GapMind for catabolism of small carbon sources

 

L-valine catabolism in Williamsia sterculiae CPCC 203464

Best path

livF, livG, livJ, livH, livM, ofo, acdH, ech, bch, mmsB, mmsA, prpC, prpD, acn, prpB

Rules

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.

47 steps (34 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-valine ABC transporter, ATPase component 1 (LivF/BraG) BW971_RS17380 BW971_RS17385
livG L-valine ABC transporter, ATPase component 2 (LivG/BraF) BW971_RS17385 BW971_RS12525
livJ L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) BW971_RS17400
livH L-valine ABC transporter, permease component 1 (LivH/BraD) BW971_RS17395
livM L-valine ABC transporter, permease component 2 (LivM/BraE) BW971_RS17390
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused BW971_RS03235
acdH isobutyryl-CoA dehydrogenase BW971_RS03250 BW971_RS05230
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase BW971_RS12060 BW971_RS00105
bch 3-hydroxyisobutyryl-CoA hydrolase BW971_RS03885 BW971_RS12060
mmsB 3-hydroxyisobutyrate dehydrogenase BW971_RS14530
mmsA methylmalonate-semialdehyde dehydrogenase BW971_RS07620 BW971_RS14520
prpC 2-methylcitrate synthase BW971_RS12705 BW971_RS15410
prpD 2-methylcitrate dehydratase BW971_RS12715
acn (2R,3S)-2-methylcitrate dehydratase BW971_RS06960
prpB 2-methylisocitrate lyase BW971_RS08040 BW971_RS12710
Alternative steps:
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) BW971_RS06960
Bap2 L-valine permease Bap2 BW971_RS01220 BW971_RS09675
bcaP L-valine uptake transporter BcaP/CitA BW971_RS15225 BW971_RS14700
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 BW971_RS13135
brnQ L-valine:cation symporter BrnQ/BraZ/BraB
dddA 3-hydroxypropionate dehydrogenase BW971_RS00545
epi methylmalonyl-CoA epimerase BW971_RS20370
hpcD 3-hydroxypropionyl-CoA dehydratase BW971_RS12060 BW971_RS16050
iolA malonate semialdehyde dehydrogenase (CoA-acylating) BW971_RS14520 BW971_RS07620
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component BW971_RS08065 BW971_RS14205
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit BW971_RS07055
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit BW971_RS07055
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components BW971_RS07055
natA L-valine ABC transporter, ATPase component 1 (NatA) BW971_RS17385 BW971_RS19660
natB L-valine ABC transporter, substrate-binding component NatB
natC L-valine ABC transporter, permease component 1 (NatC)
natD L-valine ABC transporter, permease component 2 (NatD)
natE L-valine ABC transporter, ATPase component 2 (NatE) BW971_RS17380 BW971_RS17385
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 BW971_RS05105 BW971_RS03245
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit BW971_RS05105 BW971_RS03245
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit BW971_RS14635
pccB propionyl-CoA carboxylase, beta subunit BW971_RS05175 BW971_RS18180
pco propanyl-CoA oxidase BW971_RS02040 BW971_RS08610
phtJ L-valine uptake permease PhtJ
prpF methylaconitate isomerase
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