GapMind for catabolism of small carbon sources

 

L-isoleucine catabolism in Pseudovibrio axinellae Ad2

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 (35 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-isoleucine ABC transporter, ATPase component 1 (LivF/BraG) PsAD2_RS02820 PsAD2_RS08270
livG L-isoleucine ABC transporter, ATPase component 2 (LivG/BraF) PsAD2_RS02825 PsAD2_RS06010
livJ L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) PsAD2_RS02810 PsAD2_RS08260
livH L-isoleucine ABC transporter, permease component 1 (LivH/BraD) PsAD2_RS02835 PsAD2_RS08285
livM L-isoleucine ABC transporter, permease component 2 (LivM/BraE) PsAD2_RS02830 PsAD2_RS08280
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused PsAD2_RS22995 PsAD2_RS02870
acdH (2S)-2-methylbutanoyl-CoA dehydrogenase PsAD2_RS16670 PsAD2_RS17745
ech 2-methyl-3-hydroxybutyryl-CoA hydro-lyase PsAD2_RS08800 PsAD2_RS22445
ivdG 3-hydroxy-2-methylbutyryl-CoA dehydrogenase PsAD2_RS04975 PsAD2_RS01750
fadA 2-methylacetoacetyl-CoA thiolase PsAD2_RS01745 PsAD2_RS08175
pccA propionyl-CoA carboxylase, alpha subunit PsAD2_RS02130 PsAD2_RS22235
pccB propionyl-CoA carboxylase, beta subunit PsAD2_RS02145 PsAD2_RS22230
epi methylmalonyl-CoA epimerase PsAD2_RS01440
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit PsAD2_RS04560 PsAD2_RS15690
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit PsAD2_RS04560 PsAD2_RS15690
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase PsAD2_RS01920
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) PsAD2_RS01920
Bap2 L-isoleucine permease Bap2
bcaP L-isoleucine uptake transporter BcaP/CitA
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit PsAD2_RS19465
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit PsAD2_RS19470
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component PsAD2_RS06990 PsAD2_RS19475
brnQ L-isoleucine:cation symporter BrnQ/BraZ/BraB
dddA 3-hydroxypropionate dehydrogenase PsAD2_RS05370 PsAD2_RS08720
hpcD 3-hydroxypropionyl-CoA dehydratase PsAD2_RS08800 PsAD2_RS16425
iolA malonate semialdehyde dehydrogenase (CoA-acylating) PsAD2_RS05090 PsAD2_RS08865
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component PsAD2_RS19485 PsAD2_RS06985
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components PsAD2_RS04560 PsAD2_RS15690
natA L-isoleucine ABC transporter, ATPase component 1 (NatA) PsAD2_RS07405 PsAD2_RS06010
natB L-isoleucine ABC transporter, substrate-binding component NatB
natC L-isoleucine ABC transporter, permease component 1 (NatC) PsAD2_RS07420
natD L-isoleucine ABC transporter, permease component 2 (NatD) PsAD2_RS07415 PsAD2_RS09795
natE L-isoleucine ABC transporter, ATPase component 2 (NatE) PsAD2_RS07410 PsAD2_RS02820
ofoA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit OfoA
ofoB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit OfoB PsAD2_RS09655
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit PsAD2_RS02130 PsAD2_RS01215
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pco propanyl-CoA oxidase PsAD2_RS08770
prpB 2-methylisocitrate lyase PsAD2_RS12285 PsAD2_RS18050
prpC 2-methylcitrate synthase PsAD2_RS01570
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase PsAD2_RS13785
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