GapMind for catabolism of small carbon sources

 

L-isoleucine catabolism in Cupriavidus basilensis 4G11

Best path

livF, livG, livJ, livH, livM, ofo, acdH, ech, ivdG, fadA, prpC, acnD, prpF, acn, prpB

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 (35 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-isoleucine ABC transporter, ATPase component 1 (LivF/BraG) RR42_RS16960 RR42_RS14405
livG L-isoleucine ABC transporter, ATPase component 2 (LivG/BraF) RR42_RS16965 RR42_RS14410
livJ L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) RR42_RS14425 RR42_RS16980
livH L-isoleucine ABC transporter, permease component 1 (LivH/BraD) RR42_RS16975 RR42_RS14420
livM L-isoleucine ABC transporter, permease component 2 (LivM/BraE) RR42_RS14415 RR42_RS16970
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused RR42_RS19540 RR42_RS34245
acdH (2S)-2-methylbutanoyl-CoA dehydrogenase RR42_RS00895 RR42_RS28565
ech 2-methyl-3-hydroxybutyryl-CoA hydro-lyase RR42_RS02510 RR42_RS18250
ivdG 3-hydroxy-2-methylbutyryl-CoA dehydrogenase RR42_RS03440 RR42_RS25375
fadA 2-methylacetoacetyl-CoA thiolase RR42_RS07610 RR42_RS25455
prpC 2-methylcitrate synthase RR42_RS11265 RR42_RS14475
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) RR42_RS11270 RR42_RS14490
prpF methylaconitate isomerase RR42_RS11275 RR42_RS23050
acn (2R,3S)-2-methylcitrate dehydratase RR42_RS11270 RR42_RS23515
prpB 2-methylisocitrate lyase RR42_RS12200 RR42_RS11260
Alternative steps:
Bap2 L-isoleucine permease Bap2 RR42_RS11100 RR42_RS28305
bcaP L-isoleucine uptake transporter BcaP/CitA RR42_RS01585
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit RR42_RS33045 RR42_RS10655
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit RR42_RS33050 RR42_RS21730
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component RR42_RS33055 RR42_RS07370
brnQ L-isoleucine:cation symporter BrnQ/BraZ/BraB
dddA 3-hydroxypropionate dehydrogenase RR42_RS20290 RR42_RS29710
epi methylmalonyl-CoA epimerase
hpcD 3-hydroxypropionyl-CoA dehydratase RR42_RS23710 RR42_RS18250
iolA malonate semialdehyde dehydrogenase (CoA-acylating) RR42_RS01580 RR42_RS34225
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component RR42_RS07380 RR42_RS26115
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit RR42_RS01600
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components RR42_RS01600
natA L-isoleucine ABC transporter, ATPase component 1 (NatA) RR42_RS16965 RR42_RS14410
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) RR42_RS34785 RR42_RS14420
natE L-isoleucine ABC transporter, ATPase component 2 (NatE) RR42_RS20235 RR42_RS14405
ofoA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit OfoA
ofoB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit OfoB
pccA propionyl-CoA carboxylase, alpha subunit RR42_RS26895 RR42_RS32735
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit RR42_RS17700 RR42_RS29420
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit RR42_RS26895
pccB propionyl-CoA carboxylase, beta subunit RR42_RS26905 RR42_RS29410
pco propanyl-CoA oxidase RR42_RS08770 RR42_RS15400
prpD 2-methylcitrate dehydratase RR42_RS14485
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