GapMind for catabolism of small carbon sources

 

L-isoleucine catabolism in Xenophilus azovorans DSM 13620

Best path

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

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-isoleucine ABC transporter, ATPase component 1 (LivF/BraG) Q392_RS11630 Q392_RS06000
livG L-isoleucine ABC transporter, ATPase component 2 (LivG/BraF) Q392_RS11635 Q392_RS20785
livJ L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) Q392_RS28895 Q392_RS05395
livH L-isoleucine ABC transporter, permease component 1 (LivH/BraD) Q392_RS11645 Q392_RS07410
livM L-isoleucine ABC transporter, permease component 2 (LivM/BraE) Q392_RS11640 Q392_RS01960
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused Q392_RS04890
acdH (2S)-2-methylbutanoyl-CoA dehydrogenase Q392_RS19315 Q392_RS06805
ech 2-methyl-3-hydroxybutyryl-CoA hydro-lyase Q392_RS25070 Q392_RS00345
ivdG 3-hydroxy-2-methylbutyryl-CoA dehydrogenase Q392_RS22870 Q392_RS15125
fadA 2-methylacetoacetyl-CoA thiolase Q392_RS19325 Q392_RS22590
pccA propionyl-CoA carboxylase, alpha subunit Q392_RS30710 Q392_RS01765
pccB propionyl-CoA carboxylase, beta subunit Q392_RS30700 Q392_RS02190
epi methylmalonyl-CoA epimerase Q392_RS30720
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit Q392_RS30690
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit Q392_RS30690
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase Q392_RS16570 Q392_RS13930
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) Q392_RS16570
Bap2 L-isoleucine permease Bap2
bcaP L-isoleucine uptake transporter BcaP/CitA
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit Q392_RS04360 Q392_RS02555
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit Q392_RS02550 Q392_RS04365
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component Q392_RS16810 Q392_RS02540
brnQ L-isoleucine:cation symporter BrnQ/BraZ/BraB
dddA 3-hydroxypropionate dehydrogenase Q392_RS18190 Q392_RS22945
hpcD 3-hydroxypropionyl-CoA dehydratase Q392_RS02070 Q392_RS02515
iolA malonate semialdehyde dehydrogenase (CoA-acylating) Q392_RS18175 Q392_RS06795
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component Q392_RS16820 Q392_RS16865
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components Q392_RS30690
natA L-isoleucine ABC transporter, ATPase component 1 (NatA) Q392_RS11635 Q392_RS12265
natB L-isoleucine ABC transporter, substrate-binding component NatB Q392_RS00200
natC L-isoleucine ABC transporter, permease component 1 (NatC)
natD L-isoleucine ABC transporter, permease component 2 (NatD) Q392_RS07410 Q392_RS11645
natE L-isoleucine ABC transporter, ATPase component 2 (NatE) Q392_RS11630 Q392_RS28465
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 Q392_RS30710 Q392_RS17540
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pco propanyl-CoA oxidase Q392_RS20240 Q392_RS27255
prpB 2-methylisocitrate lyase Q392_RS30945 Q392_RS19625
prpC 2-methylcitrate synthase Q392_RS19615 Q392_RS13875
prpD 2-methylcitrate dehydratase Q392_RS19620
prpF methylaconitate isomerase Q392_RS04105 Q392_RS13440
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