GapMind for catabolism of small carbon sources

 

L-isoleucine catabolism in Amycolatopsis halophila YIM 93223

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) AMYHA_RS16245 AMYHA_RS07110
natB L-isoleucine ABC transporter, substrate-binding component NatB AMYHA_RS16235
natC L-isoleucine ABC transporter, permease component 1 (NatC)
natD L-isoleucine ABC transporter, permease component 2 (NatD) AMYHA_RS16255 AMYHA_RS10530
natE L-isoleucine ABC transporter, ATPase component 2 (NatE) AMYHA_RS16240 AMYHA_RS20895
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit AMYHA_RS03550 AMYHA_RS07890
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit AMYHA_RS07885 AMYHA_RS03555
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component AMYHA_RS07880 AMYHA_RS03560
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component AMYHA_RS04850 AMYHA_RS18755
acdH (2S)-2-methylbutanoyl-CoA dehydrogenase AMYHA_RS09585 AMYHA_RS19255
ech 2-methyl-3-hydroxybutyryl-CoA hydro-lyase AMYHA_RS01145 AMYHA_RS20710
ivdG 3-hydroxy-2-methylbutyryl-CoA dehydrogenase AMYHA_RS02615 AMYHA_RS23710
fadA 2-methylacetoacetyl-CoA thiolase AMYHA_RS06545 AMYHA_RS06490
pccA propionyl-CoA carboxylase, alpha subunit AMYHA_RS25215 AMYHA_RS19995
pccB propionyl-CoA carboxylase, beta subunit AMYHA_RS25160 AMYHA_RS19150
epi methylmalonyl-CoA epimerase AMYHA_RS10325
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit AMYHA_RS25265 AMYHA_RS22150
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit AMYHA_RS25265 AMYHA_RS22150
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase AMYHA_RS15065
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) AMYHA_RS15065
Bap2 L-isoleucine permease Bap2
bcaP L-isoleucine uptake transporter BcaP/CitA
brnQ L-isoleucine:cation symporter BrnQ/BraZ/BraB
dddA 3-hydroxypropionate dehydrogenase AMYHA_RS20340 AMYHA_RS26645
hpcD 3-hydroxypropionyl-CoA dehydratase AMYHA_RS20710 AMYHA_RS06590
iolA malonate semialdehyde dehydrogenase (CoA-acylating) AMYHA_RS14120 AMYHA_RS20335
livF L-isoleucine ABC transporter, ATPase component 1 (LivF/BraG) AMYHA_RS20895 AMYHA_RS07105
livG L-isoleucine ABC transporter, ATPase component 2 (LivG/BraF) AMYHA_RS05545 AMYHA_RS20900
livH L-isoleucine ABC transporter, permease component 1 (LivH/BraD) AMYHA_RS04370 AMYHA_RS10530
livJ L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3)
livM L-isoleucine ABC transporter, permease component 2 (LivM/BraE) AMYHA_RS10525 AMYHA_RS20915
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components AMYHA_RS25265 AMYHA_RS16400
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 AMYHA_RS01155
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit AMYHA_RS19995 AMYHA_RS25215
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pco propanyl-CoA oxidase AMYHA_RS24060 AMYHA_RS09585
prpB 2-methylisocitrate lyase AMYHA_RS20455 AMYHA_RS10340
prpC 2-methylcitrate synthase AMYHA_RS06260 AMYHA_RS06280
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 AMYHA_RS01150
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