GapMind for catabolism of small carbon sources

 

L-valine catabolism in Jannaschia aquimarina GSW-M26

Best path

Bap2, ofo, acdH, ech, bch, mmsB, mmsA, pccA, pccB, epi, mcm-large, mcm-small

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
Bap2 L-valine permease Bap2
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused jaqu_RS05420
acdH isobutyryl-CoA dehydrogenase jaqu_RS04205 jaqu_RS10025
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase jaqu_RS12650 jaqu_RS00375
bch 3-hydroxyisobutyryl-CoA hydrolase jaqu_RS10020
mmsB 3-hydroxyisobutyrate dehydrogenase jaqu_RS10015 jaqu_RS11725
mmsA methylmalonate-semialdehyde dehydrogenase jaqu_RS11085 jaqu_RS03630
pccA propionyl-CoA carboxylase, alpha subunit jaqu_RS11645 jaqu_RS04250
pccB propionyl-CoA carboxylase, beta subunit jaqu_RS11615 jaqu_RS04230
epi methylmalonyl-CoA epimerase jaqu_RS11880
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit jaqu_RS11670 jaqu_RS02675
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit jaqu_RS11670 jaqu_RS02675
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase jaqu_RS11455
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) jaqu_RS11455
bcaP L-valine uptake transporter BcaP/CitA
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit jaqu_RS03175 jaqu_RS05150
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit jaqu_RS03180 jaqu_RS05145
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component jaqu_RS05140 jaqu_RS05835
brnQ L-valine:cation symporter BrnQ/BraZ/BraB
dddA 3-hydroxypropionate dehydrogenase jaqu_RS12755 jaqu_RS03625
hpcD 3-hydroxypropionyl-CoA dehydratase jaqu_RS12650 jaqu_RS05030
iolA malonate semialdehyde dehydrogenase (CoA-acylating) jaqu_RS11085 jaqu_RS03630
livF L-valine ABC transporter, ATPase component 1 (LivF/BraG) jaqu_RS14620 jaqu_RS18395
livG L-valine ABC transporter, ATPase component 2 (LivG/BraF) jaqu_RS14580 jaqu_RS07830
livH L-valine ABC transporter, permease component 1 (LivH/BraD) jaqu_RS07820 jaqu_RS09840
livJ L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3)
livM L-valine ABC transporter, permease component 2 (LivM/BraE) jaqu_RS14610 jaqu_RS07825
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component jaqu_RS04615 jaqu_RS19795
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components jaqu_RS11670 jaqu_RS02675
natA L-valine ABC transporter, ATPase component 1 (NatA) jaqu_RS04915 jaqu_RS14580
natB L-valine ABC transporter, substrate-binding component NatB
natC L-valine ABC transporter, permease component 1 (NatC) jaqu_RS07825
natD L-valine ABC transporter, permease component 2 (NatD) jaqu_RS04940 jaqu_RS14600
natE L-valine ABC transporter, ATPase component 2 (NatE) jaqu_RS04925 jaqu_RS14620
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 jaqu_RS11645 jaqu_RS18415
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit jaqu_RS18410
pco propanyl-CoA oxidase jaqu_RS05745 jaqu_RS01820
phtJ L-valine uptake permease PhtJ
prpB 2-methylisocitrate lyase jaqu_RS01445
prpC 2-methylcitrate synthase jaqu_RS06305
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
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