GapMind for catabolism of small carbon sources

 

L-isoleucine catabolism in Marivita geojedonensis DPG-138

Best path

natA, natB, natC, natD, natE, 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 (34 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
natA L-isoleucine ABC transporter, ATPase component 1 (NatA) MGEO_RS19860 MGEO_RS14455
natB L-isoleucine ABC transporter, substrate-binding component NatB MGEO_RS14450
natC L-isoleucine ABC transporter, permease component 1 (NatC) MGEO_RS14470
natD L-isoleucine ABC transporter, permease component 2 (NatD) MGEO_RS19850 MGEO_RS14465
natE L-isoleucine ABC transporter, ATPase component 2 (NatE) MGEO_RS14460 MGEO_RS19855
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused MGEO_RS11165
acdH (2S)-2-methylbutanoyl-CoA dehydrogenase MGEO_RS13880 MGEO_RS05735
ech 2-methyl-3-hydroxybutyryl-CoA hydro-lyase MGEO_RS17480 MGEO_RS15835
ivdG 3-hydroxy-2-methylbutyryl-CoA dehydrogenase MGEO_RS14675 MGEO_RS04630
fadA 2-methylacetoacetyl-CoA thiolase MGEO_RS09905 MGEO_RS17560
pccA propionyl-CoA carboxylase, alpha subunit MGEO_RS05495 MGEO_RS05760
pccB propionyl-CoA carboxylase, beta subunit MGEO_RS05475 MGEO_RS05755
epi methylmalonyl-CoA epimerase MGEO_RS18700
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit MGEO_RS05505 MGEO_RS00155
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit MGEO_RS05505 MGEO_RS00155
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase MGEO_RS14690
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) MGEO_RS14690
Bap2 L-isoleucine permease Bap2
bcaP L-isoleucine uptake transporter BcaP/CitA
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit MGEO_RS05650 MGEO_RS04995
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit MGEO_RS04990 MGEO_RS05645
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component MGEO_RS09570 MGEO_RS04975
brnQ L-isoleucine:cation symporter BrnQ/BraZ/BraB
dddA 3-hydroxypropionate dehydrogenase MGEO_RS07505 MGEO_RS02655
hpcD 3-hydroxypropionyl-CoA dehydratase MGEO_RS17480 MGEO_RS00470
iolA malonate semialdehyde dehydrogenase (CoA-acylating) MGEO_RS13860 MGEO_RS17260
livF L-isoleucine ABC transporter, ATPase component 1 (LivF/BraG) MGEO_RS05250 MGEO_RS04030
livG L-isoleucine ABC transporter, ATPase component 2 (LivG/BraF) MGEO_RS04005 MGEO_RS05255
livH L-isoleucine ABC transporter, permease component 1 (LivH/BraD) MGEO_RS04010 MGEO_RS10635
livJ L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3)
livM L-isoleucine ABC transporter, permease component 2 (LivM/BraE) MGEO_RS19845 MGEO_RS14470
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component MGEO_RS09565 MGEO_RS18755
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components MGEO_RS05505 MGEO_RS00155
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 MGEO_RS05495 MGEO_RS14815
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pco propanyl-CoA oxidase MGEO_RS11945
prpB 2-methylisocitrate lyase MGEO_RS11935
prpC 2-methylcitrate synthase MGEO_RS02490 MGEO_RS11295
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase MGEO_RS06775
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