GapMind for catabolism of small carbon sources

 

L-isoleucine catabolism in Desulfatiglans anilini DSM 4660

Best path

livF, livG, livJ, livH, livM, vorA*, vorB, vorC, 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 (29 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-isoleucine ABC transporter, ATPase component 1 (LivF/BraG) H567_RS0109140 H567_RS0107395
livG L-isoleucine ABC transporter, ATPase component 2 (LivG/BraF) H567_RS23995 H567_RS23835
livJ L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) H567_RS0109120
livH L-isoleucine ABC transporter, permease component 1 (LivH/BraD) H567_RS0109125 H567_RS0115930
livM L-isoleucine ABC transporter, permease component 2 (LivM/BraE) H567_RS0109130 H567_RS0108380
vorA* branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit VorA H567_RS0102585 with H567_RS0102580 H567_RS0100385
vorB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit VorB H567_RS0100390 H567_RS0102590
vorC branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC H567_RS0102595
acdH (2S)-2-methylbutanoyl-CoA dehydrogenase H567_RS0110860 H567_RS0104145
ech 2-methyl-3-hydroxybutyryl-CoA hydro-lyase H567_RS0110895 H567_RS0115475
ivdG 3-hydroxy-2-methylbutyryl-CoA dehydrogenase H567_RS0117055 H567_RS0106010
fadA 2-methylacetoacetyl-CoA thiolase H567_RS0110730 H567_RS0110065
pccA propionyl-CoA carboxylase, alpha subunit
pccB propionyl-CoA carboxylase, beta subunit H567_RS0106055 H567_RS0118015
epi methylmalonyl-CoA epimerase H567_RS0112715 H567_RS0121800
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit H567_RS0106035 H567_RS0120695
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit H567_RS0120700 H567_RS0110880
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase H567_RS0109540
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming)
Bap2 L-isoleucine permease Bap2
bcaP L-isoleucine uptake transporter BcaP/CitA
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit H567_RS0119820
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit H567_RS0119825
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component
brnQ L-isoleucine:cation symporter BrnQ/BraZ/BraB
dddA 3-hydroxypropionate dehydrogenase
hpcD 3-hydroxypropionyl-CoA dehydratase H567_RS0110895 H567_RS0118000
iolA malonate semialdehyde dehydrogenase (CoA-acylating)
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component H567_RS0118430 H567_RS25615
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components H567_RS0106035 H567_RS0120695
natA L-isoleucine ABC transporter, ATPase component 1 (NatA) H567_RS0114755 H567_RS0107400
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) H567_RS0109125 H567_RS0115930
natE L-isoleucine ABC transporter, ATPase component 2 (NatE) H567_RS0109140 H567_RS0108405
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
ofoA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit OfoA H567_RS0121655 H567_RS0116420
ofoB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit OfoB H567_RS0111775 H567_RS0116415
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pco propanyl-CoA oxidase H567_RS0117635 H567_RS0110050
prpB 2-methylisocitrate lyase
prpC 2-methylcitrate synthase H567_RS0101215
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase

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