GapMind for catabolism of small carbon sources

 

L-isoleucine catabolism in Desulfacinum infernum DSM 9756

Best path

livF, livG, livJ, livH, livM, 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 (32 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-isoleucine ABC transporter, ATPase component 1 (LivF/BraG) BUB04_RS02700 BUB04_RS00760
livG L-isoleucine ABC transporter, ATPase component 2 (LivG/BraF) BUB04_RS02695 BUB04_RS13190
livJ L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) BUB04_RS13175 BUB04_RS14530
livH L-isoleucine ABC transporter, permease component 1 (LivH/BraD) BUB04_RS14535 BUB04_RS02685
livM L-isoleucine ABC transporter, permease component 2 (LivM/BraE) BUB04_RS13185 BUB04_RS14540
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit BUB04_RS01335 BUB04_RS01455
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit BUB04_RS01340 BUB04_RS01450
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component BUB04_RS01345 BUB04_RS07775
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component BUB04_RS03960 BUB04_RS01350
acdH (2S)-2-methylbutanoyl-CoA dehydrogenase BUB04_RS03730 BUB04_RS01095
ech 2-methyl-3-hydroxybutyryl-CoA hydro-lyase BUB04_RS15240 BUB04_RS01090
ivdG 3-hydroxy-2-methylbutyryl-CoA dehydrogenase BUB04_RS07485 BUB04_RS18395
fadA 2-methylacetoacetyl-CoA thiolase BUB04_RS03720 BUB04_RS17410
pccA propionyl-CoA carboxylase, alpha subunit BUB04_RS08790
pccB propionyl-CoA carboxylase, beta subunit BUB04_RS05245 BUB04_RS02735
epi methylmalonyl-CoA epimerase BUB04_RS00980
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit BUB04_RS00960 BUB04_RS13745
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit BUB04_RS00965 BUB04_RS13740
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase BUB04_RS02125
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) BUB04_RS02125
Bap2 L-isoleucine permease Bap2
bcaP L-isoleucine uptake transporter BcaP/CitA
brnQ L-isoleucine:cation symporter BrnQ/BraZ/BraB
dddA 3-hydroxypropionate dehydrogenase
hpcD 3-hydroxypropionyl-CoA dehydratase BUB04_RS03725 BUB04_RS07705
iolA malonate semialdehyde dehydrogenase (CoA-acylating) BUB04_RS04110 BUB04_RS13170
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components BUB04_RS00960 BUB04_RS13745
natA L-isoleucine ABC transporter, ATPase component 1 (NatA) BUB04_RS02695 BUB04_RS14545
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) BUB04_RS13180 BUB04_RS02685
natE L-isoleucine ABC transporter, ATPase component 2 (NatE) BUB04_RS14475 BUB04_RS02700
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
ofoA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit OfoA BUB04_RS11735 BUB04_RS05910
ofoB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit OfoB BUB04_RS02325 BUB04_RS11740
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit BUB04_RS08790
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pco propanyl-CoA oxidase BUB04_RS12135
prpB 2-methylisocitrate lyase
prpC 2-methylcitrate synthase BUB04_RS10620
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 BUB04_RS02330 BUB04_RS05910
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