Finding step acdH for L-valine catabolism in Thioalkalivibrio halophilus HL17
No candidates for acdH: isobutyryl-CoA dehydrogenase
GapMind classifies a step as low confidence even if it does not find any candidates. You can still try to find candidates by using Curated BLAST (which searches the 6-frame translation) or by text search of the annotations (which may indicate weak homology, under 30% identity or 50% coverage, that GapMind does not consider). See the links below.
Definition of step acdH
- Curated proteins or TIGRFams with EC 1.3.8.5 (search)
- Ignore hits to 200844 when looking for 'other' hits (2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5))
- Ignore hits to GFF2715 when looking for 'other' hits (2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5))
- Ignore hits to Ac3H11_2996 when looking for 'other' hits (2-methyl-branched-chain-enoyl-CoA reductase (EC 1.3.8.5))
- Ignore hits to GFF2397 when looking for 'other' hits (2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5))
- Ignore hits to Pf1N1B4_4787 when looking for 'other' hits (2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5))
- Ignore hits to AO356_26355 when looking for 'other' hits (2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5))
- Ignore hits to Pf6N2E2_1146 when looking for 'other' hits (2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5))
- Ignore hits to PfGW456L13_2983 when looking for 'other' hits (Short-chain acyl-CoA dehydrogenase (EC 1.3.8.1))
- Curated sequence GFF2392: isobutyryl-CoA dehydrogenase (EC 1.3.8.1)
- Ignore hits to MONOMER-17424 when looking for 'other' hits (short-chain acyl-CoA dehydrogenase monomer (EC 1.3.8.1))
- Comment: EC 1.3.8.5 includes isobutyryl-CoA dehydrogenases and sometimes (2S)-2-methylbutanoyl-CoA dehydrogenases (involved in isoleucine degradation, usually given EC 1.3.8.5 as well) or 3-methylbutanoyl-CoA dehydrogenases (involved in leucine degradation, usually given EC 1.3.8.4). Some enzymes act on all three methylacyl-CoA substrates. Other genes are required only for isoleucine degradation and their activity on isobutyryl-CoA is uncertain, so they are marked ignore. Also add Psest_2440 (GFF2392), given a different EC number, and ignore PfGW456L13_2983 (given a different EC but involved in isoleucine degradation) and PP_2216 (MONOMER-17424), also involved in isoleucine degradation.
Or cluster all characterized acdH proteins
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.
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About GapMind
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:
- ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
- HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.
where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").
Otherwise, a candidate is "medium confidence" if either:
- ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
- ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
- HMMer finds a hit (regardless of coverage or other bits).
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:
- our ignorance of proteins' functions,
- omissions in the gene models,
- frame-shift errors in the genome sequence, or
- the organism lacks the pathway.
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