GapMind for catabolism of small carbon sources

 

L-leucine catabolism in Thermoactinomyces daqus H-18

Best path

leuT, ilvE, bkdA, bkdB, bkdC, lpd, 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 (23 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
leuT L-leucine:Na+ symporter LeuT
ilvE L-leucine transaminase JG50_RS0100835 JG50_RS0108415
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit JG50_RS0114955 JG50_RS0105840
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit JG50_RS0114950 JG50_RS0105845
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component JG50_RS0105630 JG50_RS0105850
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component JG50_RS0114960 JG50_RS0105635
liuA isovaleryl-CoA dehydrogenase JG50_RS0113945 JG50_RS0107230
liuB 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit JG50_RS0115085 JG50_RS0106100
liuD 3-methylcrotonyl-CoA carboxylase, beta subunit JG50_RS0106120 JG50_RS0114535
liuC 3-methylglutaconyl-CoA hydratase JG50_RS0106115 JG50_RS0106695
liuE hydroxymethylglutaryl-CoA lyase JG50_RS0106110 JG50_RS0109905
aacS acetoacetyl-CoA synthetase JG50_RS0113940 JG50_RS0105805
atoB acetyl-CoA C-acetyltransferase JG50_RS0107240 JG50_RS0101445
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) JG50_RS0100595 JG50_RS0106735
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP JG50_RS0106730 JG50_RS0104015
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 JG50_RS0115245 JG50_RS0105800
bcaP L-leucine uptake transporter BcaP JG50_RS0106450 JG50_RS0102490
brnQ L-leucine:Na+ symporter BrnQ/BraB
livF L-leucine ABC transporter, ATPase component 1 (LivF/BraG) JG50_RS0104015 JG50_RS0100825
livG L-leucine ABC transporter, ATPase component 2 (LivG/BraF) JG50_RS0103120 JG50_RS0111270
livH L-leucine ABC transporter, permease component 1 (LivH/BraD)
livJ L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3)
livM L-leucine ABC transporter, permease component 2 (LivM/BraE)
natA L-leucine ABC transporter, ATPase component 1 (NatA) JG50_RS0106730 JG50_RS0104015
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)
natE L-leucine ABC transporter, ATPase component 2 (NatE) JG50_RS0106810 JG50_RS0100950
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
ofoA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit OfoA JG50_RS0103260
ofoB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit OfoB JG50_RS0103265
vorA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit VorA
vorB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit VorB JG50_RS0103260
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 24 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 (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