GapMind for catabolism of small carbon sources

 

L-isoleucine catabolism in Bacteroides fluxus YIT 12057

Best path

Bap2, 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 (25 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
Bap2 L-isoleucine permease Bap2
vorA* branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit VorA HMPREF9446_RS03160 with HMPREF9446_RS03165
vorB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit VorB HMPREF9446_RS03155 HMPREF9446_RS13130
vorC branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC HMPREF9446_RS03150
acdH (2S)-2-methylbutanoyl-CoA dehydrogenase HMPREF9446_RS00545
ech 2-methyl-3-hydroxybutyryl-CoA hydro-lyase HMPREF9446_RS13610
ivdG 3-hydroxy-2-methylbutyryl-CoA dehydrogenase HMPREF9446_RS05935 HMPREF9446_RS09995
fadA 2-methylacetoacetyl-CoA thiolase
pccA propionyl-CoA carboxylase, alpha subunit HMPREF9446_RS10475
pccB propionyl-CoA carboxylase, beta subunit HMPREF9446_RS00070 HMPREF9446_RS10485
epi methylmalonyl-CoA epimerase HMPREF9446_RS00075
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit HMPREF9446_RS11995
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit HMPREF9446_RS11995
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming)
bcaP L-isoleucine uptake transporter BcaP/CitA HMPREF9446_RS06370
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit HMPREF9446_RS06135
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit HMPREF9446_RS06135
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component HMPREF9446_RS06130
brnQ L-isoleucine:cation symporter BrnQ/BraZ/BraB
dddA 3-hydroxypropionate dehydrogenase
hpcD 3-hydroxypropionyl-CoA dehydratase HMPREF9446_RS13610
iolA malonate semialdehyde dehydrogenase (CoA-acylating)
livF L-isoleucine ABC transporter, ATPase component 1 (LivF/BraG) HMPREF9446_RS09630 HMPREF9446_RS13805
livG L-isoleucine ABC transporter, ATPase component 2 (LivG/BraF) HMPREF9446_RS09630 HMPREF9446_RS13805
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 HMPREF9446_RS12300 HMPREF9446_RS05445
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components HMPREF9446_RS11995 HMPREF9446_RS11990
natA L-isoleucine ABC transporter, ATPase component 1 (NatA) HMPREF9446_RS09630
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) HMPREF9446_RS09630 HMPREF9446_RS16325
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 HMPREF9446_RS13125
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit HMPREF9446_RS10475
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pco propanyl-CoA oxidase
prpB 2-methylisocitrate lyase
prpC 2-methylcitrate synthase HMPREF9446_RS05250
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