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#59 PTHR11615 (nitrate, formate, iron dehydrogenase)
Hi,
Although the family name says dehydrogenase, annotations are diverse. Here is a summary of the propagations I would do for this family-
* Fungi node-PTN000906804: Iron-sulfur cluster binding (GO:51536), iron -sulfur cluster assembly(GO:16226) and cytosol (GO:5829) to the
* PTN 000177281: NADH dehydrogenase (Ub) activity (GO:8137), mitochondrial electron transport, NADH to Ub (GO:6120), mitochondrial inner membrane(GO:5743) to node
*PTN000177330 don't know how to deal with the plant node
* PTN000177461: propagate 4-Iron-sulfur cluster binding (GO:51539), NADH dehydrogenase activity (GO:3954), plasma membrane (GO:5886)
* PTN000906908: propagate trimethylamine-N-oxide reductase (cytochrome c) activity (GO:50626)
* PTN000177620 propagate formate dehydrogenase (GO:8863)
* PTN000177398 propagate nitrate reductase activity (GO8940)
* PTN000745948 looks like the manual annotations for fdhF need to be examined
*PTN000906990 Ecoli dmsa is a dimethyl sulfoxate (although there are no manual annotations to that term) and others are selenate reductase. Iam not confident of propagating anything.
Rama
Hi Rama,
In general, I agree with your annotations. The main things I would suggest are:
1) trying to infer the function of the common ancestor (root of the tree), and
2) propagate to a node that follows a duplication
Here's a summary of what I would do:
Root:
These two functions are present in nearly all clades except for NAR1, so they are likely to be ancestral. Annotate to root
- MF oxidoreductase activity and iron-sulfur cluster binding
- BP cellular respiration
NAR1 (yeast) clade (PTN177495):
Based on annotations to human NARFL and yeast NAR1, these orthologs are involved in maturation of Fe-S containing proteins
- MF iron-sulfur cluster binding inherited from root, NOT oxidoreductase
- CC cytosol
- BP: NOT cellular respiration. No other annotation for now. Would like to annotate GO:0097428 but unfortunately the yeast and human orthologs are annotated instead to iron-sulfur cluster assembly (suggest reannotation as from the abstracts these are apparently involved in maturation of Fe-S containing proteins, not necessarily assembly of the cluster itself)
-- NARF subfamily of this clade: MF lamin binding (NOT iron-sulfur cluster binding as no evidence for this), CC lamin filament (NOT cytosol as no evidence for this)
nuoG (E.coli) clade:
Based on widespread annotations, these are aerobic respiratory electron chain oxidoreductases, in the mitochondria of eukaryotes.
- MF NADH dehydrogenase (ubiquinone)-- verified in SwissProt record that even the E. coli uses ubiquinone as acceptor
- CC respiratory complex I to root of clade; mitochondrial resp comp I to root of eukaryotes, plasma membrane resp comp I to root of bacteria
- BP aerobic respiration to root of clade
--There are several divergent subfamilies in plants (all except the one containing EMB1467). These should have a NOT for all above annotations. The CASP-containing subfamily (PTN177419) has additional annotations: CC Casparian strip, BP cell wall modification and cell-cell junction assembly
torA (E. coli) clade (PTN177395):
- MF molybdenum binding (should be molybdopterin instead, suggest reannotation), NOT Fe-S binding
- BP anaerobic respiration, aerobic respiration
fdoG (E.coli) clade (PTN177620):
- MF molybdopterin binding, formate dehydrogenase activity, NOT Fe-S binding
-CC cytoplasm
- BP anaerobic respiration
napA (E.coli) clade (PTN177407):
- MF molybdenum binding (should be molybdopterin instead, suggest reannotation), nitrate reductase
- CC periplasmic space
- BP anaerobic respiration
fdhF (E.coli) clade (PTN745948):
- MF molybdenum binding (should be molybdopterin instead, suggest reannotation), suggest annotation of formate dehydrogenase activity
- BP no propagation now but suggest annotation of anaerobic respiration
narG (E.coli) clade (PTN906979):
- MF molybdenum binding (should be molybdopterin instead, suggest reannotation)
- CC plasma membrane
- BP anaerobic respiration
dmsA/ynf (E.coli) clade (PTN906990):
- MF molybdenum binding (should be molybdopterin instead, suggest reannotation)
- BP anaerobic respiration
Hi Paul,
According to http://dehydrogenase.co.uk/
I think these proteins are dehydrogenases and not oxidoreductases; does that sound right to you ?
Hi Paul, Rama,
I reviewed the annotations, trying to implement Paul's suggestions. This is a summary of what I've done
Disputed
Root:
These two functions are present in nearly all clades except for NAR1, so they are likely to be ancestral. Annotate to root
NAR1 (yeast) clade (PTN177495):
Based on annotations to human NARFL and yeast NAR1, these orthologs are involved in maturation of Fe-S containing proteins
-- NARF subfamily of this clade: MF lamin binding (NOT iron-sulfur cluster binding as no evidence for this), CC lamin filament (NOT cytosol as no evidence for this) -> did not propagate anything to this cade; data too scarce
nuoG (E.coli) clade:
Based on widespread annotations, these are aerobic respiratory electron chain oxidoreductases, in the mitochondria of eukaryotes.
--There are several divergent subfamilies in plants (all except the one containing EMB1467). These should have a NOT for all above annotations. The CASP-containing subfamily (PTN177419) has additional annotations: CC Casparian strip, BP cell wall modification and cell-cell junction assembly
-> This clade now has aanerobic bacteria; did not propgate anything special
torA (E. coli) clade (PTN177395):
fdoG (E.coli) clade (PTN177620):
-CC cytoplasm -> membrane
napA (E.coli) clade (PTN177407):
fdhF (E.coli) clade (PTN745948):
narG (E.coli) clade (PTN906979):
dmsA/ynf (E.coli) clade (PTN906990): (annotated as torA)
NDFUS1
(If there are no more comments, this issue can be closed. I'll leave it open for now)