GapMind for catabolism of small carbon sources

 

L-isoleucine catabolism in Sporolactobacillus vineae SL153

Best path

bcaP, bkdA, bkdB, bkdC, lpd, acdH, ech, ivdG, fadA, prpC, prpD, acn, prpB

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 (27 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
bcaP L-isoleucine uptake transporter BcaP/CitA RH97_RS02450 RH97_RS05565
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit RH97_RS10575 RH97_RS04120
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit RH97_RS10580 RH97_RS04115
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component RH97_RS10585 RH97_RS04110
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component RH97_RS04105 RH97_RS10570
acdH (2S)-2-methylbutanoyl-CoA dehydrogenase RH97_RS08905
ech 2-methyl-3-hydroxybutyryl-CoA hydro-lyase RH97_RS08930 RH97_RS07390
ivdG 3-hydroxy-2-methylbutyryl-CoA dehydrogenase RH97_RS03700 RH97_RS10960
fadA 2-methylacetoacetyl-CoA thiolase RH97_RS08940 RH97_RS04710
prpC 2-methylcitrate synthase RH97_RS00850
prpD 2-methylcitrate dehydratase RH97_RS04485
acn (2R,3S)-2-methylcitrate dehydratase RH97_RS05105
prpB 2-methylisocitrate lyase RH97_RS04480 RH97_RS04375
Alternative steps:
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) RH97_RS05105
Bap2 L-isoleucine permease Bap2 RH97_RS02150 RH97_RS12570
brnQ L-isoleucine:cation symporter BrnQ/BraZ/BraB
dddA 3-hydroxypropionate dehydrogenase
epi methylmalonyl-CoA epimerase
hpcD 3-hydroxypropionyl-CoA dehydratase RH97_RS08930 RH97_RS07390
iolA malonate semialdehyde dehydrogenase (CoA-acylating) RH97_RS06770 RH97_RS06550
livF L-isoleucine ABC transporter, ATPase component 1 (LivF/BraG) RH97_RS07250 RH97_RS07245
livG L-isoleucine ABC transporter, ATPase component 2 (LivG/BraF) RH97_RS07245 RH97_RS08020
livH L-isoleucine ABC transporter, permease component 1 (LivH/BraD) RH97_RS07235
livJ L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) RH97_RS07230
livM L-isoleucine ABC transporter, permease component 2 (LivM/BraE) RH97_RS07240
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components
natA L-isoleucine ABC transporter, ATPase component 1 (NatA) RH97_RS07245 RH97_RS07250
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) RH97_RS07235
natE L-isoleucine ABC transporter, ATPase component 2 (NatE) RH97_RS07250 RH97_RS08365
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
pccA propionyl-CoA carboxylase, alpha subunit RH97_RS08700 RH97_RS04065
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit RH97_RS08700 RH97_RS04065
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit
pco propanyl-CoA oxidase
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 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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 (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). 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. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. 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:

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