GapMind for catabolism of small carbon sources

 

L-isoleucine catabolism in Croceitalea dokdonensis DOKDO 023

Best path

Bap2, 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 (24 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
Bap2 L-isoleucine permease Bap2
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit I595_RS01360 I595_RS04535
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit I595_RS01360 I595_RS03900
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component I595_RS09520 I595_RS11630
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component I595_RS15795 I595_RS02270
acdH (2S)-2-methylbutanoyl-CoA dehydrogenase I595_RS04620 I595_RS00270
ech 2-methyl-3-hydroxybutyryl-CoA hydro-lyase I595_RS07175 I595_RS00285
ivdG 3-hydroxy-2-methylbutyryl-CoA dehydrogenase I595_RS12125 I595_RS01130
fadA 2-methylacetoacetyl-CoA thiolase I595_RS00280 I595_RS15570
pccA propionyl-CoA carboxylase, alpha subunit I595_RS09845 I595_RS12865
pccB propionyl-CoA carboxylase, beta subunit I595_RS09840 I595_RS00620
epi methylmalonyl-CoA epimerase I595_RS13045
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit I595_RS09870 I595_RS14700
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit I595_RS09870
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming)
bcaP L-isoleucine uptake transporter BcaP/CitA
brnQ L-isoleucine:cation symporter BrnQ/BraZ/BraB I595_RS13805
dddA 3-hydroxypropionate dehydrogenase
hpcD 3-hydroxypropionyl-CoA dehydratase I595_RS07175
iolA malonate semialdehyde dehydrogenase (CoA-acylating) I595_RS01520
livF L-isoleucine ABC transporter, ATPase component 1 (LivF/BraG) I595_RS10080 I595_RS12740
livG L-isoleucine ABC transporter, ATPase component 2 (LivG/BraF) I595_RS10080 I595_RS09645
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 I595_RS14700 I595_RS09870
natA L-isoleucine ABC transporter, ATPase component 1 (NatA) I595_RS10080
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) I595_RS10080 I595_RS12780
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 I595_RS09845 I595_RS12865
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pco propanyl-CoA oxidase I595_RS11880 I595_RS08845
prpB 2-methylisocitrate lyase
prpC 2-methylcitrate synthase I595_RS12380
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.

Links

Downloads

Related tools

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