GapMind for catabolism of small carbon sources

 

L-isoleucine catabolism in Halioglobus japonicus S1-36

Best path

Bap2, ofo, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small

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 C0029_RS00155
acdH (2S)-2-methylbutanoyl-CoA dehydrogenase C0029_RS01670 C0029_RS16975
ech 2-methyl-3-hydroxybutyryl-CoA hydro-lyase C0029_RS18685 C0029_RS01675
ivdG 3-hydroxy-2-methylbutyryl-CoA dehydrogenase C0029_RS02360 C0029_RS03475
fadA 2-methylacetoacetyl-CoA thiolase C0029_RS18680 C0029_RS06075
pccA propionyl-CoA carboxylase, alpha subunit C0029_RS03860 C0029_RS16990
pccB propionyl-CoA carboxylase, beta subunit C0029_RS16980 C0029_RS11170
epi methylmalonyl-CoA epimerase C0029_RS11180 C0029_RS05365
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit C0029_RS11185
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit C0029_RS11185
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase C0029_RS10190
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming)
bcaP L-isoleucine uptake transporter BcaP/CitA
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit C0029_RS01085
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component C0029_RS07525 C0029_RS01080
brnQ L-isoleucine:cation symporter BrnQ/BraZ/BraB
dddA 3-hydroxypropionate dehydrogenase C0029_RS03565 C0029_RS09135
hpcD 3-hydroxypropionyl-CoA dehydratase C0029_RS09615 C0029_RS01675
iolA malonate semialdehyde dehydrogenase (CoA-acylating) C0029_RS01440 C0029_RS01630
livF L-isoleucine ABC transporter, ATPase component 1 (LivF/BraG) C0029_RS00525 C0029_RS18690
livG L-isoleucine ABC transporter, ATPase component 2 (LivG/BraF) C0029_RS00525 C0029_RS12860
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 C0029_RS10915 C0029_RS12865
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components C0029_RS11185
natA L-isoleucine ABC transporter, ATPase component 1 (NatA) C0029_RS00525
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) C0029_RS10470 C0029_RS12860
ofoA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit OfoA
ofoB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit OfoB C0029_RS10820
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit C0029_RS15355 C0029_RS16990
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit C0029_RS02495
pco propanyl-CoA oxidase C0029_RS13310
prpB 2-methylisocitrate lyase
prpC 2-methylcitrate synthase C0029_RS13155 C0029_RS10890
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 C0029_RS10815
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.

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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 (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