Enzymes to search for. Selected pathways involved in carbon fixation are shown below, along with enzymes in each pathway. (Key enzymes specific to each pathway are indicated in italics.) Organisms that possess this pathway and have sequenced genomes are suggested below as sources for sequences to use as queries.
|
Pathway |
Enzymes |
Suggested
organism |
Searcher |
Result |
|
Calvin cycle (reductive pentose-Pi pathway) |
Ribulose-1,5-bisphosphate carboxylase/oxygenase |
Rhodobacter, Synechocystis |
KR |
No homolog found |
|
Transadolase |
Rhodobacter, Synechocystis |
|
|
|
|
Transketolase |
Rhodobacter, Synechocystis |
|
|
|
|
Phosphoribulokinase |
Rhodobacter, Synechocystis |
KTR |
No homolog found |
|
|
3-phosphoglycerate kinase |
Rhodobacter, Synechocystis |
|
|
|
|
glyceraldehyde-3-Pi dehydrogenase |
Rhodobacter, Synechocystis |
WH |
3 good homologs found on contigs 3, 39, & 16 |
|
|
Sedoheptulose-1,7-bisphosphatase |
Rhodobacter, Synechocystis |
|
|
|
|
Ribulosephosphate 3-epimerase |
Rhodobacter, Synechocystis |
|
|
|
|
Phosphopentose isomerase |
Rhodobacter, Synechocystis |
|
|
|
|
Reverse TCA cycle |
Ferredoxin-dependent a-ketoglutarate
dehydrogenase |
Chlorobium |
RL |
No homolog found |
|
Ferredoxin-dependent pyruvate dehydrogenase |
Chlorobium |
RL |
Very weak homolog (probably not real) in contig 22 |
|
|
Citrate lyase |
Chlorobium |
RL |
Possible homologs for subunits 1 and 2 found in contig 22 |
|
|
Fumarase |
Chlorobium |
WH |
No convincing homolog |
|
|
Succinate dehydrogenase |
Chlorobium |
WH |
Obvious homolog in contig 22 |
|
|
Succinyl-CoA synthetase |
Chlorobium |
WH |
Obvious homolog in contig 22 |
|
|
Isocitrate dehydrogenase |
Chlorobium |
RL |
Obvious homolog in contig 3 |
|
|
Hydroxypropionate & glyoxylate pathways |
Acetyl-CoA carboxylase |
Chloroflexus |
VY |
Obvious homolog in contig 22 |
|
Malonate-CoA reductase |
Chloroflexus |
VY |
No homolog found |
|
|
Propionyl-CoA synthase |
Chloroflexus |
KR/LW |
Potential homolog in contig 34 |
|
|
Propionyl-CoA carboxylase |
Chloroflexus |
|
|
|
|
Methylmalonyl-CoA epimerase |
Chloroflexus |
|
|
|
|
Methylmalonyl-CoA mutase |
Chloroflexus |
|
|
|
|
Succinyl-CoA:Malyl-CoA transferase |
Chloroflexus |
|
|
|
|
L-malyl-CoA lyase/ |
Chloroflexus |
LW |
No homolog found |
|
|
Methylmalyl-CoA synthase? |
Chloroflexus |
|
|
|
|
Mesaconyl-CoA hydratase? |
Chloroflexus |
|
|
|
|
R-Citramalyl-CoA lyase |
Chloroflexus |
LW |
No homolog found |
|
|
Ribulose-monophosphate pathway |
3-Hexulose-6-phosphate synthase |
Methylococcus |
BB |
No homolog found |
|
6-Phospho-3-hexulose isomerase |
Methylococcus |
BB |
No homolog found |
|
|
Formate dehydrogenase |
Methylococcus |
BB |
Potential homolog of a subunit in contig 17 |
|
|
Formaldehyde dehydrogenase |
Methylococcus |
BB |
No homolog found |
|
|
Serine pathway |
Serine transhydroxymethylase |
Methylosinus |
JMM |
Homolog in contig 38 |
|
|
Glycerate dehydrogenase |
Methylosinus |
|
|
|
|
Glycerate kinase |
Methylosinus |
|
|
|
|
Phosphoenolpyruvate carboxylase |
Methylosinus |
JMM |
No homolog found |
|
|
Malyl-CoA synthetase |
Methylosinus |
JMM |
Homolog in contig 22 |
|
|
Malyl-CoA lyase |
Methylosinus |
JMM |
No homolog found |
|
Acetyl-CoA pathway |
CO dehydrogenase |
Methanosarcina |
|
|
|
Substrate oxidation pathways |
Lactate dehydrogenase |
|
|
|
|
Alcohol dehydrogenase |
|
|
|
|
|
Hydrogenases (Fe only and |
|
KTR |
Several homologs found |
|
|
Sulfide:quinone oxidoreductase |
|
KTR |
No convincing homolog |