GapMind for catabolism of small carbon sources

 

L-leucine catabolism in Hyphomicrobium sulfonivorans WDL6

Best path

livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB

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 (21 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-leucine ABC transporter, ATPase component 1 (LivF/BraG) APY04_RS10575 APY04_RS08095
livG L-leucine ABC transporter, ATPase component 2 (LivG/BraF) APY04_RS10570 APY04_RS08115
livJ L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) APY04_RS10585
livH L-leucine ABC transporter, permease component 1 (LivH/BraD) APY04_RS10560 APY04_RS13100
livM L-leucine ABC transporter, permease component 2 (LivM/BraE) APY04_RS10565 APY04_RS08105
ilvE L-leucine transaminase APY04_RS16460 APY04_RS17235
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
liuA isovaleryl-CoA dehydrogenase APY04_RS04790 APY04_RS09545
liuB 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit APY04_RS01365 APY04_RS04340
liuD 3-methylcrotonyl-CoA carboxylase, beta subunit APY04_RS01350
liuC 3-methylglutaconyl-CoA hydratase APY04_RS10815 APY04_RS07375
liuE hydroxymethylglutaryl-CoA lyase
aacS acetoacetyl-CoA synthetase APY04_RS00535 APY04_RS01545
atoB acetyl-CoA C-acetyltransferase APY04_RS12555 APY04_RS12615
Alternative steps:
AAP1 L-leucine permease AAP1
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ APY04_RS14665
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM)
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP APY04_RS07015 APY04_RS12335
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ)
atoA acetoacetyl-CoA transferase, A subunit
atoD acetoacetyl-CoA transferase, B subunit
Bap2 L-leucine permease Bap2
bcaP L-leucine uptake transporter BcaP
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit APY04_RS12515
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit APY04_RS12520
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component APY04_RS06750 APY04_RS12525
brnQ L-leucine:Na+ symporter BrnQ/BraB
leuT L-leucine:Na+ symporter LeuT
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component APY04_RS12540 APY04_RS06755
natA L-leucine ABC transporter, ATPase component 1 (NatA) APY04_RS08115 APY04_RS10570
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) APY04_RS10560
natE L-leucine ABC transporter, ATPase component 2 (NatE) APY04_RS10575 APY04_RS08095
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 Apr 09 2024. 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 (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). 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. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. 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:

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