GapMind for catabolism of small carbon sources

 

L-isoleucine catabolism in Ruegeria conchae TW15

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 (32 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-isoleucine ABC transporter, ATPase component 1 (LivF/BraG) G7G_RS0115355 G7G_RS0107125
livG L-isoleucine ABC transporter, ATPase component 2 (LivG/BraF) G7G_RS0107130 G7G_RS0115350
livJ L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3)
livH L-isoleucine ABC transporter, permease component 1 (LivH/BraD) G7G_RS0101020 G7G_RS0115340
livM L-isoleucine ABC transporter, permease component 2 (LivM/BraE) G7G_RS0107135 G7G_RS0118395
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused G7G_RS0106765 G7G_RS0102470
acdH (2S)-2-methylbutanoyl-CoA dehydrogenase G7G_RS0106645 G7G_RS0117695
ech 2-methyl-3-hydroxybutyryl-CoA hydro-lyase G7G_RS0116465 G7G_RS0102205
ivdG 3-hydroxy-2-methylbutyryl-CoA dehydrogenase G7G_RS0108810 G7G_RS0114145
fadA 2-methylacetoacetyl-CoA thiolase G7G_RS0122070 G7G_RS0109505
pccA propionyl-CoA carboxylase, alpha subunit G7G_RS0113355 G7G_RS0117665
pccB propionyl-CoA carboxylase, beta subunit G7G_RS0113330 G7G_RS0117675
epi methylmalonyl-CoA epimerase G7G_RS0112770
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit G7G_RS0113370 G7G_RS0117980
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit G7G_RS0113370 G7G_RS0117980
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase G7G_RS0113975 G7G_RS0120980
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) G7G_RS0113975
Bap2 L-isoleucine permease Bap2
bcaP L-isoleucine uptake transporter BcaP/CitA
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit G7G_RS0114335
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit G7G_RS0114330 G7G_RS0110015
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component G7G_RS0122175 G7G_RS0114320
brnQ L-isoleucine:cation symporter BrnQ/BraZ/BraB
dddA 3-hydroxypropionate dehydrogenase G7G_RS0101190 G7G_RS0113310
hpcD 3-hydroxypropionyl-CoA dehydratase G7G_RS0116465 G7G_RS0122460
iolA malonate semialdehyde dehydrogenase (CoA-acylating) G7G_RS0106675 G7G_RS0111640
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component G7G_RS0114415 G7G_RS0122165
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components G7G_RS0113370 G7G_RS0117980
natA L-isoleucine ABC transporter, ATPase component 1 (NatA) G7G_RS0107430 G7G_RS0101005
natB L-isoleucine ABC transporter, substrate-binding component NatB G7G_RS0107425
natC L-isoleucine ABC transporter, permease component 1 (NatC)
natD L-isoleucine ABC transporter, permease component 2 (NatD) G7G_RS0107445 G7G_RS0115340
natE L-isoleucine ABC transporter, ATPase component 2 (NatE) G7G_RS0107435 G7G_RS0107125
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 G7G_RS0113355 G7G_RS0120085
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit G7G_RS0120080
pco propanyl-CoA oxidase G7G_RS0107335 G7G_RS0117695
prpB 2-methylisocitrate lyase
prpC 2-methylcitrate synthase G7G_RS0107985
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