GapMind for catabolism of small carbon sources

 

L-leucine catabolism in Dechlorosoma suillum PS

Best path

livF, livG, livJ, livH, livM, ilvE, ofo, 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 (22 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-leucine ABC transporter, ATPase component 1 (LivF/BraG) Dsui_0626 Dsui_2057
livG L-leucine ABC transporter, ATPase component 2 (LivG/BraF) Dsui_0627 Dsui_2058
livJ L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) Dsui_0630 Dsui_2061
livH L-leucine ABC transporter, permease component 1 (LivH/BraD) Dsui_0629 Dsui_2060
livM L-leucine ABC transporter, permease component 2 (LivM/BraE) Dsui_0628 Dsui_2059
ilvE L-leucine transaminase Dsui_1904 Dsui_3339
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused Dsui_0379
liuA isovaleryl-CoA dehydrogenase Dsui_0975 Dsui_0977
liuB 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit Dsui_0982 Dsui_0516
liuD 3-methylcrotonyl-CoA carboxylase, beta subunit Dsui_0980 Dsui_0517
liuC 3-methylglutaconyl-CoA hydratase Dsui_0981 Dsui_1378
liuE hydroxymethylglutaryl-CoA lyase Dsui_0984
aacS acetoacetyl-CoA synthetase Dsui_2297 Dsui_3212
atoB acetyl-CoA C-acetyltransferase Dsui_0976 Dsui_3239
Alternative steps:
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) Dsui_0637
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP Dsui_0638 Dsui_2068
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
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component Dsui_1577 Dsui_2218
brnQ L-leucine:Na+ symporter BrnQ/BraB
leuT L-leucine:Na+ symporter LeuT
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component Dsui_1576 Dsui_2219
natA L-leucine ABC transporter, ATPase component 1 (NatA) Dsui_2058 Dsui_0627
natB L-leucine ABC transporter, substrate-binding component NatB
natC L-leucine ABC transporter, permease component 1 (NatC) Dsui_0628
natD L-leucine ABC transporter, permease component 2 (NatD) Dsui_0629 Dsui_2060
natE L-leucine ABC transporter, ATPase component 2 (NatE) Dsui_0841 Dsui_2057
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, 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