livF, livG, livJ, livH, livM, ofo, acdH, ech, bch, mmsB, mmsA, pccA, pccB, epi, mcm-large, mcm-small
Overview: Valine degradation in GapMind is based on MetaCyc pathway L-valine degradation I (link). The other pathways do not produce any fixed carbon and are not included.
Or see definitions of steps
Step | Description | Best candidate | 2nd candidate |
---|---|---|---|
livF | L-valine ABC transporter, ATPase component 1 (LivF/BraG) | AZC_RS15220 | AZC_RS20900 |
livG | L-valine ABC transporter, ATPase component 2 (LivG/BraF) | AZC_RS15215 | AZC_RS01005 |
livJ | L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | AZC_RS15230 | AZC_RS00990 |
livH | L-valine ABC transporter, permease component 1 (LivH/BraD) | AZC_RS15205 | AZC_RS02445 |
livM | L-valine ABC transporter, permease component 2 (LivM/BraE) | AZC_RS15210 | AZC_RS01000 |
ofo | branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | AZC_RS03575 | |
acdH | isobutyryl-CoA dehydrogenase | AZC_RS02925 | AZC_RS14650 |
ech | (S)-3-hydroxybutanoyl-CoA hydro-lyase | AZC_RS04085 | AZC_RS14860 |
bch | 3-hydroxyisobutyryl-CoA hydrolase | AZC_RS07970 | AZC_RS12935 |
mmsB | 3-hydroxyisobutyrate dehydrogenase | AZC_RS02930 | AZC_RS17945 |
mmsA | methylmalonate-semialdehyde dehydrogenase | AZC_RS21125 | AZC_RS02920 |
pccA | propionyl-CoA carboxylase, alpha subunit | AZC_RS09205 | AZC_RS23530 |
pccB | propionyl-CoA carboxylase, beta subunit | AZC_RS09210 | AZC_RS23520 |
epi | methylmalonyl-CoA epimerase | AZC_RS08740 | |
mcm-large | methylmalonyl-CoA mutase, large (catalytic) subunit | AZC_RS09195 | AZC_RS05085 |
mcm-small | methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit | AZC_RS09195 | AZC_RS05085 |
Alternative steps: | |||
acn | (2R,3S)-2-methylcitrate dehydratase | AZC_RS22880 | |
acnD | 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) | AZC_RS22880 | |
Bap2 | L-valine permease Bap2 | ||
bcaP | L-valine uptake transporter BcaP/CitA | ||
bkdA | branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit | AZC_RS09025 | AZC_RS09895 |
bkdB | branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit | AZC_RS09035 | AZC_RS09890 |
bkdC | branched-chain alpha-ketoacid dehydrogenase, E2 component | AZC_RS20570 | AZC_RS09040 |
brnQ | L-valine:cation symporter BrnQ/BraZ/BraB | ||
dddA | 3-hydroxypropionate dehydrogenase | AZC_RS16840 | AZC_RS06090 |
hpcD | 3-hydroxypropionyl-CoA dehydratase | AZC_RS04085 | AZC_RS12935 |
iolA | malonate semialdehyde dehydrogenase (CoA-acylating) | AZC_RS02920 | AZC_RS21125 |
lpd | branched-chain alpha-ketoacid dehydrogenase, E3 component | AZC_RS09050 | AZC_RS20560 |
mcmA | methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components | AZC_RS09195 | AZC_RS05085 |
natA | L-valine ABC transporter, ATPase component 1 (NatA) | AZC_RS15510 | AZC_RS10930 |
natB | L-valine ABC transporter, substrate-binding component NatB | AZC_RS15495 | |
natC | L-valine ABC transporter, permease component 1 (NatC) | ||
natD | L-valine ABC transporter, permease component 2 (NatD) | AZC_RS15500 | AZC_RS10920 |
natE | L-valine ABC transporter, ATPase component 2 (NatE) | AZC_RS15520 | AZC_RS09785 |
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 | AZC_RS09205 | AZC_RS15865 |
pccA2 | propionyl-CoA carboxylase, biotin carboxylase subunit | ||
pco | propanyl-CoA oxidase | AZC_RS18305 | AZC_RS14650 |
phtJ | L-valine uptake permease PhtJ | ||
prpB | 2-methylisocitrate lyase | AZC_RS10945 | |
prpC | 2-methylcitrate synthase | AZC_RS08870 | |
prpD | 2-methylcitrate dehydratase | ||
prpF | methylaconitate isomerase | AZC_RS13820 | AZC_RS04500 |
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.
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:
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