GapMind for catabolism of small carbon sources

 

L-leucine catabolism in Shewanella loihica PV-4

Best path

brnQ, ilvE, bkdA, bkdB, bkdC, lpd, 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
brnQ L-leucine:Na+ symporter BrnQ/BraB Shew_0769
ilvE L-leucine transaminase Shew_0291 Shew_0278
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit Shew_1925
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit Shew_1926 Shew_0901
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component Shew_1927 Shew_3430
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component Shew_3429 Shew_3660
liuA isovaleryl-CoA dehydrogenase Shew_2570 Shew_1669
liuB 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit Shew_2573 Shew_3365
liuD 3-methylcrotonyl-CoA carboxylase, beta subunit Shew_2571
liuC 3-methylglutaconyl-CoA hydratase Shew_2572 Shew_1670
liuE hydroxymethylglutaryl-CoA lyase Shew_2574
atoA acetoacetyl-CoA transferase, A subunit Shew_2575
atoD acetoacetyl-CoA transferase, B subunit Shew_2576
atoB acetyl-CoA C-acetyltransferase Shew_1667 Shew_0018
Alternative steps:
aacS acetoacetyl-CoA synthetase Shew_2593
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 Shew_3164 Shew_0974
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ)
Bap2 L-leucine permease Bap2
bcaP L-leucine uptake transporter BcaP
leuT L-leucine:Na+ symporter LeuT Shew_2896
livF L-leucine ABC transporter, ATPase component 1 (LivF/BraG) Shew_2606 Shew_3310
livG L-leucine ABC transporter, ATPase component 2 (LivG/BraF) Shew_2611 Shew_3310
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) Shew_2608
natA L-leucine ABC transporter, ATPase component 1 (NatA) Shew_2611 Shew_3310
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) Shew_2609
natE L-leucine ABC transporter, ATPase component 2 (NatE) Shew_2606 Shew_3164
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