GapMind for catabolism of small carbon sources

 

L-leucine catabolism in Cupriavidus basilensis 4G11

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 (28 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-leucine ABC transporter, ATPase component 1 (LivF/BraG) RR42_RS16960 RR42_RS14405
livG L-leucine ABC transporter, ATPase component 2 (LivG/BraF) RR42_RS16965 RR42_RS14410
livJ L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) RR42_RS14425 RR42_RS16980
livH L-leucine ABC transporter, permease component 1 (LivH/BraD) RR42_RS16975 RR42_RS14420
livM L-leucine ABC transporter, permease component 2 (LivM/BraE) RR42_RS14415 RR42_RS16970
ilvE L-leucine transaminase RR42_RS25890 RR42_RS14595
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused RR42_RS19540 RR42_RS34245
liuA isovaleryl-CoA dehydrogenase RR42_RS26910 RR42_RS00870
liuB 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit RR42_RS26895 RR42_RS29420
liuD 3-methylcrotonyl-CoA carboxylase, beta subunit RR42_RS26905 RR42_RS29410
liuC 3-methylglutaconyl-CoA hydratase RR42_RS26900 RR42_RS00955
liuE hydroxymethylglutaryl-CoA lyase RR42_RS00955 RR42_RS13255
atoA acetoacetyl-CoA transferase, A subunit RR42_RS06555 RR42_RS35925
atoD acetoacetyl-CoA transferase, B subunit RR42_RS06560 RR42_RS35920
atoB acetyl-CoA C-acetyltransferase RR42_RS07610 RR42_RS25455
Alternative steps:
aacS acetoacetyl-CoA synthetase RR42_RS26915 RR42_RS10085
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) RR42_RS27120 RR42_RS09485
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP RR42_RS16370 RR42_RS02590
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) RR42_RS31740 RR42_RS16450
Bap2 L-leucine permease Bap2 RR42_RS11100 RR42_RS28305
bcaP L-leucine uptake transporter BcaP RR42_RS01585
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit RR42_RS33045 RR42_RS10655
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit RR42_RS33050 RR42_RS21730
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component RR42_RS33055 RR42_RS07370
brnQ L-leucine:Na+ symporter BrnQ/BraB
leuT L-leucine:Na+ symporter LeuT
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component RR42_RS07380 RR42_RS26115
natA L-leucine ABC transporter, ATPase component 1 (NatA) RR42_RS14410 RR42_RS16965
natB L-leucine ABC transporter, substrate-binding component NatB
natC L-leucine ABC transporter, permease component 1 (NatC)
natD L-leucine ABC transporter, permease component 2 (NatD) RR42_RS34785 RR42_RS14420
natE L-leucine ABC transporter, ATPase component 2 (NatE) RR42_RS20235 RR42_RS14405
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