GapMind for catabolism of small carbon sources

 

L-isoleucine catabolism in Pandoraea thiooxydans ATSB16

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 (34 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-isoleucine ABC transporter, ATPase component 1 (LivF/BraG) PATSB16_RS01010 PATSB16_RS05700
livG L-isoleucine ABC transporter, ATPase component 2 (LivG/BraF) PATSB16_RS01005 PATSB16_RS12750
livJ L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) PATSB16_RS00990 PATSB16_RS19595
livH L-isoleucine ABC transporter, permease component 1 (LivH/BraD) PATSB16_RS00995 PATSB16_RS05685
livM L-isoleucine ABC transporter, permease component 2 (LivM/BraE) PATSB16_RS01000 PATSB16_RS05690
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit PATSB16_RS05825
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit PATSB16_RS05820
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component PATSB16_RS05815 PATSB16_RS05315
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component PATSB16_RS05325 PATSB16_RS05810
acdH (2S)-2-methylbutanoyl-CoA dehydrogenase PATSB16_RS16820 PATSB16_RS00750
ech 2-methyl-3-hydroxybutyryl-CoA hydro-lyase PATSB16_RS15750 PATSB16_RS20735
ivdG 3-hydroxy-2-methylbutyryl-CoA dehydrogenase PATSB16_RS00815 PATSB16_RS07890
fadA 2-methylacetoacetyl-CoA thiolase PATSB16_RS05650 PATSB16_RS05675
prpC 2-methylcitrate synthase PATSB16_RS04015 PATSB16_RS12065
prpD 2-methylcitrate dehydratase PATSB16_RS04020
acn (2R,3S)-2-methylcitrate dehydratase PATSB16_RS12110
prpB 2-methylisocitrate lyase PATSB16_RS10440 PATSB16_RS04010
Alternative steps:
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) PATSB16_RS12110
Bap2 L-isoleucine permease Bap2 PATSB16_RS09985 PATSB16_RS11290
bcaP L-isoleucine uptake transporter BcaP/CitA
brnQ L-isoleucine:cation symporter BrnQ/BraZ/BraB
dddA 3-hydroxypropionate dehydrogenase PATSB16_RS19040 PATSB16_RS13975
epi methylmalonyl-CoA epimerase
hpcD 3-hydroxypropionyl-CoA dehydratase PATSB16_RS20735 PATSB16_RS06150
iolA malonate semialdehyde dehydrogenase (CoA-acylating) PATSB16_RS19035 PATSB16_RS01900
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit PATSB16_RS16985
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components PATSB16_RS16985
natA L-isoleucine ABC transporter, ATPase component 1 (NatA) PATSB16_RS03645 PATSB16_RS01005
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) PATSB16_RS03635 PATSB16_RS05685
natE L-isoleucine ABC transporter, ATPase component 2 (NatE) PATSB16_RS03650 PATSB16_RS05700
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused PATSB16_RS19815 PATSB16_RS19020
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 PATSB16_RS16865 PATSB16_RS00325
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit PATSB16_RS00325 PATSB16_RS07865
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit PATSB16_RS16865
pccB propionyl-CoA carboxylase, beta subunit PATSB16_RS16835
pco propanyl-CoA oxidase PATSB16_RS19095 PATSB16_RS01745
prpF methylaconitate isomerase PATSB16_RS19520 PATSB16_RS17580
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