GapMind for catabolism of small carbon sources

 

L-leucine catabolism in Echinicola vietnamensis KMM 6221, DSM 17526

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 (18 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
leuT L-leucine:Na+ symporter LeuT
ilvE L-leucine transaminase Echvi_2202 Echvi_1626
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit Echvi_1750 Echvi_1221
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit Echvi_3823 Echvi_1750
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component Echvi_2446 Echvi_0772
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component Echvi_4609 Echvi_0770
liuA isovaleryl-CoA dehydrogenase Echvi_1473 Echvi_1212
liuB 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit Echvi_3962 Echvi_0191
liuD 3-methylcrotonyl-CoA carboxylase, beta subunit Echvi_0113 Echvi_0160
liuC 3-methylglutaconyl-CoA hydratase Echvi_0343 Echvi_4069
liuE hydroxymethylglutaryl-CoA lyase Echvi_3855
atoA acetoacetyl-CoA transferase, A subunit Echvi_3272
atoD acetoacetyl-CoA transferase, B subunit Echvi_3271
atoB acetyl-CoA C-acetyltransferase Echvi_3705 Echvi_1071
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 Echvi_1582 Echvi_4044
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
brnQ L-leucine:Na+ symporter BrnQ/BraB
livF L-leucine ABC transporter, ATPase component 1 (LivF/BraG) Echvi_1333 Echvi_1022
livG L-leucine ABC transporter, ATPase component 2 (LivG/BraF) Echvi_1333 Echvi_1582
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) Echvi_1333 Echvi_1022
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) Echvi_1333 Echvi_4044
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