GapMind for catabolism of small carbon sources

 

L-isoleucine catabolism in Nitriliruptor alkaliphilus DSM 45188

Best path

natA, natB, natC, natD, natE, 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 (33 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
natA L-isoleucine ABC transporter, ATPase component 1 (NatA) NITAL_RS06630 NITAL_RS26090
natB L-isoleucine ABC transporter, substrate-binding component NatB
natC L-isoleucine ABC transporter, permease component 1 (NatC) NITAL_RS00060 NITAL_RS06635
natD L-isoleucine ABC transporter, permease component 2 (NatD) NITAL_RS00065 NITAL_RS06640
natE L-isoleucine ABC transporter, ATPase component 2 (NatE) NITAL_RS26090 NITAL_RS06625
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit NITAL_RS11440
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit NITAL_RS11445 NITAL_RS10280
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component NITAL_RS11450 NITAL_RS19475
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component NITAL_RS19470 NITAL_RS11455
acdH (2S)-2-methylbutanoyl-CoA dehydrogenase NITAL_RS22860 NITAL_RS10175
ech 2-methyl-3-hydroxybutyryl-CoA hydro-lyase NITAL_RS10870 NITAL_RS09215
ivdG 3-hydroxy-2-methylbutyryl-CoA dehydrogenase NITAL_RS22540 NITAL_RS22550
fadA 2-methylacetoacetyl-CoA thiolase NITAL_RS12720 NITAL_RS12465
pccA propionyl-CoA carboxylase, alpha subunit NITAL_RS10130 NITAL_RS15990
pccB propionyl-CoA carboxylase, beta subunit NITAL_RS22865 NITAL_RS10155
epi methylmalonyl-CoA epimerase NITAL_RS10825
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit NITAL_RS10065 NITAL_RS00965
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit NITAL_RS01120 NITAL_RS00965
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase NITAL_RS17910
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) NITAL_RS17910
Bap2 L-isoleucine permease Bap2
bcaP L-isoleucine uptake transporter BcaP/CitA
brnQ L-isoleucine:cation symporter BrnQ/BraZ/BraB
dddA 3-hydroxypropionate dehydrogenase NITAL_RS02760 NITAL_RS19580
hpcD 3-hydroxypropionyl-CoA dehydratase NITAL_RS09215 NITAL_RS12715
iolA malonate semialdehyde dehydrogenase (CoA-acylating) NITAL_RS09035 NITAL_RS05175
livF L-isoleucine ABC transporter, ATPase component 1 (LivF/BraG) NITAL_RS01180 NITAL_RS08785
livG L-isoleucine ABC transporter, ATPase component 2 (LivG/BraF) NITAL_RS08790 NITAL_RS01175
livH L-isoleucine ABC transporter, permease component 1 (LivH/BraD) NITAL_RS08770 NITAL_RS01165
livJ L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3)
livM L-isoleucine ABC transporter, permease component 2 (LivM/BraE) NITAL_RS01160 NITAL_RS08775
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components NITAL_RS22060 NITAL_RS10065
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 NITAL_RS19955
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit NITAL_RS10130 NITAL_RS22870
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pco propanyl-CoA oxidase NITAL_RS24285 NITAL_RS23005
prpB 2-methylisocitrate lyase
prpC 2-methylcitrate synthase NITAL_RS14580
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase
vorA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit VorA NITAL_RS19955
vorB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit VorB NITAL_RS19960
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