GapMind for catabolism of small carbon sources

 

L-isoleucine catabolism in Azorhizobium caulinodans ORS 571

Best path

livF, livG, livJ, livH, livM, ofo, 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 (34 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-isoleucine ABC transporter, ATPase component 1 (LivF/BraG) AZC_RS15220 AZC_RS10935
livG L-isoleucine ABC transporter, ATPase component 2 (LivG/BraF) AZC_RS15215 AZC_RS01005
livJ L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) AZC_RS15230 AZC_RS00990
livH L-isoleucine ABC transporter, permease component 1 (LivH/BraD) AZC_RS15205 AZC_RS02445
livM L-isoleucine ABC transporter, permease component 2 (LivM/BraE) AZC_RS15210 AZC_RS01000
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused AZC_RS03575
acdH (2S)-2-methylbutanoyl-CoA dehydrogenase AZC_RS02925 AZC_RS14650
ech 2-methyl-3-hydroxybutyryl-CoA hydro-lyase AZC_RS04085 AZC_RS14860
ivdG 3-hydroxy-2-methylbutyryl-CoA dehydrogenase AZC_RS04790 AZC_RS10620
fadA 2-methylacetoacetyl-CoA thiolase AZC_RS01555 AZC_RS15355
pccA propionyl-CoA carboxylase, alpha subunit AZC_RS09205 AZC_RS23530
pccB propionyl-CoA carboxylase, beta subunit AZC_RS09210 AZC_RS23520
epi methylmalonyl-CoA epimerase AZC_RS08740
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit AZC_RS09195 AZC_RS05085
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit AZC_RS09195 AZC_RS05085
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase AZC_RS22880
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) AZC_RS22880
Bap2 L-isoleucine permease Bap2
bcaP L-isoleucine uptake transporter BcaP/CitA
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit AZC_RS09025 AZC_RS09895
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit AZC_RS09035 AZC_RS09890
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component AZC_RS20570 AZC_RS09040
brnQ L-isoleucine:cation symporter BrnQ/BraZ/BraB
dddA 3-hydroxypropionate dehydrogenase AZC_RS16840 AZC_RS06090
hpcD 3-hydroxypropionyl-CoA dehydratase AZC_RS04085 AZC_RS12935
iolA malonate semialdehyde dehydrogenase (CoA-acylating) AZC_RS02920 AZC_RS21125
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component AZC_RS09050 AZC_RS20560
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components AZC_RS09195 AZC_RS05085
natA L-isoleucine ABC transporter, ATPase component 1 (NatA) AZC_RS15510 AZC_RS10930
natB L-isoleucine ABC transporter, substrate-binding component NatB AZC_RS15495
natC L-isoleucine ABC transporter, permease component 1 (NatC)
natD L-isoleucine ABC transporter, permease component 2 (NatD) AZC_RS15500 AZC_RS10920
natE L-isoleucine ABC transporter, ATPase component 2 (NatE) AZC_RS15520 AZC_RS09785
ofoA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit OfoA
ofoB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit OfoB
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit AZC_RS09205 AZC_RS15865
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pco propanyl-CoA oxidase AZC_RS18305 AZC_RS14650
prpB 2-methylisocitrate lyase AZC_RS10945
prpC 2-methylcitrate synthase AZC_RS08870
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase AZC_RS13820 AZC_RS04500
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