GapMind for catabolism of small carbon sources

 

L-isoleucine catabolism in Thiothrix lacustris DSM 21227

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 (21 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-isoleucine ABC transporter, ATPase component 1 (LivF/BraG) Q394_RS0102930 Q394_RS0106660
livG L-isoleucine ABC transporter, ATPase component 2 (LivG/BraF) Q394_RS0102925 Q394_RS0106655
livJ L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) Q394_RS0102910
livH L-isoleucine ABC transporter, permease component 1 (LivH/BraD) Q394_RS0102915 Q394_RS0106645
livM L-isoleucine ABC transporter, permease component 2 (LivM/BraE) Q394_RS0102920
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
acdH (2S)-2-methylbutanoyl-CoA dehydrogenase
ech 2-methyl-3-hydroxybutyryl-CoA hydro-lyase Q394_RS0112850
ivdG 3-hydroxy-2-methylbutyryl-CoA dehydrogenase Q394_RS0114510 Q394_RS0118475
fadA 2-methylacetoacetyl-CoA thiolase Q394_RS0118420 Q394_RS0100445
prpC 2-methylcitrate synthase Q394_RS0100855 Q394_RS0102885
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) Q394_RS0100860
prpF methylaconitate isomerase Q394_RS0100865
acn (2R,3S)-2-methylcitrate dehydratase Q394_RS0100860 Q394_RS0102890
prpB 2-methylisocitrate lyase Q394_RS0115650 Q394_RS0100850
Alternative steps:
Bap2 L-isoleucine permease Bap2
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 Q394_RS0108510 Q394_RS0102865
brnQ L-isoleucine:cation symporter BrnQ/BraZ/BraB
dddA 3-hydroxypropionate dehydrogenase
epi methylmalonyl-CoA epimerase
hpcD 3-hydroxypropionyl-CoA dehydratase
iolA malonate semialdehyde dehydrogenase (CoA-acylating) Q394_RS0104930 Q394_RS0117580
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component Q394_RS0108515 Q394_RS0106590
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components
natA L-isoleucine ABC transporter, ATPase component 1 (NatA) Q394_RS0102925 Q394_RS0106655
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) Q394_RS0102915
natE L-isoleucine ABC transporter, ATPase component 2 (NatE) Q394_RS0102930 Q394_RS0106660
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 Q394_RS0109800 Q394_RS0109245
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit Q394_RS0109800 Q394_RS0109245
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