As text, or see rules and steps
# Leucine biosynthesis in GapMind is based on MetaCyc pathway L-leucine biosynthesis (metacyc:LEUSYN-PWY). # This begins with the initial steps of # valine biosynthesis (see metacyc:VALSYN-PWY), up to 3-methyloxobutanoate. import val.steps:3-methyl-2-oxobutanoate import ile.steps:leuB leuC leuD # Ignore CharProtDB entries with no EC number. # Add Echvi_3833 (uniprot:L0G5E1_ECHVK) and CA265_RS15855 (uniprot:A0A1X9Z750_9SPHI), which are supported by fitness data. # uniprot:P85362 is ignored because it is just 9 amino acids. # uniprot:S3D9F8 and uniprot:K0E4E5 are involved in secondary metabolite synthesis and it is not # clear if they actually have this activity, so they are ignored. leuA 2-isopropylmalate synthase EC:2.3.3.13 uniprot:L0G5E1_ECHVK uniprot:A0A1X9Z750_9SPHI ignore_other:isopropylmalate synthase ignore:SwissProt::P85362 ignore:SwissProt::S3D9F8 ignore:SwissProt::K0E4E5 # Q8NS92 is ignored because it is primarily a transcriptional regulator. # Similarity to aromatic amino acid transaminases or tyrosine transaminases is ignored as they # are often non-specific. ilvE leucine transaminase EC:2.6.1.6 EC:2.6.1.42 ignore:SwissProt::Q8NS92 ignore_other:2.6.1.57 ignore_other:2.6.1.5 all: 3-methyl-2-oxobutanoate leuA leuC leuD leuB ilvE
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