GapMind for catabolism of small carbon sources

 

L-isoleucine catabolism in Nostoc punctiforme ATCC 29133; PCC 73102

Best path

natA, natB, natC, natD, natE, ofo, 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 (22 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
natA L-isoleucine ABC transporter, ATPase component 1 (NatA) NPUN_RS19810 NPUN_RS25685
natB L-isoleucine ABC transporter, substrate-binding component NatB NPUN_RS13990
natC L-isoleucine ABC transporter, permease component 1 (NatC) NPUN_RS19815
natD L-isoleucine ABC transporter, permease component 2 (NatD) NPUN_RS19325 NPUN_RS25705
natE L-isoleucine ABC transporter, ATPase component 2 (NatE) NPUN_RS05940 NPUN_RS25665
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
acdH (2S)-2-methylbutanoyl-CoA dehydrogenase NPUN_RS17395
ech 2-methyl-3-hydroxybutyryl-CoA hydro-lyase NPUN_RS20040 NPUN_RS16025
ivdG 3-hydroxy-2-methylbutyryl-CoA dehydrogenase NPUN_RS11785 NPUN_RS09090
fadA 2-methylacetoacetyl-CoA thiolase
prpC 2-methylcitrate synthase NPUN_RS28465
prpD 2-methylcitrate dehydratase
acn (2R,3S)-2-methylcitrate dehydratase NPUN_RS09725
prpB 2-methylisocitrate lyase
Alternative steps:
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming)
Bap2 L-isoleucine permease Bap2
bcaP L-isoleucine uptake transporter BcaP/CitA
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit NPUN_RS28225
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit NPUN_RS19450 NPUN_RS16000
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component
brnQ L-isoleucine:cation symporter BrnQ/BraZ/BraB
dddA 3-hydroxypropionate dehydrogenase NPUN_RS25690 NPUN_RS10325
epi methylmalonyl-CoA epimerase
hpcD 3-hydroxypropionyl-CoA dehydratase NPUN_RS20040
iolA malonate semialdehyde dehydrogenase (CoA-acylating) NPUN_RS06130 NPUN_RS26800
livF L-isoleucine ABC transporter, ATPase component 1 (LivF/BraG) NPUN_RS25665 NPUN_RS05940
livG L-isoleucine ABC transporter, ATPase component 2 (LivG/BraF) NPUN_RS25685 NPUN_RS19810
livH L-isoleucine ABC transporter, permease component 1 (LivH/BraD) NPUN_RS25705 NPUN_RS19325
livJ L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3)
livM L-isoleucine ABC transporter, permease component 2 (LivM/BraE) NPUN_RS25695
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component NPUN_RS21095 NPUN_RS04680
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
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 NPUN_RS30115
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit NPUN_RS30115
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit
pco propanyl-CoA oxidase
prpF methylaconitate isomerase
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