GapMind for catabolism of small carbon sources

 

L-valine catabolism in Fibrella aestuarina BUZ 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 (26 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 FAES_RS05745
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit FAES_RS23665 FAES_RS27810
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component FAES_RS09445 FAES_RS10545
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component FAES_RS05180 FAES_RS09435
acdH isobutyryl-CoA dehydrogenase FAES_RS02510 FAES_RS08980
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase FAES_RS08085 FAES_RS12260
bch 3-hydroxyisobutyryl-CoA hydrolase FAES_RS12260 FAES_RS00115
mmsB 3-hydroxyisobutyrate dehydrogenase
mmsA methylmalonate-semialdehyde dehydrogenase FAES_RS15720 FAES_RS15000
pccA propionyl-CoA carboxylase, alpha subunit FAES_RS03420 FAES_RS04740
pccB propionyl-CoA carboxylase, beta subunit FAES_RS12880 FAES_RS22580
epi methylmalonyl-CoA epimerase FAES_RS25665
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit FAES_RS03310 FAES_RS13525
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit FAES_RS03310
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase FAES_RS13575
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming)
bcaP L-valine uptake transporter BcaP/CitA FAES_RS17155 FAES_RS08355
brnQ L-valine:cation symporter BrnQ/BraZ/BraB
dddA 3-hydroxypropionate dehydrogenase FAES_RS25950
hpcD 3-hydroxypropionyl-CoA dehydratase FAES_RS12260 FAES_RS14305
iolA malonate semialdehyde dehydrogenase (CoA-acylating) FAES_RS15720
livF L-valine ABC transporter, ATPase component 1 (LivF/BraG) FAES_RS24920 FAES_RS25660
livG L-valine ABC transporter, ATPase component 2 (LivG/BraF) FAES_RS24920 FAES_RS04920
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 FAES_RS13525 FAES_RS03310
natA L-valine ABC transporter, ATPase component 1 (NatA) FAES_RS24920
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) FAES_RS24920 FAES_RS11020
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 FAES_RS03420 FAES_RS04740
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pco propanyl-CoA oxidase FAES_RS13760 FAES_RS08980
phtJ L-valine uptake permease PhtJ
prpB 2-methylisocitrate lyase
prpC 2-methylcitrate synthase FAES_RS04095
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