GapMind for catabolism of small carbon sources

 

L-isoleucine catabolism in Hydrogenophaga taeniospiralis CCUG 15921 NBRC 102512

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 (33 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-isoleucine ABC transporter, ATPase component 1 (LivF/BraG) HTA01S_RS16505 HTA01S_RS04375
livG L-isoleucine ABC transporter, ATPase component 2 (LivG/BraF) HTA01S_RS16510 HTA01S_RS05080
livJ L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) HTA01S_RS07615
livH L-isoleucine ABC transporter, permease component 1 (LivH/BraD) HTA01S_RS16520 HTA01S_RS04360
livM L-isoleucine ABC transporter, permease component 2 (LivM/BraE) HTA01S_RS16515 HTA01S_RS08705
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused HTA01S_RS23185
acdH (2S)-2-methylbutanoyl-CoA dehydrogenase HTA01S_RS11060 HTA01S_RS11035
ech 2-methyl-3-hydroxybutyryl-CoA hydro-lyase HTA01S_RS04710 HTA01S_RS03890
ivdG 3-hydroxy-2-methylbutyryl-CoA dehydrogenase HTA01S_RS18355 HTA01S_RS14275
fadA 2-methylacetoacetyl-CoA thiolase HTA01S_RS11050 HTA01S_RS02090
pccA propionyl-CoA carboxylase, alpha subunit HTA01S_RS06730 HTA01S_RS11160
pccB propionyl-CoA carboxylase, beta subunit HTA01S_RS06725 HTA01S_RS11130
epi methylmalonyl-CoA epimerase HTA01S_RS06740
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit HTA01S_RS06715 HTA01S_RS04855
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit HTA01S_RS06715 HTA01S_RS09875
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase HTA01S_RS17335 HTA01S_RS17285
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) HTA01S_RS17335
Bap2 L-isoleucine permease Bap2
bcaP L-isoleucine uptake transporter BcaP/CitA
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit HTA01S_RS06615
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit HTA01S_RS06620 HTA01S_RS01230
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component HTA01S_RS06625 HTA01S_RS00010
brnQ L-isoleucine:cation symporter BrnQ/BraZ/BraB
dddA 3-hydroxypropionate dehydrogenase HTA01S_RS09515 HTA01S_RS06370
hpcD 3-hydroxypropionyl-CoA dehydratase HTA01S_RS03890 HTA01S_RS03885
iolA malonate semialdehyde dehydrogenase (CoA-acylating) HTA01S_RS06165 HTA01S_RS16360
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component HTA01S_RS00005 HTA01S_RS07650
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components HTA01S_RS06715 HTA01S_RS04855
natA L-isoleucine ABC transporter, ATPase component 1 (NatA) HTA01S_RS16510 HTA01S_RS14295
natB L-isoleucine ABC transporter, substrate-binding component NatB
natC L-isoleucine ABC transporter, permease component 1 (NatC)
natD L-isoleucine ABC transporter, permease component 2 (NatD) HTA01S_RS16520 HTA01S_RS05630
natE L-isoleucine ABC transporter, ATPase component 2 (NatE) HTA01S_RS14300 HTA01S_RS16505
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 HTA01S_RS06730 HTA01S_RS04010
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pco propanyl-CoA oxidase HTA01S_RS14830 HTA01S_RS11035
prpB 2-methylisocitrate lyase HTA01S_RS22560
prpC 2-methylcitrate synthase HTA01S_RS17235
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase HTA01S_RS19850 HTA01S_RS18160
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 Apr 09 2024. 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