GapMind for catabolism of small carbon sources

 

L-valine catabolism in Polaribacter dokdonensis DSW-5

Best path

brnQ, bkdA, bkdB, bkdC, lpd, 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 (25 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
brnQ L-valine:cation symporter BrnQ/BraZ/BraB I602_RS06720
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit I602_RS11120 I602_RS12260
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit I602_RS11120 I602_RS02910
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component I602_RS13065 I602_RS06855
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component I602_RS12805 I602_RS04785
acdH isobutyryl-CoA dehydrogenase I602_RS01265 I602_RS00765
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase I602_RS05270 I602_RS12910
bch 3-hydroxyisobutyryl-CoA hydrolase I602_RS05270
mmsB 3-hydroxyisobutyrate dehydrogenase
mmsA methylmalonate-semialdehyde dehydrogenase I602_RS02060 I602_RS06450
pccA propionyl-CoA carboxylase, alpha subunit I602_RS05480
pccB propionyl-CoA carboxylase, beta subunit I602_RS09370
epi methylmalonyl-CoA epimerase I602_RS05035
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit I602_RS00950 I602_RS08695
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit I602_RS00950
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase I602_RS10495 I602_RS10500
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) I602_RS10500
Bap2 L-valine permease Bap2
bcaP L-valine uptake transporter BcaP/CitA
dddA 3-hydroxypropionate dehydrogenase
hpcD 3-hydroxypropionyl-CoA dehydratase I602_RS05270
iolA malonate semialdehyde dehydrogenase (CoA-acylating) I602_RS02060
livF L-valine ABC transporter, ATPase component 1 (LivF/BraG) I602_RS11370 I602_RS09395
livG L-valine ABC transporter, ATPase component 2 (LivG/BraF) I602_RS11370 I602_RS02165
livH L-valine ABC transporter, permease component 1 (LivH/BraD)
livJ L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3)
livM L-valine ABC transporter, permease component 2 (LivM/BraE)
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components I602_RS08695 I602_RS00950
natA L-valine ABC transporter, ATPase component 1 (NatA) I602_RS11370 I602_RS06375
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)
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
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 I602_RS05480
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pco propanyl-CoA oxidase I602_RS04215 I602_RS01265
phtJ L-valine uptake permease PhtJ
prpB 2-methylisocitrate lyase
prpC 2-methylcitrate synthase I602_RS02205
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