GapMind for catabolism of small carbon sources

 

L-leucine catabolism in Dyella japonica UNC79MFTsu3.2

Best path

leuT, ilvE, bkdA, bkdB, bkdC, lpd, 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 (21 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
leuT L-leucine:Na+ symporter LeuT
ilvE L-leucine transaminase N515DRAFT_2015 N515DRAFT_0573
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit N515DRAFT_0356
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit N515DRAFT_0355 N515DRAFT_0481
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component N515DRAFT_2156 N515DRAFT_0354
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component N515DRAFT_2155 N515DRAFT_2778
liuA isovaleryl-CoA dehydrogenase N515DRAFT_0941 N515DRAFT_0492
liuB 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit N515DRAFT_0927 N515DRAFT_3374
liuD 3-methylcrotonyl-CoA carboxylase, beta subunit N515DRAFT_0936
liuC 3-methylglutaconyl-CoA hydratase N515DRAFT_0930 N515DRAFT_1164
liuE hydroxymethylglutaryl-CoA lyase N515DRAFT_0926
atoA acetoacetyl-CoA transferase, A subunit N515DRAFT_1736
atoD acetoacetyl-CoA transferase, B subunit N515DRAFT_1736
atoB acetyl-CoA C-acetyltransferase N515DRAFT_0938 N515DRAFT_2688
Alternative steps:
aacS acetoacetyl-CoA synthetase N515DRAFT_1417
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 N515DRAFT_1085 N515DRAFT_1562
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ)
Bap2 L-leucine permease Bap2 N515DRAFT_2630 N515DRAFT_3653
bcaP L-leucine uptake transporter BcaP N515DRAFT_0722 N515DRAFT_2925
brnQ L-leucine:Na+ symporter BrnQ/BraB
livF L-leucine ABC transporter, ATPase component 1 (LivF/BraG) N515DRAFT_3950 N515DRAFT_1248
livG L-leucine ABC transporter, ATPase component 2 (LivG/BraF) N515DRAFT_3950 N515DRAFT_1562
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) N515DRAFT_3950 N515DRAFT_1687
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) N515DRAFT_3950 N515DRAFT_1687
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
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.

Links

Downloads

Related tools

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