As text, or see rules and steps
# Ethanol can pass through biological membranes, so no transporter is required. # Ethanol degradation in GapMind is based on MetaCyc pathways # ethanol degradation I (oxidation to acetyl-CoA, metacyc:ETOH-ACETYLCOA-ANA-PWY) # and II (oxidation to acetate and activation, metacyc:PWY66-21). # Pathways III (with ethanol monooxygenase, metacyc:PWY66-161) and # IV (with ethanol peroxidase, metacyc:PWY66-162) are not reported to # occur in prokaryotes and are not included. # CH_121261 seems to be a sequence fragment etoh-dh-nad ethanol dehydrogenase (NAD(P)) EC:1.1.1.1 ignore:CharProtDB::CH_121261 EC:1.1.1.71 etoh-dh-c ethanol dehydrogenase (cytochrome c) EC:1.1.2.8 ignore_other:1.1.2.8 # (The enzyme from Zymomonas is NAD-dependent, but is misannotated as quinone-dependent in MetaCyc.) adhAqn ethanol dehydrogenase (quinone), subunit I curated:BRENDA::Q44002 curated:BRENDA::P18278 curated:BRENDA::Q93RE9 curated:SwissProt::O05542 curated:SwissProt::P28036 ignore_other:1.1.2.8 adhBqn ethanol dehydrogenase (quinone), subunit II curated:SwissProt::P0A388 curated:SwissProt::Q47945 ignore_other:1.1.2.8 adhSqn ethanol dehydrogenase (quinone), subunit III curated:SwissProt::O05544 # Bacterial quinone-dependent enzymes (EC 1.1.5.5) have 3 subunits. etoh-dh-qn: adhAqn adhBqn adhSqn # Three types of ethanol dehydrogenases: NAD(P) dependent, cytochrome c dependent, or quinone dependent. etoh-dh: etoh-dh-nad etoh-dh: etoh-dh-c etoh-dh: etoh-dh-qn # Many enzymes are multifunctional alcohol/acetaldehyde dehydrogenases, # and many close homologs have just one annotation. # EC:1.2.1.57 is acylating butanal dehydrogenase, which may also act on acetaldehyde. # Q2XQZ7 is probably misannotated. ald-dh-CoA acetaldehyde dehydrogenase, acylating EC:1.2.1.10 ignore_other:1.1.1.1 ignore_other:1.1.1.71 ignore_other:1.2.1.57 ignore:BRENDA::Q2XQZ7 adh acetaldehyde dehydrogenase (not acylating) EC:1.2.1.3 acs acetyl-CoA synthetase, AMP-forming EC:6.2.1.1 ackA acetate kinase EC:2.7.2.1 EC:2.7.2.15 # BRENDA misannotates yeast's carnitine acetyltransferase with EC:2.3.1.8 pta phosphate acetyltransferase EC:2.3.1.8 ignore:BRENDA::P32796 # Acetaldehyde can be oxidized to acetyl-CoA, or oxidized to acetate and activated to acetyl-CoA # by either acetyl-CoA synthetase (acs) # or by acetate kinase (ackA) and phosphate acetyltransferase (pta). acetaldehyde-degradation: ald-dh-CoA acetaldehyde-degradation: adh acs acetaldehyde-degradation: adh ackA pta # Ethanol is consumed by oxidation to acetaldehyde all: etoh-dh acetaldehyde-degradation
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory