GapMind for catabolism of small carbon sources

 

L-isoleucine catabolism in Sphingobium czechense LL01

Best path

Bap2, 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 (32 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
Bap2 L-isoleucine permease Bap2
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit V473_RS07890 V473_RS09780
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit V473_RS07885 V473_RS09775
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component V473_RS07880 V473_RS02805
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component V473_RS06640 V473_RS22020
acdH (2S)-2-methylbutanoyl-CoA dehydrogenase V473_RS17555 V473_RS04405
ech 2-methyl-3-hydroxybutyryl-CoA hydro-lyase V473_RS04380 V473_RS05770
ivdG 3-hydroxy-2-methylbutyryl-CoA dehydrogenase V473_RS17565 V473_RS08625
fadA 2-methylacetoacetyl-CoA thiolase V473_RS07145 V473_RS00635
pccA propionyl-CoA carboxylase, alpha subunit V473_RS08265 V473_RS17405
pccB propionyl-CoA carboxylase, beta subunit V473_RS08285 V473_RS17400
epi methylmalonyl-CoA epimerase V473_RS08280
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit V473_RS08275
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit V473_RS08275
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase V473_RS10350 V473_RS10360
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) V473_RS10350
bcaP L-isoleucine uptake transporter BcaP/CitA V473_RS03185 V473_RS00330
brnQ L-isoleucine:cation symporter BrnQ/BraZ/BraB
dddA 3-hydroxypropionate dehydrogenase V473_RS05495 V473_RS16770
hpcD 3-hydroxypropionyl-CoA dehydratase V473_RS04380 V473_RS08215
iolA malonate semialdehyde dehydrogenase (CoA-acylating) V473_RS17900 V473_RS05490
livF L-isoleucine ABC transporter, ATPase component 1 (LivF/BraG) V473_RS04120 V473_RS13485
livG L-isoleucine ABC transporter, ATPase component 2 (LivG/BraF) V473_RS04115 V473_RS13485
livH L-isoleucine ABC transporter, permease component 1 (LivH/BraD) V473_RS04105
livJ L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3)
livM L-isoleucine ABC transporter, permease component 2 (LivM/BraE)
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components V473_RS08275
natA L-isoleucine ABC transporter, ATPase component 1 (NatA) V473_RS04115 V473_RS13485
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) V473_RS04105
natE L-isoleucine ABC transporter, ATPase component 2 (NatE) V473_RS04120 V473_RS13485
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused V473_RS08130
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 V473_RS08265 V473_RS02840
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pco propanyl-CoA oxidase V473_RS16975 V473_RS16860
prpB 2-methylisocitrate lyase V473_RS16720
prpC 2-methylcitrate synthase V473_RS07650
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase V473_RS20175
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