GapMind for catabolism of small carbon sources

 

L-isoleucine catabolism in Pantoea rwandensis LMG 26275

Best path

livF, livG, livJ, livH, livM, ofo, acdH, ech, ivdG, fadA, prpC, acnD, prpF, 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 (27 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-isoleucine ABC transporter, ATPase component 1 (LivF/BraG) HA51_RS18890 HA51_RS15825
livG L-isoleucine ABC transporter, ATPase component 2 (LivG/BraF) HA51_RS18895 HA51_RS15830
livJ L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) HA51_RS18910 HA51_RS15845
livH L-isoleucine ABC transporter, permease component 1 (LivH/BraD) HA51_RS18905 HA51_RS15840
livM L-isoleucine ABC transporter, permease component 2 (LivM/BraE) HA51_RS18900 HA51_RS15835
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
acdH (2S)-2-methylbutanoyl-CoA dehydrogenase
ech 2-methyl-3-hydroxybutyryl-CoA hydro-lyase HA51_RS26560 HA51_RS11045
ivdG 3-hydroxy-2-methylbutyryl-CoA dehydrogenase HA51_RS14510 HA51_RS25235
fadA 2-methylacetoacetyl-CoA thiolase HA51_RS11040 HA51_RS26555
prpC 2-methylcitrate synthase HA51_RS24035
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) HA51_RS08735
prpF methylaconitate isomerase HA51_RS13265 HA51_RS12775
acn (2R,3S)-2-methylcitrate dehydratase HA51_RS25755 HA51_RS08735
prpB 2-methylisocitrate lyase HA51_RS25015
Alternative steps:
Bap2 L-isoleucine permease Bap2 HA51_RS22655 HA51_RS07520
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 HA51_RS25775 HA51_RS24005
brnQ L-isoleucine:cation symporter BrnQ/BraZ/BraB HA51_RS17315 HA51_RS08425
dddA 3-hydroxypropionate dehydrogenase HA51_RS01030 HA51_RS03810
epi methylmalonyl-CoA epimerase
hpcD 3-hydroxypropionyl-CoA dehydratase HA51_RS04965 HA51_RS11045
iolA malonate semialdehyde dehydrogenase (CoA-acylating) HA51_RS03420 HA51_RS17570
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component HA51_RS25770 HA51_RS16010
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit HA51_RS25000
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components
natA L-isoleucine ABC transporter, ATPase component 1 (NatA) HA51_RS18895 HA51_RS09630
natB L-isoleucine ABC transporter, substrate-binding component NatB
natC L-isoleucine ABC transporter, permease component 1 (NatC) HA51_RS18900
natD L-isoleucine ABC transporter, permease component 2 (NatD) HA51_RS18905
natE L-isoleucine ABC transporter, ATPase component 2 (NatE) HA51_RS18890 HA51_RS15825
ofoA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit OfoA
ofoB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit OfoB
pccA propionyl-CoA carboxylase, alpha subunit HA51_RS24830 HA51_RS07090
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit HA51_RS24830 HA51_RS07090
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit
pco propanyl-CoA oxidase
prpD 2-methylcitrate dehydratase
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.

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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