GapMind for catabolism of small carbon sources

 

L-isoleucine catabolism in Sphingomonas histidinilytica UM2

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 (32 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
Bap2 L-isoleucine permease Bap2 B5X82_RS24315
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit B5X82_RS20775 B5X82_RS23215
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit B5X82_RS20780 B5X82_RS23210
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component B5X82_RS23205 B5X82_RS20785
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component B5X82_RS09200 B5X82_RS23200
acdH (2S)-2-methylbutanoyl-CoA dehydrogenase B5X82_RS04280 B5X82_RS24130
ech 2-methyl-3-hydroxybutyryl-CoA hydro-lyase B5X82_RS16345 B5X82_RS23095
ivdG 3-hydroxy-2-methylbutyryl-CoA dehydrogenase B5X82_RS24290 B5X82_RS22365
fadA 2-methylacetoacetyl-CoA thiolase B5X82_RS11200 B5X82_RS18105
pccA propionyl-CoA carboxylase, alpha subunit B5X82_RS15605 B5X82_RS20675
pccB propionyl-CoA carboxylase, beta subunit B5X82_RS15580 B5X82_RS20680
epi methylmalonyl-CoA epimerase B5X82_RS15590 B5X82_RS20505
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit B5X82_RS15595
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit B5X82_RS15595
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase B5X82_RS13120 B5X82_RS13125
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) B5X82_RS13120
bcaP L-isoleucine uptake transporter BcaP/CitA B5X82_RS10835 B5X82_RS14620
brnQ L-isoleucine:cation symporter BrnQ/BraZ/BraB
dddA 3-hydroxypropionate dehydrogenase B5X82_RS01105 B5X82_RS24480
hpcD 3-hydroxypropionyl-CoA dehydratase B5X82_RS16885 B5X82_RS23050
iolA malonate semialdehyde dehydrogenase (CoA-acylating) B5X82_RS24135 B5X82_RS22960
livF L-isoleucine ABC transporter, ATPase component 1 (LivF/BraG) B5X82_RS15520 B5X82_RS22845
livG L-isoleucine ABC transporter, ATPase component 2 (LivG/BraF) B5X82_RS15520 B5X82_RS16780
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 B5X82_RS15595
natA L-isoleucine ABC transporter, ATPase component 1 (NatA) B5X82_RS15520 B5X82_RS23320
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) B5X82_RS15520 B5X82_RS23320
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused B5X82_RS07995
ofoA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit OfoA
ofoB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit OfoB B5X82_RS11955
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit B5X82_RS15605 B5X82_RS00390
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pco propanyl-CoA oxidase B5X82_RS20375
prpB 2-methylisocitrate lyase B5X82_RS11255
prpC 2-methylcitrate synthase B5X82_RS12080
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase
vorA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit VorA
vorB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit VorB B5X82_RS11960
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.

Links

Downloads

Related tools

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