GapMind for catabolism of small carbon sources

 

L-leucine catabolism in Burkholderia phytofirmans PsJN

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 (29 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-leucine ABC transporter, ATPase component 1 (LivF/BraG) BPHYT_RS15590 BPHYT_RS31755
livG L-leucine ABC transporter, ATPase component 2 (LivG/BraF) BPHYT_RS15595 BPHYT_RS31750
livJ L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) BPHYT_RS01885 BPHYT_RS15610
livH L-leucine ABC transporter, permease component 1 (LivH/BraD) BPHYT_RS15605 BPHYT_RS31740
livM L-leucine ABC transporter, permease component 2 (LivM/BraE) BPHYT_RS15600 BPHYT_RS31745
ilvE L-leucine transaminase BPHYT_RS16285 BPHYT_RS05965
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused BPHYT_RS18305 BPHYT_RS02015
liuA isovaleryl-CoA dehydrogenase BPHYT_RS23260 BPHYT_RS18740
liuB 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit BPHYT_RS23275 BPHYT_RS25975
liuD 3-methylcrotonyl-CoA carboxylase, beta subunit BPHYT_RS23265
liuC 3-methylglutaconyl-CoA hydratase BPHYT_RS23270 BPHYT_RS28020
liuE hydroxymethylglutaryl-CoA lyase BPHYT_RS02130 BPHYT_RS34520
atoA acetoacetyl-CoA transferase, A subunit BPHYT_RS13675 BPHYT_RS21415
atoD acetoacetyl-CoA transferase, B subunit BPHYT_RS13670 BPHYT_RS21420
atoB acetyl-CoA C-acetyltransferase BPHYT_RS09150 BPHYT_RS09180
Alternative steps:
aacS acetoacetyl-CoA synthetase BPHYT_RS19375 BPHYT_RS23420
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) BPHYT_RS24645 BPHYT_RS34460
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP BPHYT_RS16685 BPHYT_RS34455
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) BPHYT_RS21915 BPHYT_RS16695
Bap2 L-leucine permease Bap2 BPHYT_RS15500 BPHYT_RS21680
bcaP L-leucine uptake transporter BcaP BPHYT_RS33230 BPHYT_RS01785
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit BPHYT_RS29360
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit BPHYT_RS29355
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component BPHYT_RS12835 BPHYT_RS08115
brnQ L-leucine:Na+ symporter BrnQ/BraB
leuT L-leucine:Na+ symporter LeuT
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component BPHYT_RS12830 BPHYT_RS08120
natA L-leucine ABC transporter, ATPase component 1 (NatA) BPHYT_RS15595 BPHYT_RS04435
natB L-leucine ABC transporter, substrate-binding component NatB
natC L-leucine ABC transporter, permease component 1 (NatC) BPHYT_RS31745
natD L-leucine ABC transporter, permease component 2 (NatD) BPHYT_RS32510 BPHYT_RS31740
natE L-leucine ABC transporter, ATPase component 2 (NatE) BPHYT_RS19445 BPHYT_RS15590
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