Finding step amaB for L-lysine catabolism in Lactobacillus oryzae SG293
No candidates for amaB: L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd)
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 amaB
- Curated proteins or TIGRFams with EC 1.2.1.31 (search)
- Ignore hits to Q4L235 when looking for 'other' hits (Beta-alanine-activating enzyme; Acyl-CoA synthetase family member 4; Protein NRPS998; EC 6.2.1.-. L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31))
- Do not include HMM TIGR03443 (when considering EC numbers)
- Ignore hits to P83402 when looking for 'other' hits (Alpha-aminoadipic semialdehyde dehydrogenase; Alpha-AASA dehydrogenase; Aldehyde dehydrogenase family 7 member A1; Antiquitin-1; Delta1-piperideine-6-carboxylate dehydrogenase; P6c dehydrogenase; EC 1.2.1.31)
- Ignore hits to P84463 when looking for 'other' hits (Alpha-aminoadipic semialdehyde dehydrogenase; Alpha-AASA dehydrogenase; Aldehyde dehydrogenase family 7 member A1; Antiquitin-1; Delta1-piperideine-6-carboxylate dehydrogenase; P6c dehydrogenase; EC 1.2.1.31)
- Curated sequence MONOMER-12387: Δ1-piperideine-6-carboxylate dehydrogenase
- UniProt sequence Q88CC3: SubName: Full=L-piperidine-6-carboxylate dehydrogenase {ECO:0000313|EMBL:AAN70823.1}; EC=1.2.1.21 {ECO:0000313|EMBL:AAN70823.1};
- UniProt sequence Q92L07: SubName: Full=Putative aldehyde dehydrogenase transmembrane protein {ECO:0000313|EMBL:CAC47869.1}; EC=1.2.1.3 {ECO:0000313|EMBL:CAC47869.1};
- Comment: Q4L235 is misannotated in BRENDA. TIGR03443 hits both amaB and the ATP-hydrolyzing L-2-aminoadipate reductase. P83402 and P84463 are short sequence fragments. In MetaCyc, MONOMER-20455 is annotated as performing this reaction but was not given this EC number. PP_5258 (Q88CC3) is in a newer version of metacyc. SMc04385 (Q92L07) was identified using fitness data.
Or cluster all characterized amaB proteins
This GapMind analysis is from Sep 24 2021. 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