GapMind for catabolism of small carbon sources

 

L-valine catabolism in Erythrobacter gangjinensis K7-2

Best path

Bap2, 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 (29 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
Bap2 L-valine permease Bap2
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit AAW01_RS01595 AAW01_RS02710
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit AAW01_RS01600 AAW01_RS02700
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component AAW01_RS01605 AAW01_RS02590
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component AAW01_RS02605 AAW01_RS00490
acdH isobutyryl-CoA dehydrogenase AAW01_RS10540 AAW01_RS07145
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase AAW01_RS13205 AAW01_RS11465
bch 3-hydroxyisobutyryl-CoA hydrolase AAW01_RS10535 AAW01_RS13205
mmsB 3-hydroxyisobutyrate dehydrogenase AAW01_RS13215 AAW01_RS06075
mmsA methylmalonate-semialdehyde dehydrogenase AAW01_RS13220 AAW01_RS09770
pccA propionyl-CoA carboxylase, alpha subunit AAW01_RS04050 AAW01_RS10650
pccB propionyl-CoA carboxylase, beta subunit AAW01_RS04080 AAW01_RS07130
epi methylmalonyl-CoA epimerase AAW01_RS04070
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit AAW01_RS04065
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit AAW01_RS04065 AAW01_RS04365
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase AAW01_RS12810
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) AAW01_RS12810
bcaP L-valine uptake transporter BcaP/CitA
brnQ L-valine:cation symporter BrnQ/BraZ/BraB
dddA 3-hydroxypropionate dehydrogenase
hpcD 3-hydroxypropionyl-CoA dehydratase AAW01_RS13205 AAW01_RS03435
iolA malonate semialdehyde dehydrogenase (CoA-acylating) AAW01_RS13220 AAW01_RS09770
livF L-valine ABC transporter, ATPase component 1 (LivF/BraG) AAW01_RS09360 AAW01_RS06625
livG L-valine ABC transporter, ATPase component 2 (LivG/BraF) AAW01_RS09360 AAW01_RS07155
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 AAW01_RS04065
natA L-valine ABC transporter, ATPase component 1 (NatA) AAW01_RS09360
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) AAW01_RS09360 AAW01_RS07015
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
ofoA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit OfoA AAW01_RS01480
ofoB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit OfoB AAW01_RS01485
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit AAW01_RS04050 AAW01_RS04105
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pco propanyl-CoA oxidase AAW01_RS11555 AAW01_RS07145
phtJ L-valine uptake permease PhtJ
prpB 2-methylisocitrate lyase
prpC 2-methylcitrate synthase AAW01_RS02830
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 AAW01_RS01480
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