GapMind for catabolism of small carbon sources

 

L-isoleucine catabolism in Kyrpidia tusciae DSM 2912

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 (34 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-isoleucine ABC transporter, ATPase component 1 (LivF/BraG) BTUS_RS08510 BTUS_RS06880
livG L-isoleucine ABC transporter, ATPase component 2 (LivG/BraF) BTUS_RS08505 BTUS_RS06875
livJ L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) BTUS_RS08490 BTUS_RS06860
livH L-isoleucine ABC transporter, permease component 1 (LivH/BraD) BTUS_RS08495 BTUS_RS06865
livM L-isoleucine ABC transporter, permease component 2 (LivM/BraE) BTUS_RS08500 BTUS_RS06870
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit BTUS_RS06515 BTUS_RS03115
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit BTUS_RS06520 BTUS_RS03120
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component BTUS_RS01575 BTUS_RS06525
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component BTUS_RS01580 BTUS_RS13955
acdH (2S)-2-methylbutanoyl-CoA dehydrogenase BTUS_RS16285 BTUS_RS16280
ech 2-methyl-3-hydroxybutyryl-CoA hydro-lyase BTUS_RS02935 BTUS_RS01510
ivdG 3-hydroxy-2-methylbutyryl-CoA dehydrogenase BTUS_RS15475 BTUS_RS02380
fadA 2-methylacetoacetyl-CoA thiolase BTUS_RS16115 BTUS_RS05310
pccA propionyl-CoA carboxylase, alpha subunit BTUS_RS03690 BTUS_RS01500
pccB propionyl-CoA carboxylase, beta subunit BTUS_RS06545 BTUS_RS08590
epi methylmalonyl-CoA epimerase BTUS_RS06540
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit BTUS_RS06535 BTUS_RS02370
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit BTUS_RS06540 BTUS_RS02375
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase BTUS_RS12735
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) BTUS_RS12735
Bap2 L-isoleucine permease Bap2 BTUS_RS13730 BTUS_RS15100
bcaP L-isoleucine uptake transporter BcaP/CitA
brnQ L-isoleucine:cation symporter BrnQ/BraZ/BraB
dddA 3-hydroxypropionate dehydrogenase
hpcD 3-hydroxypropionyl-CoA dehydratase BTUS_RS02935 BTUS_RS06165
iolA malonate semialdehyde dehydrogenase (CoA-acylating) BTUS_RS15380 BTUS_RS06175
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components BTUS_RS05290 BTUS_RS06535
natA L-isoleucine ABC transporter, ATPase component 1 (NatA) BTUS_RS06875 BTUS_RS08505
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) BTUS_RS08495 BTUS_RS08110
natE L-isoleucine ABC transporter, ATPase component 2 (NatE) BTUS_RS08510 BTUS_RS06880
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
ofoA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit OfoA BTUS_RS02485
ofoB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit OfoB BTUS_RS02480
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit BTUS_RS03690 BTUS_RS01500
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pco propanyl-CoA oxidase BTUS_RS03960 BTUS_RS01775
prpB 2-methylisocitrate lyase BTUS_RS05055
prpC 2-methylcitrate synthase BTUS_RS11895 BTUS_RS12050
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 BTUS_RS02485
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.

Links

Downloads

Related tools

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