GapMind for catabolism of small carbon sources

 

L-isoleucine catabolism in Novosphingobium barchaimii LL02

Best path

Bap2, bkdA, bkdB, bkdC, lpd, 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 (29 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
Bap2 L-isoleucine permease Bap2
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit V474_RS02435 V474_RS09600
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit V474_RS02440 V474_RS19420
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component V474_RS02445 V474_RS07635
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component V474_RS03825 V474_RS11040
acdH (2S)-2-methylbutanoyl-CoA dehydrogenase V474_RS01300 V474_RS05240
ech 2-methyl-3-hydroxybutyryl-CoA hydro-lyase V474_RS01310 V474_RS20080
ivdG 3-hydroxy-2-methylbutyryl-CoA dehydrogenase V474_RS00850 V474_RS19955
fadA 2-methylacetoacetyl-CoA thiolase V474_RS02980 V474_RS05390
pccA propionyl-CoA carboxylase, alpha subunit V474_RS05365 V474_RS18360
pccB propionyl-CoA carboxylase, beta subunit V474_RS05395 V474_RS18370
epi methylmalonyl-CoA epimerase V474_RS05385
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit V474_RS05380
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit V474_RS05380
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase V474_RS13470 V474_RS08450
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) V474_RS13470 V474_RS10030
bcaP L-isoleucine uptake transporter BcaP/CitA V474_RS08715 V474_RS02665
brnQ L-isoleucine:cation symporter BrnQ/BraZ/BraB
dddA 3-hydroxypropionate dehydrogenase V474_RS12195 V474_RS23920
hpcD 3-hydroxypropionyl-CoA dehydratase V474_RS01310 V474_RS16345
iolA malonate semialdehyde dehydrogenase (CoA-acylating) V474_RS10060 V474_RS17175
livF L-isoleucine ABC transporter, ATPase component 1 (LivF/BraG) V474_RS15730 V474_RS07795
livG L-isoleucine ABC transporter, ATPase component 2 (LivG/BraF) V474_RS07795 V474_RS15730
livH L-isoleucine ABC transporter, permease component 1 (LivH/BraD)
livJ L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3)
livM L-isoleucine ABC transporter, permease component 2 (LivM/BraE)
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components V474_RS05380
natA L-isoleucine ABC transporter, ATPase component 1 (NatA) V474_RS15730
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) V474_RS15730 V474_RS16575
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 V474_RS04820
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit V474_RS05365 V474_RS22420
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pco propanyl-CoA oxidase
prpB 2-methylisocitrate lyase V474_RS10075 V474_RS09690
prpC 2-methylcitrate synthase V474_RS03125
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase V474_RS09055
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