GapMind for catabolism of small carbon sources

 

L-leucine catabolism in Pseudomonas fluorescens GW456-L13

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 (28 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-leucine ABC transporter, ATPase component 1 (LivF/BraG) PfGW456L13_4611 PfGW456L13_120
livG L-leucine ABC transporter, ATPase component 2 (LivG/BraF) PfGW456L13_4610 PfGW456L13_121
livJ L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) PfGW456L13_4606 PfGW456L13_124
livH L-leucine ABC transporter, permease component 1 (LivH/BraD) PfGW456L13_4608 PfGW456L13_123
livM L-leucine ABC transporter, permease component 2 (LivM/BraE) PfGW456L13_4609 PfGW456L13_122
ilvE L-leucine transaminase PfGW456L13_3544 PfGW456L13_4923
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit PfGW456L13_3540
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit PfGW456L13_3541
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component PfGW456L13_3542 PfGW456L13_215
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component PfGW456L13_3543 PfGW456L13_4267
liuA isovaleryl-CoA dehydrogenase PfGW456L13_2591 PfGW456L13_1387
liuB 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit PfGW456L13_2588 PfGW456L13_2284
liuD 3-methylcrotonyl-CoA carboxylase, beta subunit PfGW456L13_2590 PfGW456L13_2287
liuC 3-methylglutaconyl-CoA hydratase PfGW456L13_2589 PfGW456L13_2434
liuE hydroxymethylglutaryl-CoA lyase PfGW456L13_2594 PfGW456L13_4547
aacS acetoacetyl-CoA synthetase PfGW456L13_2872 PfGW456L13_2593
atoB acetyl-CoA C-acetyltransferase PfGW456L13_2411 PfGW456L13_2982
Alternative steps:
AAP1 L-leucine permease AAP1
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ PfGW456L13_1698
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) PfGW456L13_1700 PfGW456L13_4772
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP PfGW456L13_1701 PfGW456L13_4773
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) PfGW456L13_1699
atoA acetoacetyl-CoA transferase, A subunit
atoD acetoacetyl-CoA transferase, B subunit
Bap2 L-leucine permease Bap2 PfGW456L13_3211 PfGW456L13_4790
bcaP L-leucine uptake transporter BcaP
brnQ L-leucine:Na+ symporter BrnQ/BraB PfGW456L13_4264
leuT L-leucine:Na+ symporter LeuT
natA L-leucine ABC transporter, ATPase component 1 (NatA) PfGW456L13_4610 PfGW456L13_84
natB L-leucine ABC transporter, substrate-binding component NatB
natC L-leucine ABC transporter, permease component 1 (NatC) PfGW456L13_4609
natD L-leucine ABC transporter, permease component 2 (NatD) PfGW456L13_4608
natE L-leucine ABC transporter, ATPase component 2 (NatE) PfGW456L13_4611 PfGW456L13_120
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused PfGW456L13_3456
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