GapMind for catabolism of small carbon sources

 

L-isoleucine catabolism in Pseudomonas fluorescens GW456-L13

Best path

livF, livG, livJ, livH, livM, bkdA, bkdB, bkdC, lpd, acdH, ech, ivdG, fadA, prpC, acnD, prpF, acn, prpB

Also see fitness data for the top candidates

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) PfGW456L13_4611 PfGW456L13_120
livG L-isoleucine ABC transporter, ATPase component 2 (LivG/BraF) PfGW456L13_4610 PfGW456L13_121
livJ L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) PfGW456L13_4606 PfGW456L13_124
livH L-isoleucine ABC transporter, permease component 1 (LivH/BraD) PfGW456L13_4608 PfGW456L13_123
livM L-isoleucine ABC transporter, permease component 2 (LivM/BraE) PfGW456L13_4609 PfGW456L13_122
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit PfGW456L13_3540
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit PfGW456L13_3541
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component PfGW456L13_3542 PfGW456L13_215
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component PfGW456L13_3543 PfGW456L13_4267
acdH (2S)-2-methylbutanoyl-CoA dehydrogenase PfGW456L13_2983 PfGW456L13_2985
ech 2-methyl-3-hydroxybutyryl-CoA hydro-lyase PfGW456L13_4041 PfGW456L13_2434
ivdG 3-hydroxy-2-methylbutyryl-CoA dehydrogenase PfGW456L13_2981 PfGW456L13_1761
fadA 2-methylacetoacetyl-CoA thiolase PfGW456L13_4040 PfGW456L13_2982
prpC 2-methylcitrate synthase PfGW456L13_4117 PfGW456L13_4274
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) PfGW456L13_4116 PfGW456L13_4052
prpF methylaconitate isomerase PfGW456L13_4115
acn (2R,3S)-2-methylcitrate dehydratase PfGW456L13_4116 PfGW456L13_3378
prpB 2-methylisocitrate lyase PfGW456L13_4118 PfGW456L13_2633
Alternative steps:
Bap2 L-isoleucine permease Bap2 PfGW456L13_3211 PfGW456L13_4790
bcaP L-isoleucine uptake transporter BcaP/CitA
brnQ L-isoleucine:cation symporter BrnQ/BraZ/BraB PfGW456L13_4264
dddA 3-hydroxypropionate dehydrogenase PfGW456L13_3561 PfGW456L13_1082
epi methylmalonyl-CoA epimerase PfGW456L13_3114 PfGW456L13_1425
hpcD 3-hydroxypropionyl-CoA dehydratase PfGW456L13_3427 PfGW456L13_2984
iolA malonate semialdehyde dehydrogenase (CoA-acylating) PfGW456L13_2 PfGW456L13_5146
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
natA L-isoleucine ABC transporter, ATPase component 1 (NatA) PfGW456L13_4610 PfGW456L13_84
natB L-isoleucine ABC transporter, substrate-binding component NatB
natC L-isoleucine ABC transporter, permease component 1 (NatC) PfGW456L13_4609
natD L-isoleucine ABC transporter, permease component 2 (NatD) PfGW456L13_4608
natE L-isoleucine ABC transporter, ATPase component 2 (NatE) PfGW456L13_4611 PfGW456L13_120
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused PfGW456L13_3456
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 PfGW456L13_2284 PfGW456L13_2588
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit PfGW456L13_728 PfGW456L13_52
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit PfGW456L13_2590 PfGW456L13_2287
pco propanyl-CoA oxidase PfGW456L13_554 PfGW456L13_2983
prpD 2-methylcitrate dehydratase PfGW456L13_4114
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 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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