GapMind for catabolism of small carbon sources

 

L-leucine catabolism in Pedobacter sp. GW460-11-11-14-LB5

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 (19 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
leuT L-leucine:Na+ symporter LeuT
ilvE L-leucine transaminase CA265_RS22650 CA265_RS15785
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit CA265_RS18405 CA265_RS19580
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit CA265_RS18405 CA265_RS18860
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component CA265_RS09070 CA265_RS19585
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component CA265_RS05155 CA265_RS24150
liuA isovaleryl-CoA dehydrogenase CA265_RS02820 CA265_RS22715
liuB 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit CA265_RS02215 CA265_RS18365
liuD 3-methylcrotonyl-CoA carboxylase, beta subunit CA265_RS10640 CA265_RS16635
liuC 3-methylglutaconyl-CoA hydratase CA265_RS09125 CA265_RS20005
liuE hydroxymethylglutaryl-CoA lyase CA265_RS13115
atoA acetoacetyl-CoA transferase, A subunit CA265_RS06305
atoD acetoacetyl-CoA transferase, B subunit CA265_RS06310
atoB acetyl-CoA C-acetyltransferase CA265_RS06590 CA265_RS17585
Alternative steps:
aacS acetoacetyl-CoA synthetase
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 CA265_RS04175 CA265_RS04345
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ)
Bap2 L-leucine permease Bap2
bcaP L-leucine uptake transporter BcaP CA265_RS17395 CA265_RS15000
brnQ L-leucine:Na+ symporter BrnQ/BraB
livF L-leucine ABC transporter, ATPase component 1 (LivF/BraG) CA265_RS25230 CA265_RS04345
livG L-leucine ABC transporter, ATPase component 2 (LivG/BraF) CA265_RS25230 CA265_RS16020
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) CA265_RS25230 CA265_RS15245
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) CA265_RS25230 CA265_RS04345
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.

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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, the preprint on GapMind for carbon sources, 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