pgaudet commented 5 years ago

Not in GO - do not add xref:

7.5.2.6 ABC-type lipid A-core oligosaccharide transporter 7.4.2.9 ABC-type dipeptide transporter -> closest is GO:0071916 dipeptide transmembrane transporter activity but also annotated with non-ABC transporters 7.4.2.7 ABC-type alpha-factor-pheromone transporter

geneontology / go-ontology

Fix EC class 7 - transporters #17359

Additions

Merges