GapMind for catabolism of small carbon sources

 

L-leucine catabolism in Sinorhizobium meliloti 1021

Best path

livF, livG, livJ, livH, livM, ilvE, bkdA, bkdB, bkdC, lpd, 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 (25 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-leucine ABC transporter, ATPase component 1 (LivF/BraG) SMc01948 SMc02358
livG L-leucine ABC transporter, ATPase component 2 (LivG/BraF) SMc01949 SMc02357
livJ L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) SMc01946 SMc00078
livH L-leucine ABC transporter, permease component 1 (LivH/BraD) SMc01951 SMc02359
livM L-leucine ABC transporter, permease component 2 (LivM/BraE) SMc01950
ilvE L-leucine transaminase SMc02896 SMc04323
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit SMc03201 SMc01030
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit SMc03202 SM_b20020
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component SMc03203 SM_b20019
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component SMc03204 SMc01035
liuA isovaleryl-CoA dehydrogenase SM_b21121 SMc01359
liuB 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit SM_b21124 SM_b20756
liuD 3-methylcrotonyl-CoA carboxylase, beta subunit SM_b21122 SM_b20755
liuC 3-methylglutaconyl-CoA hydratase SM_b21126 SMc01153
liuE hydroxymethylglutaryl-CoA lyase SM_b21125
aacS acetoacetyl-CoA synthetase SMc00774 SMc02162
atoB acetyl-CoA C-acetyltransferase SMc03879 SMa1450
Alternative steps:
AAP1 L-leucine permease AAP1
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ SMc02118 SMc00676
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) SMc02120 SMc03865
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP SMc02121 SMc03135
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) SMc02119 SMc03865
atoA acetoacetyl-CoA transferase, A subunit
atoD acetoacetyl-CoA transferase, B subunit
Bap2 L-leucine permease Bap2
bcaP L-leucine uptake transporter BcaP
brnQ L-leucine:Na+ symporter BrnQ/BraB
leuT L-leucine:Na+ symporter LeuT
natA L-leucine ABC transporter, ATPase component 1 (NatA) SMc03120 SMc02357
natB L-leucine ABC transporter, substrate-binding component NatB SMc01946
natC L-leucine ABC transporter, permease component 1 (NatC)
natD L-leucine ABC transporter, permease component 2 (NatD) SM_b20604 SMc03118
natE L-leucine ABC transporter, ATPase component 2 (NatE) SMc01948 SMc02358
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
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