GapMind for catabolism of small carbon sources

 

L-isoleucine catabolism in Stutzerimonas stutzeri A1501

Best path

livF, livG, livJ, livH, livM, ofo, acdH, ech, ivdG, fadA, prpC, acnD, prpF, acn, prpB

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 (31 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-isoleucine ABC transporter, ATPase component 1 (LivF/BraG) PST_RS14970 PST_RS02165
livG L-isoleucine ABC transporter, ATPase component 2 (LivG/BraF) PST_RS14965 PST_RS16095
livJ L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) PST_RS14950
livH L-isoleucine ABC transporter, permease component 1 (LivH/BraD) PST_RS14955 PST_RS02160
livM L-isoleucine ABC transporter, permease component 2 (LivM/BraE) PST_RS14960 PST_RS16075
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused PST_RS04430
acdH (2S)-2-methylbutanoyl-CoA dehydrogenase PST_RS09700 PST_RS09725
ech 2-methyl-3-hydroxybutyryl-CoA hydro-lyase PST_RS08735 PST_RS09740
ivdG 3-hydroxy-2-methylbutyryl-CoA dehydrogenase PST_RS09690 PST_RS15785
fadA 2-methylacetoacetyl-CoA thiolase PST_RS08740 PST_RS03530
prpC 2-methylcitrate synthase PST_RS10310 PST_RS09470
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) PST_RS10315 PST_RS09345
prpF methylaconitate isomerase PST_RS10320
acn (2R,3S)-2-methylcitrate dehydratase PST_RS10315 PST_RS10365
prpB 2-methylisocitrate lyase PST_RS10305 PST_RS18590
Alternative steps:
Bap2 L-isoleucine permease Bap2 PST_RS13100
bcaP L-isoleucine uptake transporter BcaP/CitA
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component PST_RS19185 PST_RS09500
brnQ L-isoleucine:cation symporter BrnQ/BraZ/BraB PST_RS09520
dddA 3-hydroxypropionate dehydrogenase PST_RS08840 PST_RS03140
epi methylmalonyl-CoA epimerase
hpcD 3-hydroxypropionyl-CoA dehydratase PST_RS09740 PST_RS03120
iolA malonate semialdehyde dehydrogenase (CoA-acylating) PST_RS09745 PST_RS02550
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component PST_RS09505 PST_RS13275
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components
natA L-isoleucine ABC transporter, ATPase component 1 (NatA) PST_RS14965 PST_RS16095
natB L-isoleucine ABC transporter, substrate-binding component NatB
natC L-isoleucine ABC transporter, permease component 1 (NatC) PST_RS14960
natD L-isoleucine ABC transporter, permease component 2 (NatD) PST_RS16080
natE L-isoleucine ABC transporter, ATPase component 2 (NatE) PST_RS14970 PST_RS16090
ofoA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit OfoA
ofoB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit OfoB
pccA propionyl-CoA carboxylase, alpha subunit PST_RS16135 PST_RS16440
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit PST_RS00965 PST_RS16440
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit PST_RS07020
pccB propionyl-CoA carboxylase, beta subunit PST_RS16125
pco propanyl-CoA oxidase PST_RS02285
prpD 2-methylcitrate dehydratase
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