GapMind for catabolism of small carbon sources

 

L-leucine catabolism in Caulobacter crescentus NA1000

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 (22 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
leuT L-leucine:Na+ symporter LeuT
ilvE L-leucine transaminase CCNA_02244 CCNA_03024
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused CCNA_03280
liuA isovaleryl-CoA dehydrogenase CCNA_02254 CCNA_01875
liuB 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit CCNA_02250 CCNA_02261
liuD 3-methylcrotonyl-CoA carboxylase, beta subunit CCNA_02252 CCNA_02054
liuC 3-methylglutaconyl-CoA hydratase CCNA_02251 CCNA_00006
liuE hydroxymethylglutaryl-CoA lyase CCNA_00500
atoA acetoacetyl-CoA transferase, A subunit CCNA_00206 CCNA_02488
atoD acetoacetyl-CoA transferase, B subunit CCNA_00207 CCNA_02489
atoB acetyl-CoA C-acetyltransferase CCNA_00820 CCNA_00544
Alternative steps:
aacS acetoacetyl-CoA synthetase CCNA_01017 CCNA_01382
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) CCNA_01507
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP CCNA_01506 CCNA_02751
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 CCNA_01242 CCNA_00435
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit CCNA_01799
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit CCNA_01800
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component CCNA_00343 CCNA_01803
brnQ L-leucine:Na+ symporter BrnQ/BraB
livF L-leucine ABC transporter, ATPase component 1 (LivF/BraG) CCNA_03714 CCNA_03235
livG L-leucine ABC transporter, ATPase component 2 (LivG/BraF) CCNA_03714 CCNA_03235
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)
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component CCNA_00346 CCNA_01805
natA L-leucine ABC transporter, ATPase component 1 (NatA) CCNA_03714 CCNA_02751
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) CCNA_03714 CCNA_01670
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