GapMind for catabolism of small carbon sources

 

L-isoleucine catabolism in Moritella dasanensis ArB 0140

Best path

brnQ, bkdA, bkdB, bkdC, lpd, acdH, ech, ivdG, fadA, prpC, acnD, prpF, 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
brnQ L-isoleucine:cation symporter BrnQ/BraZ/BraB A923_RS0120070 A923_RS0115990
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit A923_RS0101130
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit A923_RS0101135
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component A923_RS0101140 A923_RS22235
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component A923_RS0111095 A923_RS0119140
acdH (2S)-2-methylbutanoyl-CoA dehydrogenase A923_RS0101015
ech 2-methyl-3-hydroxybutyryl-CoA hydro-lyase A923_RS0119830 A923_RS0104120
ivdG 3-hydroxy-2-methylbutyryl-CoA dehydrogenase A923_RS0108700 A923_RS0119400
fadA 2-methylacetoacetyl-CoA thiolase A923_RS0104115 A923_RS0119825
prpC 2-methylcitrate synthase A923_RS0100240 A923_RS0113605
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) A923_RS0100245
prpF methylaconitate isomerase A923_RS0100250
acn (2R,3S)-2-methylcitrate dehydratase A923_RS0111105 A923_RS0100245
prpB 2-methylisocitrate lyase A923_RS0100235
Alternative steps:
Bap2 L-isoleucine permease Bap2
bcaP L-isoleucine uptake transporter BcaP/CitA
dddA 3-hydroxypropionate dehydrogenase A923_RS0108520
epi methylmalonyl-CoA epimerase
hpcD 3-hydroxypropionyl-CoA dehydratase A923_RS0116325 A923_RS0104120
iolA malonate semialdehyde dehydrogenase (CoA-acylating) A923_RS0115330 A923_RS0108515
livF L-isoleucine ABC transporter, ATPase component 1 (LivF/BraG) A923_RS0116415 A923_RS0110810
livG L-isoleucine ABC transporter, ATPase component 2 (LivG/BraF) A923_RS0110810 A923_RS0116420
livH L-isoleucine ABC transporter, permease component 1 (LivH/BraD) A923_RS0116430
livJ L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3)
livM L-isoleucine ABC transporter, permease component 2 (LivM/BraE)
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit A923_RS0101145
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components A923_RS0101145
natA L-isoleucine ABC transporter, ATPase component 1 (NatA) A923_RS0110810 A923_RS0116420
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) A923_RS0116415 A923_RS0106420
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 A923_RS0118365 A923_RS0101000
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit A923_RS0118365 A923_RS0101000
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit A923_RS0101010
pco propanyl-CoA oxidase
prpD 2-methylcitrate dehydratase
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.

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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