GapMind for catabolism of small carbon sources

 

L-leucine catabolism in Bacteroides thetaiotaomicron VPI-5482

Best path

leuT, ilvE, vorA*, vorB, vorC, liuA, liuB, liuD, liuC, liuE, aacS, 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 (20 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
leuT L-leucine:Na+ symporter LeuT BT3642
ilvE L-leucine transaminase BT3892
vorA* branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit VorA BT0330 with BT0329
vorB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit VorB BT0331 BT2836
vorC branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC BT0333
liuA isovaleryl-CoA dehydrogenase BT1806
liuB 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit BT1915 BT1449
liuD 3-methylcrotonyl-CoA carboxylase, beta subunit BT1686 BT1917
liuC 3-methylglutaconyl-CoA hydratase BT4702
liuE hydroxymethylglutaryl-CoA lyase
aacS acetoacetyl-CoA synthetase BT2782
atoB acetyl-CoA C-acetyltransferase
Alternative steps:
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)
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP BT2494 BT1751
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ)
atoA acetoacetyl-CoA transferase, A subunit
atoD acetoacetyl-CoA transferase, B subunit
Bap2 L-leucine permease Bap2
bcaP L-leucine uptake transporter BcaP
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit BT0312
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit BT0312
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component BT0311
brnQ L-leucine:Na+ symporter BrnQ/BraB
livF L-leucine ABC transporter, ATPase component 1 (LivF/BraG) BT3837 BT1291
livG L-leucine ABC transporter, ATPase component 2 (LivG/BraF) BT3837 BT1291
livH L-leucine ABC transporter, permease component 1 (LivH/BraD)
livJ L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3)
livM L-leucine ABC transporter, permease component 2 (LivM/BraE)
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component BT3186 BT0309
natA L-leucine ABC transporter, ATPase component 1 (NatA) BT3837 BT3640
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)
natE L-leucine ABC transporter, ATPase component 2 (NatE) BT3837 BT0562
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
ofoA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit OfoA
ofoB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit OfoB BT2837

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, 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