GapMind for catabolism of small carbon sources

 

L-isoleucine catabolism in Phyllobacterium brassicacearum STM 196

Best path

livF, livG, livJ, livH, livM, bkdA, bkdB, bkdC, lpd, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcmA

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 (30 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-isoleucine ABC transporter, ATPase component 1 (LivF/BraG) CU102_RS21785 CU102_RS03080
livG L-isoleucine ABC transporter, ATPase component 2 (LivG/BraF) CU102_RS21790 CU102_RS23505
livJ L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) CU102_RS07510 CU102_RS21775
livH L-isoleucine ABC transporter, permease component 1 (LivH/BraD) CU102_RS21800 CU102_RS20135
livM L-isoleucine ABC transporter, permease component 2 (LivM/BraE) CU102_RS21795 CU102_RS23520
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit CU102_RS13235 CU102_RS26895
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit CU102_RS13240 CU102_RS26900
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component CU102_RS13245 CU102_RS19110
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component CU102_RS13250 CU102_RS08205
acdH (2S)-2-methylbutanoyl-CoA dehydrogenase CU102_RS06015 CU102_RS00185
ech 2-methyl-3-hydroxybutyryl-CoA hydro-lyase CU102_RS13700 CU102_RS14135
ivdG 3-hydroxy-2-methylbutyryl-CoA dehydrogenase CU102_RS28465 CU102_RS21700
fadA 2-methylacetoacetyl-CoA thiolase CU102_RS21705 CU102_RS10795
pccA propionyl-CoA carboxylase, alpha subunit CU102_RS07640 CU102_RS00195
pccB propionyl-CoA carboxylase, beta subunit CU102_RS16335 CU102_RS00190
epi methylmalonyl-CoA epimerase CU102_RS16505
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components CU102_RS00630
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase CU102_RS19205
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) CU102_RS19205
Bap2 L-isoleucine permease Bap2
bcaP L-isoleucine uptake transporter BcaP/CitA
brnQ L-isoleucine:cation symporter BrnQ/BraZ/BraB
dddA 3-hydroxypropionate dehydrogenase CU102_RS20125 CU102_RS04440
hpcD 3-hydroxypropionyl-CoA dehydratase CU102_RS18480 CU102_RS13700
iolA malonate semialdehyde dehydrogenase (CoA-acylating) CU102_RS21825 CU102_RS00695
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit CU102_RS00630
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit CU102_RS00630
natA L-isoleucine ABC transporter, ATPase component 1 (NatA) CU102_RS03085 CU102_RS20145
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)
natE L-isoleucine ABC transporter, ATPase component 2 (NatE) CU102_RS21785 CU102_RS03080
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
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 CU102_RS07640 CU102_RS25290
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pco propanyl-CoA oxidase CU102_RS01740
prpB 2-methylisocitrate lyase CU102_RS02270
prpC 2-methylcitrate synthase CU102_RS08045
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 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