GapMind for catabolism of small carbon sources

 

L-isoleucine catabolism in Aquimarina macrocephali JAMB N27

Best path

brnQ, bkdA, bkdB, bkdC, lpd, 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
brnQ L-isoleucine:cation symporter BrnQ/BraZ/BraB Z054_RS0102630
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit Z054_RS0105825 Z054_RS0121170
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit Z054_RS0105825 Z054_RS0113525
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component Z054_RS0121175 Z054_RS0117330
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component Z054_RS0112740 Z054_RS0110780
acdH (2S)-2-methylbutanoyl-CoA dehydrogenase Z054_RS0121070 Z054_RS0104505
ech 2-methyl-3-hydroxybutyryl-CoA hydro-lyase Z054_RS0106865 Z054_RS0124795
ivdG 3-hydroxy-2-methylbutyryl-CoA dehydrogenase Z054_RS0106690 Z054_RS0109740
fadA 2-methylacetoacetyl-CoA thiolase Z054_RS0106210 Z054_RS0115825
pccA propionyl-CoA carboxylase, alpha subunit Z054_RS0117505 Z054_RS0101825
pccB propionyl-CoA carboxylase, beta subunit Z054_RS0117500 Z054_RS0107360
epi methylmalonyl-CoA epimerase Z054_RS0101730
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit Z054_RS0103245 Z054_RS0121655
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit Z054_RS0103245
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming)
Bap2 L-isoleucine permease Bap2
bcaP L-isoleucine uptake transporter BcaP/CitA
dddA 3-hydroxypropionate dehydrogenase
hpcD 3-hydroxypropionyl-CoA dehydratase Z054_RS0108580 Z054_RS0106865
iolA malonate semialdehyde dehydrogenase (CoA-acylating) Z054_RS0121915 Z054_RS0121900
livF L-isoleucine ABC transporter, ATPase component 1 (LivF/BraG) Z054_RS0104130 Z054_RS0126330
livG L-isoleucine ABC transporter, ATPase component 2 (LivG/BraF) Z054_RS0104130 Z054_RS0126330
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)
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components Z054_RS0121655 Z054_RS0103245
natA L-isoleucine ABC transporter, ATPase component 1 (NatA) Z054_RS0104130
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) Z054_RS0104130 Z054_RS0108435
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
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit Z054_RS0117505 Z054_RS0101825
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pco propanyl-CoA oxidase Z054_RS0123520
prpB 2-methylisocitrate lyase Z054_RS0119435
prpC 2-methylcitrate synthase Z054_RS0114905
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
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