GapMind for catabolism of small carbon sources

 

L-leucine catabolism in Phaeobacter inhibens BS107

Best path

leuT, ilvE, ofo, 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 (26 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
leuT L-leucine:Na+ symporter LeuT
ilvE L-leucine transaminase PGA1_c34110 PGA1_c34960
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused PGA1_c17080 PGA1_c04490
liuA isovaleryl-CoA dehydrogenase PGA1_c10280 PGA1_c12060
liuB 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit PGA1_c10330 PGA1_c21540
liuD 3-methylcrotonyl-CoA carboxylase, beta subunit PGA1_c10320 PGA1_c21600
liuC 3-methylglutaconyl-CoA hydratase PGA1_c10360 PGA1_c36500
liuE hydroxymethylglutaryl-CoA lyase PGA1_c10340
atoA acetoacetyl-CoA transferase, A subunit PGA1_c06210
atoD acetoacetyl-CoA transferase, B subunit PGA1_c06200
atoB acetyl-CoA C-acetyltransferase PGA1_c03400 PGA1_c33180
Alternative steps:
aacS acetoacetyl-CoA synthetase PGA1_262p01840 PGA1_c34070
AAP1 L-leucine permease AAP1
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ PGA1_c01980
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) PGA1_c02000 PGA1_c26600
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP PGA1_c02010 PGA1_262p02350
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) PGA1_c01990
Bap2 L-leucine permease Bap2
bcaP L-leucine uptake transporter BcaP
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit PGA1_c23140 PGA1_c17550
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit PGA1_c23150 PGA1_c17560
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component PGA1_c23180 PGA1_c03590
brnQ L-leucine:Na+ symporter BrnQ/BraB
livF L-leucine ABC transporter, ATPase component 1 (LivF/BraG) PGA1_c02620 PGA1_c32560
livG L-leucine ABC transporter, ATPase component 2 (LivG/BraF) PGA1_c02610 PGA1_c32620
livH L-leucine ABC transporter, permease component 1 (LivH/BraD) PGA1_c02590 PGA1_c16550
livJ L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3)
livM L-leucine ABC transporter, permease component 2 (LivM/BraE) PGA1_c02600 PGA1_c32580
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component PGA1_c17390 PGA1_c23190
natA L-leucine ABC transporter, ATPase component 1 (NatA) PGA1_c15910 PGA1_c02610
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) PGA1_c15940
natE L-leucine ABC transporter, ATPase component 2 (NatE) PGA1_c15920 PGA1_c02620
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, 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