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:ilvH ilvI ilvC ilvD # 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 leuA 2-isopropylmalate synthase EC:2.3.3.13 uniprot:L0G5E1_ECHVK uniprot:A0A1X9Z750_9SPHI ignore_other:isopropylmalate synthase # Ignore some BRENDA annotations without subunit information for LeuCD # and ignore CharProtDB::CH_122621 (leuCD fusion) which is not actually characterized. # Ignore a 2,3-methylmalate dehydratase (Q0QLE2,Q0QLE1) which is >50% identical to leuCD from DvH (DVU2982,DVU2983). # And, DvH leuC (DVU2982) has similarity to both LeuC and to homoaconitase, and fitness data confirms # its role in amino acid biosynthesis, so explicitly include it. leuC 3-isopropylmalate dehydratase, large subunit term:3-isopropylmalate dehydratase large subunit term:3-isopropylmalate dehydratase%LeuC hmm:TIGR00170 hmm:TIGR02083 hmm:TIGR02086 ignore:SwissProt::Q0QLE2 ignore_other:EC 4.2.1.33 ignore_other:EC 4.2.1.35 uniprot:LEUC_DESVH ignore:CharProtDB::CH_122621 # DvH leuD (DVU2983) has similarity to both LeuD and to homoaconitase, and fitness data confirms # its role in amino acid biosynthesis. leuD 3-isopropylmalate dehydaratase, small subunit term:3-isopropylmalate dehydratase small subunit term:3-isopropylmalate dehydratase%LeuD hmm:TIGR00171 hmm:TIGR02084 hmm:TIGR02087 ignore:SwissProt::Q0QLE1 ignore_other:EC 4.2.1.33 ignore_other:EC 4.2.1.35 uniprot:LEUD_DESVH ignore:CharProtDB::CH_122621 leuB 3-isopropylmalate dehydrogenase EC:1.1.1.85 ilvE leucine transaminase EC:2.6.1.6 EC:2.6.1.42 all: ilvH ilvI ilvC ilvD 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