GapMind for catabolism of small carbon sources

 

L-isoleucine catabolism in Desulfacinum hydrothermale DSM 13146

Best path

livF, livG, livJ, livH, livM, ofo, 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) B9A12_RS02930 B9A12_RS05170
livG L-isoleucine ABC transporter, ATPase component 2 (LivG/BraF) B9A12_RS02925 B9A12_RS14620
livJ L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) B9A12_RS14635 B9A12_RS02910
livH L-isoleucine ABC transporter, permease component 1 (LivH/BraD) B9A12_RS02915 B9A12_RS14630
livM L-isoleucine ABC transporter, permease component 2 (LivM/BraE) B9A12_RS14625 B9A12_RS00035
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
acdH (2S)-2-methylbutanoyl-CoA dehydrogenase B9A12_RS12590 B9A12_RS01200
ech 2-methyl-3-hydroxybutyryl-CoA hydro-lyase B9A12_RS10305 B9A12_RS12585
ivdG 3-hydroxy-2-methylbutyryl-CoA dehydrogenase
fadA 2-methylacetoacetyl-CoA thiolase B9A12_RS12580 B9A12_RS06945
pccA propionyl-CoA carboxylase, alpha subunit B9A12_RS08335
pccB propionyl-CoA carboxylase, beta subunit B9A12_RS03695 B9A12_RS02965
epi methylmalonyl-CoA epimerase B9A12_RS01640
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit B9A12_RS01655 B9A12_RS14285
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit B9A12_RS01650 B9A12_RS14290
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase B9A12_RS07905
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) B9A12_RS07905
Bap2 L-isoleucine permease Bap2
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 B9A12_RS11440
brnQ L-isoleucine:cation symporter BrnQ/BraZ/BraB
dddA 3-hydroxypropionate dehydrogenase
hpcD 3-hydroxypropionyl-CoA dehydratase B9A12_RS12585 B9A12_RS11510
iolA malonate semialdehyde dehydrogenase (CoA-acylating) B9A12_RS14640 B9A12_RS10445
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component B9A12_RS15430 B9A12_RS11435
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components B9A12_RS01655 B9A12_RS14285
natA L-isoleucine ABC transporter, ATPase component 1 (NatA) B9A12_RS02925 B9A12_RS14620
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) B9A12_RS14630 B9A12_RS02915
natE L-isoleucine ABC transporter, ATPase component 2 (NatE) B9A12_RS02930 B9A12_RS05170
ofoA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit OfoA B9A12_RS09930 B9A12_RS06600
ofoB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit OfoB B9A12_RS09925 B9A12_RS12525
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit B9A12_RS08335
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pco propanyl-CoA oxidase B9A12_RS07135
prpB 2-methylisocitrate lyase
prpC 2-methylcitrate synthase B9A12_RS11060
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 B9A12_RS06600 B9A12_RS02525
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