GapMind for catabolism of small carbon sources

 

L-isoleucine catabolism in Mesorhizobium ciceri biovar biserrulae WSM1271

Best path

livF, livG, livJ, livH, livM, 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 (35 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-isoleucine ABC transporter, ATPase component 1 (LivF/BraG) MESCI_RS06160 MESCI_RS31070
livG L-isoleucine ABC transporter, ATPase component 2 (LivG/BraF) MESCI_RS06155 MESCI_RS31065
livJ L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) MESCI_RS06170 MESCI_RS24305
livH L-isoleucine ABC transporter, permease component 1 (LivH/BraD) MESCI_RS06145 MESCI_RS02785
livM L-isoleucine ABC transporter, permease component 2 (LivM/BraE) MESCI_RS06150 MESCI_RS31060
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit MESCI_RS04380 MESCI_RS07285
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit MESCI_RS04385 MESCI_RS07290
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component MESCI_RS04390 MESCI_RS18620
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component MESCI_RS04395 MESCI_RS18630
acdH (2S)-2-methylbutanoyl-CoA dehydrogenase MESCI_RS17130 MESCI_RS24275
ech 2-methyl-3-hydroxybutyryl-CoA hydro-lyase MESCI_RS30135 MESCI_RS05330
ivdG 3-hydroxy-2-methylbutyryl-CoA dehydrogenase MESCI_RS10445 MESCI_RS01490
fadA 2-methylacetoacetyl-CoA thiolase MESCI_RS06630 MESCI_RS05450
pccA propionyl-CoA carboxylase, alpha subunit MESCI_RS20920 MESCI_RS24300
pccB propionyl-CoA carboxylase, beta subunit MESCI_RS18485 MESCI_RS24280
epi methylmalonyl-CoA epimerase MESCI_RS16620
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit MESCI_RS24620
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit MESCI_RS24620
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase MESCI_RS04830
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) MESCI_RS04830
Bap2 L-isoleucine permease Bap2
bcaP L-isoleucine uptake transporter BcaP/CitA
brnQ L-isoleucine:cation symporter BrnQ/BraZ/BraB
dddA 3-hydroxypropionate dehydrogenase MESCI_RS08205 MESCI_RS08645
hpcD 3-hydroxypropionyl-CoA dehydratase MESCI_RS30135 MESCI_RS09340
iolA malonate semialdehyde dehydrogenase (CoA-acylating) MESCI_RS06115 MESCI_RS01365
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components MESCI_RS24620
natA L-isoleucine ABC transporter, ATPase component 1 (NatA) MESCI_RS26210 MESCI_RS31065
natB L-isoleucine ABC transporter, substrate-binding component NatB MESCI_RS26180
natC L-isoleucine ABC transporter, permease component 1 (NatC) MESCI_RS26225
natD L-isoleucine ABC transporter, permease component 2 (NatD) MESCI_RS26220 MESCI_RS31055
natE L-isoleucine ABC transporter, ATPase component 2 (NatE) MESCI_RS26215 MESCI_RS06160
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused MESCI_RS01690
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 MESCI_RS20920 MESCI_RS17925
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit MESCI_RS06175
pco propanyl-CoA oxidase MESCI_RS09970 MESCI_RS24275
prpB 2-methylisocitrate lyase MESCI_RS12170
prpC 2-methylcitrate synthase MESCI_RS19935 MESCI_RS06645
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
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