GapMind for catabolism of small carbon sources

 

L-leucine catabolism in Pseudomonas fluorescens FW300-N2E2

Best path

livF, livG, livJ, livH, livM, 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 (29 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-leucine ABC transporter, ATPase component 1 (LivF/BraG) Pf6N2E2_2926 Pf6N2E2_3576
livG L-leucine ABC transporter, ATPase component 2 (LivG/BraF) Pf6N2E2_2925 Pf6N2E2_3577
livJ L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) Pf6N2E2_2921 Pf6N2E2_3580
livH L-leucine ABC transporter, permease component 1 (LivH/BraD) Pf6N2E2_2923 Pf6N2E2_3579
livM L-leucine ABC transporter, permease component 2 (LivM/BraE) Pf6N2E2_2924 Pf6N2E2_3578
ilvE L-leucine transaminase Pf6N2E2_477 Pf6N2E2_50
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit Pf6N2E2_481 Pf6N2E2_665
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit Pf6N2E2_480 Pf6N2E2_666
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component Pf6N2E2_479 Pf6N2E2_3675
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component Pf6N2E2_478 Pf6N2E2_5857
liuA isovaleryl-CoA dehydrogenase Pf6N2E2_2191 Pf6N2E2_5026
liuB 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit Pf6N2E2_2194 Pf6N2E2_2411
liuD 3-methylcrotonyl-CoA carboxylase, beta subunit Pf6N2E2_2192 Pf6N2E2_2409
liuC 3-methylglutaconyl-CoA hydratase Pf6N2E2_2193 Pf6N2E2_1147
liuE hydroxymethylglutaryl-CoA lyase Pf6N2E2_2189 Pf6N2E2_1040
atoA acetoacetyl-CoA transferase, A subunit Pf6N2E2_2111
atoD acetoacetyl-CoA transferase, B subunit Pf6N2E2_2112
atoB acetyl-CoA C-acetyltransferase Pf6N2E2_2113 Pf6N2E2_1145
Alternative steps:
aacS acetoacetyl-CoA synthetase Pf6N2E2_2042 Pf6N2E2_2190
AAP1 L-leucine permease AAP1
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ Pf6N2E2_5402
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) Pf6N2E2_5404 Pf6N2E2_1799
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP Pf6N2E2_5405 Pf6N2E2_5567
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) Pf6N2E2_5403
Bap2 L-leucine permease Bap2 Pf6N2E2_5459 Pf6N2E2_1423
bcaP L-leucine uptake transporter BcaP
brnQ L-leucine:Na+ symporter BrnQ/BraB Pf6N2E2_5860
leuT L-leucine:Na+ symporter LeuT
natA L-leucine ABC transporter, ATPase component 1 (NatA) Pf6N2E2_2925 Pf6N2E2_1705
natB L-leucine ABC transporter, substrate-binding component NatB
natC L-leucine ABC transporter, permease component 1 (NatC) Pf6N2E2_2924
natD L-leucine ABC transporter, permease component 2 (NatD) Pf6N2E2_3579 Pf6N2E2_3548
natE L-leucine ABC transporter, ATPase component 2 (NatE) Pf6N2E2_2926 Pf6N2E2_3576
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