GapMind for catabolism of small carbon sources

 

L-isoleucine catabolism in Herbaspirillum autotrophicum IAM 14942

Best path

livF, livG, livJ, livH, livM, ofo, acdH, ech, ivdG, fadA, prpC, acnD, prpF, 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 (34 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-isoleucine ABC transporter, ATPase component 1 (LivF/BraG) AKL27_RS04805 AKL27_RS09900
livG L-isoleucine ABC transporter, ATPase component 2 (LivG/BraF) AKL27_RS04810 AKL27_RS09905
livJ L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) AKL27_RS09920 AKL27_RS25150
livH L-isoleucine ABC transporter, permease component 1 (LivH/BraD) AKL27_RS04820 AKL27_RS09915
livM L-isoleucine ABC transporter, permease component 2 (LivM/BraE) AKL27_RS09910 AKL27_RS04815
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused AKL27_RS19660 AKL27_RS01445
acdH (2S)-2-methylbutanoyl-CoA dehydrogenase AKL27_RS01455 AKL27_RS24925
ech 2-methyl-3-hydroxybutyryl-CoA hydro-lyase AKL27_RS04630 AKL27_RS10475
ivdG 3-hydroxy-2-methylbutyryl-CoA dehydrogenase AKL27_RS24930 AKL27_RS23770
fadA 2-methylacetoacetyl-CoA thiolase AKL27_RS04650 AKL27_RS00755
prpC 2-methylcitrate synthase AKL27_RS20970 AKL27_RS06595
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) AKL27_RS02305 AKL27_RS06545
prpF methylaconitate isomerase AKL27_RS02300 AKL27_RS03710
acn (2R,3S)-2-methylcitrate dehydratase AKL27_RS02305 AKL27_RS06545
prpB 2-methylisocitrate lyase AKL27_RS07500 AKL27_RS05990
Alternative steps:
Bap2 L-isoleucine permease Bap2 AKL27_RS21895
bcaP L-isoleucine uptake transporter BcaP/CitA
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit AKL27_RS01625
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit AKL27_RS01625 AKL27_RS21790
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component AKL27_RS12255 AKL27_RS01965
brnQ L-isoleucine:cation symporter BrnQ/BraZ/BraB
dddA 3-hydroxypropionate dehydrogenase AKL27_RS14220 AKL27_RS19005
epi methylmalonyl-CoA epimerase
hpcD 3-hydroxypropionyl-CoA dehydratase AKL27_RS10475 AKL27_RS23795
iolA malonate semialdehyde dehydrogenase (CoA-acylating) AKL27_RS14215 AKL27_RS15600
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component AKL27_RS12250 AKL27_RS01640
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit AKL27_RS17280
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components
natA L-isoleucine ABC transporter, ATPase component 1 (NatA) AKL27_RS23275 AKL27_RS18995
natB L-isoleucine ABC transporter, substrate-binding component NatB
natC L-isoleucine ABC transporter, permease component 1 (NatC) AKL27_RS09910 AKL27_RS23270
natD L-isoleucine ABC transporter, permease component 2 (NatD) AKL27_RS04820 AKL27_RS15590
natE L-isoleucine ABC transporter, ATPase component 2 (NatE) AKL27_RS15575 AKL27_RS09900
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 AKL27_RS14630 AKL27_RS12940
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit AKL27_RS12940 AKL27_RS14630
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit AKL27_RS14630
pccB propionyl-CoA carboxylase, beta subunit AKL27_RS14640 AKL27_RS20520
pco propanyl-CoA oxidase AKL27_RS00355 AKL27_RS24925
prpD 2-methylcitrate dehydratase AKL27_RS20980
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