GapMind for catabolism of small carbon sources

 

L-isoleucine catabolism in Caulobacter crescentus NA1000

Best path

Bap2, ofo, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcmA

Also see fitness data for the top candidates

Rules

Overview: Isoleucine degradation in GapMind is based on MetaCyc pathway L-isoleucine degradation I (link). The other pathways are fermentative and do not lead to carbon incorporation (link, link).

45 steps (28 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
Bap2 L-isoleucine permease Bap2
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused CCNA_03280
acdH (2S)-2-methylbutanoyl-CoA dehydrogenase CCNA_00436 CCNA_01412
ech 2-methyl-3-hydroxybutyryl-CoA hydro-lyase CCNA_00006 CCNA_00996
ivdG 3-hydroxy-2-methylbutyryl-CoA dehydrogenase CCNA_00123 CCNA_01747
fadA 2-methylacetoacetyl-CoA thiolase CCNA_00544 CCNA_00938
pccA propionyl-CoA carboxylase, alpha subunit CCNA_02261 CCNA_02250
pccB propionyl-CoA carboxylase, beta subunit CCNA_02054 CCNA_02252
epi methylmalonyl-CoA epimerase CCNA_02011
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components CCNA_02459 CCNA_03177
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase CCNA_03781
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) CCNA_03781
bcaP L-isoleucine uptake transporter BcaP/CitA 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-isoleucine:cation symporter BrnQ/BraZ/BraB
dddA 3-hydroxypropionate dehydrogenase CCNA_01337 CCNA_00994
hpcD 3-hydroxypropionyl-CoA dehydratase CCNA_00006 CCNA_02658
iolA malonate semialdehyde dehydrogenase (CoA-acylating) CCNA_01360 CCNA_02357
livF L-isoleucine ABC transporter, ATPase component 1 (LivF/BraG) CCNA_03714 CCNA_03235
livG L-isoleucine ABC transporter, ATPase component 2 (LivG/BraF) CCNA_03714 CCNA_03235
livH L-isoleucine ABC transporter, permease component 1 (LivH/BraD)
livJ L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3)
livM L-isoleucine ABC transporter, permease component 2 (LivM/BraE)
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component CCNA_00346 CCNA_01805
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit CCNA_02459 CCNA_03177
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit CCNA_03177 CCNA_02459
natA L-isoleucine ABC transporter, ATPase component 1 (NatA) CCNA_03714 CCNA_02751
natB L-isoleucine ABC transporter, substrate-binding component NatB
natC L-isoleucine ABC transporter, permease component 1 (NatC)
natD L-isoleucine ABC transporter, permease component 2 (NatD)
natE L-isoleucine ABC transporter, ATPase component 2 (NatE) CCNA_03714 CCNA_00366
ofoA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit OfoA
ofoB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit OfoB
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit CCNA_02261 CCNA_01961
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pco propanyl-CoA oxidase
prpB 2-methylisocitrate lyase CCNA_01980 CCNA_01841
prpC 2-methylcitrate synthase CCNA_03757 CCNA_01983
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase
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