GapMind for Amino acid biosynthesis

 

Definition of L-leucine biosynthesis

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

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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:

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:

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