GapMind for catabolism of small carbon sources

 

L-leucine catabolism in Pseudomonas putida KT2440

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) PP_1137 PP_4863
livG L-leucine ABC transporter, ATPase component 2 (LivG/BraF) PP_1138 PP_4864
livJ L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) PP_1141 PP_4867
livH L-leucine ABC transporter, permease component 1 (LivH/BraD) PP_1140 PP_4866
livM L-leucine ABC transporter, permease component 2 (LivM/BraE) PP_1139 PP_4865
ilvE L-leucine transaminase PP_3511 PP_3590
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit PP_4401 PP_0555
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit PP_4402 PP_0554
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component PP_4403 PP_0338
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component PP_4187 PP_4404
liuA isovaleryl-CoA dehydrogenase PP_4064 PP_4780
liuB 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit PP_4067 PP_5347
liuD 3-methylcrotonyl-CoA carboxylase, beta subunit PP_4065
liuC 3-methylglutaconyl-CoA hydratase PP_4066 PP_3540
liuE hydroxymethylglutaryl-CoA lyase PP_3540 PP_3394
atoA acetoacetyl-CoA transferase, A subunit PP_3122 PP_3951
atoD acetoacetyl-CoA transferase, B subunit PP_3123 PP_3952
atoB acetyl-CoA C-acetyltransferase PP_2215 PP_4636
Alternative steps:
aacS acetoacetyl-CoA synthetase PP_3071 PP_3458
AAP1 L-leucine permease AAP1
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ PP_1297
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) PP_1299 PP_1069
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP PP_1300 PP_3597
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) PP_1298 PP_5023
Bap2 L-leucine permease Bap2 PP_3727 PP_1059
bcaP L-leucine uptake transporter BcaP
brnQ L-leucine:Na+ symporter BrnQ/BraB PP_4184
leuT L-leucine:Na+ symporter LeuT
natA L-leucine ABC transporter, ATPase component 1 (NatA) PP_1138 PP_2767
natB L-leucine ABC transporter, substrate-binding component NatB
natC L-leucine ABC transporter, permease component 1 (NatC) PP_4865
natD L-leucine ABC transporter, permease component 2 (NatD) PP_1140 PP_0618
natE L-leucine ABC transporter, ATPase component 2 (NatE) PP_1137 PP_0615
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