GapMind for catabolism of small carbon sources

 

L-isoleucine catabolism in Thioalkalivibrio paradoxus ARh 1

Best path

Bap2, ofo, 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 (18 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
acdH (2S)-2-methylbutanoyl-CoA dehydrogenase THITH_RS04140 THITH_RS06790
ech 2-methyl-3-hydroxybutyryl-CoA hydro-lyase THITH_RS06780 THITH_RS08100
ivdG 3-hydroxy-2-methylbutyryl-CoA dehydrogenase THITH_RS08455 THITH_RS10325
fadA 2-methylacetoacetyl-CoA thiolase THITH_RS10310 THITH_RS06785
prpC 2-methylcitrate synthase THITH_RS09395
prpD 2-methylcitrate dehydratase
acn (2R,3S)-2-methylcitrate dehydratase THITH_RS08500
prpB 2-methylisocitrate lyase THITH_RS05895
Alternative steps:
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) THITH_RS08500
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
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component THITH_RS14290 THITH_RS16860
brnQ L-isoleucine:cation symporter BrnQ/BraZ/BraB
dddA 3-hydroxypropionate dehydrogenase
epi methylmalonyl-CoA epimerase
hpcD 3-hydroxypropionyl-CoA dehydratase THITH_RS08100 THITH_RS06780
iolA malonate semialdehyde dehydrogenase (CoA-acylating) THITH_RS17095
livF L-isoleucine ABC transporter, ATPase component 1 (LivF/BraG) THITH_RS14200 THITH_RS08160
livG L-isoleucine ABC transporter, ATPase component 2 (LivG/BraF) THITH_RS14200 THITH_RS05085
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 THITH_RS14285 THITH_RS05975
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) THITH_RS14200
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) THITH_RS14200 THITH_RS05085
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 THITH_RS14865 THITH_RS07425
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit THITH_RS14865 THITH_RS07425
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 Apr 09 2024. 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