GapMind for catabolism of small carbon sources

 

L-leucine catabolism in Magnetospirillum magneticum AMB-1

Best path

livF, livG, livJ, livH, livM, ilvE, ofo, 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 (24 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-leucine ABC transporter, ATPase component 1 (LivF/BraG) AMB_RS09120 AMB_RS10230
livG L-leucine ABC transporter, ATPase component 2 (LivG/BraF) AMB_RS09125 AMB_RS08465
livJ L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) AMB_RS15010
livH L-leucine ABC transporter, permease component 1 (LivH/BraD) AMB_RS09135 AMB_RS08455
livM L-leucine ABC transporter, permease component 2 (LivM/BraE) AMB_RS09130 AMB_RS08460
ilvE L-leucine transaminase AMB_RS02850 AMB_RS06965
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
liuA isovaleryl-CoA dehydrogenase AMB_RS03480 AMB_RS13080
liuB 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit AMB_RS03465 AMB_RS21445
liuD 3-methylcrotonyl-CoA carboxylase, beta subunit AMB_RS03475 AMB_RS21450
liuC 3-methylglutaconyl-CoA hydratase AMB_RS03470 AMB_RS03645
liuE hydroxymethylglutaryl-CoA lyase AMB_RS03460
aacS acetoacetyl-CoA synthetase AMB_RS03000 AMB_RS13240
atoB acetyl-CoA C-acetyltransferase AMB_RS18210 AMB_RS04295
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 AMB_RS10565 AMB_RS05625
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 AMB_RS11705
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit AMB_RS11710 AMB_RS00370
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component AMB_RS20045 AMB_RS11715
brnQ L-leucine:Na+ symporter BrnQ/BraB
leuT L-leucine:Na+ symporter LeuT
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component AMB_RS11730 AMB_RS20050
natA L-leucine ABC transporter, ATPase component 1 (NatA) AMB_RS08465 AMB_RS12355
natB L-leucine ABC transporter, substrate-binding component NatB
natC L-leucine ABC transporter, permease component 1 (NatC) AMB_RS09130
natD L-leucine ABC transporter, permease component 2 (NatD) AMB_RS08455 AMB_RS14465
natE L-leucine ABC transporter, ATPase component 2 (NatE) AMB_RS10230 AMB_RS09120
ofoA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit OfoA AMB_RS10840
ofoB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit OfoB AMB_RS10845
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