GapMind for catabolism of small carbon sources

 

L-leucine catabolism in Desulfatiglans anilini DSM 4660

Best path

livF, livG, livJ, livH, livM, ilvE, vorA*, vorB, vorC, 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
livF L-leucine ABC transporter, ATPase component 1 (LivF/BraG) H567_RS0109140 H567_RS0107395
livG L-leucine ABC transporter, ATPase component 2 (LivG/BraF) H567_RS23995 H567_RS23835
livJ L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) H567_RS0109120
livH L-leucine ABC transporter, permease component 1 (LivH/BraD) H567_RS0109125 H567_RS0115930
livM L-leucine ABC transporter, permease component 2 (LivM/BraE) H567_RS0109130 H567_RS0108380
ilvE L-leucine transaminase H567_RS0103275 H567_RS0116450
vorA* branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit VorA H567_RS0102585 with H567_RS0102580 H567_RS28935
vorB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit VorB H567_RS28940 H567_RS0102590
vorC branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC H567_RS0102595
liuA isovaleryl-CoA dehydrogenase H567_RS0104145 H567_RS0110860
liuB 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit
liuD 3-methylcrotonyl-CoA carboxylase, beta subunit H567_RS0117950 H567_RS0106055
liuC 3-methylglutaconyl-CoA hydratase H567_RS0120240 H567_RS0115475
liuE hydroxymethylglutaryl-CoA lyase
aacS acetoacetyl-CoA synthetase H567_RS0110465 H567_RS0117445
atoB acetyl-CoA C-acetyltransferase H567_RS0110910 H567_RS0110905
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)
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP H567_RS0115555 H567_RS0103445
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 H567_RS0119820
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit H567_RS0119825
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component
brnQ L-leucine:Na+ symporter BrnQ/BraB
leuT L-leucine:Na+ symporter LeuT
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component H567_RS0118430 H567_RS25615
natA L-leucine ABC transporter, ATPase component 1 (NatA) H567_RS0114755 H567_RS0107400
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) H567_RS0109125 H567_RS0115930
natE L-leucine ABC transporter, ATPase component 2 (NatE) H567_RS0109140 H567_RS0108405
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
ofoA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit OfoA H567_RS0121655 H567_RS0116420
ofoB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit OfoB H567_RS0111775 H567_RS0116415

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