GapMind for catabolism of small carbon sources

 

L-leucine catabolism in Pseudomonas stutzeri RCH2

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 (30 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-leucine ABC transporter, ATPase component 1 (LivF/BraG) Psest_1308 Psest_3854
livG L-leucine ABC transporter, ATPase component 2 (LivG/BraF) Psest_1309 Psest_1089
livJ L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) Psest_1312
livH L-leucine ABC transporter, permease component 1 (LivH/BraD) Psest_1311 Psest_3855
livM L-leucine ABC transporter, permease component 2 (LivM/BraE) Psest_1310 Psest_1093
ilvE L-leucine transaminase Psest_0450 Psest_1295
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused Psest_3517
liuA isovaleryl-CoA dehydrogenase Psest_1084 Psest_0539
liuB 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit Psest_1080 Psest_4085
liuD 3-methylcrotonyl-CoA carboxylase, beta subunit Psest_1083
liuC 3-methylglutaconyl-CoA hydratase Psest_1082 Psest_1079
liuE hydroxymethylglutaryl-CoA lyase Psest_1079 Psest_2661
atoA acetoacetyl-CoA transferase, A subunit Psest_1078
atoD acetoacetyl-CoA transferase, B subunit Psest_1077
atoB acetyl-CoA C-acetyltransferase Psest_1076 Psest_2446
Alternative steps:
aacS acetoacetyl-CoA synthetase Psest_1086 Psest_1334
AAP1 L-leucine permease AAP1
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ Psest_3163
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) Psest_3161 Psest_0018
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP Psest_3160 Psest_0139
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) Psest_3162
Bap2 L-leucine permease Bap2 Psest_1697
bcaP L-leucine uptake transporter BcaP
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit Psest_2219 Psest_1429
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit Psest_1427 Psest_2218
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component Psest_0447 Psest_2217
brnQ L-leucine:Na+ symporter BrnQ/BraB Psest_2489
leuT L-leucine:Na+ symporter LeuT
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component Psest_2492 Psest_1663
natA L-leucine ABC transporter, ATPase component 1 (NatA) Psest_1309 Psest_1089
natB L-leucine ABC transporter, substrate-binding component NatB
natC L-leucine ABC transporter, permease component 1 (NatC) Psest_1310
natD L-leucine ABC transporter, permease component 2 (NatD) Psest_1311 Psest_1092
natE L-leucine ABC transporter, ATPase component 2 (NatE) Psest_1308 Psest_1090
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