GapMind for catabolism of small carbon sources

 

L-leucine catabolism in Paraburkholderia bryophila 376MFSha3.1

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 (27 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-leucine ABC transporter, ATPase component 1 (LivF/BraG) H281DRAFT_04059 H281DRAFT_01585
livG L-leucine ABC transporter, ATPase component 2 (LivG/BraF) H281DRAFT_04060 H281DRAFT_02375
livJ L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) H281DRAFT_02161 H281DRAFT_04063
livH L-leucine ABC transporter, permease component 1 (LivH/BraD) H281DRAFT_04062 H281DRAFT_06397
livM L-leucine ABC transporter, permease component 2 (LivM/BraE) H281DRAFT_04061 H281DRAFT_05513
ilvE L-leucine transaminase H281DRAFT_04193 H281DRAFT_00271
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused H281DRAFT_05847 H281DRAFT_01671
liuA isovaleryl-CoA dehydrogenase H281DRAFT_01346 H281DRAFT_05793
liuB 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit H281DRAFT_01343 H281DRAFT_03840
liuD 3-methylcrotonyl-CoA carboxylase, beta subunit H281DRAFT_01345
liuC 3-methylglutaconyl-CoA hydratase H281DRAFT_01344 H281DRAFT_01200
liuE hydroxymethylglutaryl-CoA lyase H281DRAFT_02101 H281DRAFT_03708
atoA acetoacetyl-CoA transferase, A subunit H281DRAFT_04495 H281DRAFT_01597
atoD acetoacetyl-CoA transferase, B subunit H281DRAFT_04496 H281DRAFT_01596
atoB acetyl-CoA C-acetyltransferase H281DRAFT_00852 H281DRAFT_00857
Alternative steps:
aacS acetoacetyl-CoA synthetase H281DRAFT_02398 H281DRAFT_06226
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) H281DRAFT_05402 H281DRAFT_04268
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP H281DRAFT_04267 H281DRAFT_02565
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) H281DRAFT_03349 H281DRAFT_04269
Bap2 L-leucine permease Bap2 H281DRAFT_04042 H281DRAFT_01668
bcaP L-leucine uptake transporter BcaP H281DRAFT_02180
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component H281DRAFT_00467 H281DRAFT_05114
brnQ L-leucine:Na+ symporter BrnQ/BraB
leuT L-leucine:Na+ symporter LeuT
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component H281DRAFT_00468 H281DRAFT_05115
natA L-leucine ABC transporter, ATPase component 1 (NatA) H281DRAFT_04060 H281DRAFT_02383
natB L-leucine ABC transporter, substrate-binding component NatB
natC L-leucine ABC transporter, permease component 1 (NatC) H281DRAFT_04452
natD L-leucine ABC transporter, permease component 2 (NatD) H281DRAFT_06397 H281DRAFT_04062
natE L-leucine ABC transporter, ATPase component 2 (NatE) H281DRAFT_02384 H281DRAFT_04059
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