GapMind for catabolism of small carbon sources

 

L-isoleucine catabolism in Geotalea uraniireducens Rf4

Best path

livF, livG, livJ, livH, livM, bkdA, bkdB, bkdC, lpd, acdH, ech, ivdG, fadA, prpC, prpD, acn, prpB

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) GURA_RS10775 GURA_RS00570
livG L-isoleucine ABC transporter, ATPase component 2 (LivG/BraF) GURA_RS10785 GURA_RS00575
livJ L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) GURA_RS10805
livH L-isoleucine ABC transporter, permease component 1 (LivH/BraD) GURA_RS10795
livM L-isoleucine ABC transporter, permease component 2 (LivM/BraE) GURA_RS10790
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit GURA_RS14760 GURA_RS06460
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit GURA_RS14755 GURA_RS06465
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component GURA_RS14750 GURA_RS08200
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component GURA_RS06450 GURA_RS04270
acdH (2S)-2-methylbutanoyl-CoA dehydrogenase GURA_RS15475 GURA_RS15455
ech 2-methyl-3-hydroxybutyryl-CoA hydro-lyase GURA_RS15480 GURA_RS08095
ivdG 3-hydroxy-2-methylbutyryl-CoA dehydrogenase GURA_RS09505 GURA_RS18385
fadA 2-methylacetoacetyl-CoA thiolase GURA_RS08100 GURA_RS15490
prpC 2-methylcitrate synthase GURA_RS00360 GURA_RS08025
prpD 2-methylcitrate dehydratase GURA_RS00365
acn (2R,3S)-2-methylcitrate dehydratase GURA_RS09830
prpB 2-methylisocitrate lyase GURA_RS00355
Alternative steps:
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming)
Bap2 L-isoleucine permease Bap2
bcaP L-isoleucine uptake transporter BcaP/CitA
brnQ L-isoleucine:cation symporter BrnQ/BraZ/BraB
dddA 3-hydroxypropionate dehydrogenase
epi methylmalonyl-CoA epimerase GURA_RS03330
hpcD 3-hydroxypropionyl-CoA dehydratase GURA_RS15480
iolA malonate semialdehyde dehydrogenase (CoA-acylating) GURA_RS16875 GURA_RS00565
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit GURA_RS03325 GURA_RS17755
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit GURA_RS10270 GURA_RS17760
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components GURA_RS06825 GURA_RS03325
natA L-isoleucine ABC transporter, ATPase component 1 (NatA) GURA_RS00575 GURA_RS10785
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) GURA_RS10775 GURA_RS00570
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 GURA_RS11110
pccA propionyl-CoA carboxylase, alpha subunit GURA_RS09260 GURA_RS14795
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit GURA_RS09260 GURA_RS14795
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit GURA_RS03310 GURA_RS17790
pco propanyl-CoA oxidase GURA_RS15315 GURA_RS16870
prpF methylaconitate isomerase
vorA* branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit VorA GURA_RS11365 with GURA_RS11360
vorB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit VorB GURA_RS11370 GURA_RS11115
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