GapMind for catabolism of small carbon sources

 

L-leucine catabolism in Escherichia coli BW25113

Best path

livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB

Also see fitness data for the top candidates

Rules

Overview: Leucine degradation in GapMind is based on MetaCyc pathway L-leucine degradation I, via branched alpha-keto acid dehydrogenase (link). Other pathways for are not included here because they are not linked to sequence (link) or do not result in carbon incorporation.

39 steps (23 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-leucine ABC transporter, ATPase component 1 (LivF/BraG) b3454 b3201
livG L-leucine ABC transporter, ATPase component 2 (LivG/BraF) b3455 b3201
livJ L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) b3458 b3460
livH L-leucine ABC transporter, permease component 1 (LivH/BraD) b3457
livM L-leucine ABC transporter, permease component 2 (LivM/BraE) b3456
ilvE L-leucine transaminase b4054 b3770
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
liuA isovaleryl-CoA dehydrogenase b4187 b0039
liuB 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit b3256
liuD 3-methylcrotonyl-CoA carboxylase, beta subunit
liuC 3-methylglutaconyl-CoA hydratase b1393 b0036
liuE hydroxymethylglutaryl-CoA lyase
atoA acetoacetyl-CoA transferase, A subunit b2221
atoD acetoacetyl-CoA transferase, B subunit b2222
atoB acetyl-CoA C-acetyltransferase b2224 b2844
Alternative steps:
aacS acetoacetyl-CoA synthetase b1701 b1805
AAP1 L-leucine permease AAP1
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) b3270 b1918
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP b3271 b0652
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) b3269
Bap2 L-leucine permease Bap2 b2156 b0576
bcaP L-leucine uptake transporter BcaP
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component b0115 b0727
brnQ L-leucine:Na+ symporter BrnQ/BraB b0401
leuT L-leucine:Na+ symporter LeuT
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component b0116 b3962
natA L-leucine ABC transporter, ATPase component 1 (NatA) b3455 b3201
natB L-leucine ABC transporter, substrate-binding component NatB
natC L-leucine ABC transporter, permease component 1 (NatC)
natD L-leucine ABC transporter, permease component 2 (NatD) b3457
natE L-leucine ABC transporter, ATPase component 2 (NatE) b3454 b1513
ofoA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit OfoA
ofoB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit OfoB
vorA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit VorA
vorB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit VorB
vorC branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC

Confidence: high confidence medium confidence low confidence
transporter – transporters and PTS systems are shaded because predicting their specificity is particularly challenging.

This GapMind analysis is from Sep 17 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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