GapMind for catabolism of small carbon sources

 

L-valine catabolism in Belnapia rosea CPCC 100156

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) BLR02_RS12510 BLR02_RS10300
livG L-valine ABC transporter, ATPase component 2 (LivG/BraF) BLR02_RS12515 BLR02_RS19380
livJ L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) BLR02_RS12505 BLR02_RS10280
livH L-valine ABC transporter, permease component 1 (LivH/BraD) BLR02_RS12525 BLR02_RS10285
livM L-valine ABC transporter, permease component 2 (LivM/BraE) BLR02_RS12520 BLR02_RS25430
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused BLR02_RS16560
acdH isobutyryl-CoA dehydrogenase BLR02_RS16555 BLR02_RS03525
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase BLR02_RS23955 BLR02_RS03400
bch 3-hydroxyisobutyryl-CoA hydrolase BLR02_RS23330 BLR02_RS13145
mmsB 3-hydroxyisobutyrate dehydrogenase BLR02_RS01175 BLR02_RS15295
mmsA methylmalonate-semialdehyde dehydrogenase BLR02_RS18460 BLR02_RS04250
prpC 2-methylcitrate synthase BLR02_RS19010 BLR02_RS05735
prpD 2-methylcitrate dehydratase BLR02_RS19020
acn (2R,3S)-2-methylcitrate dehydratase BLR02_RS06435
prpB 2-methylisocitrate lyase BLR02_RS15615 BLR02_RS04390
Alternative steps:
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) BLR02_RS06435
Bap2 L-valine permease Bap2
bcaP L-valine uptake transporter BcaP/CitA
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit BLR02_RS01930
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit BLR02_RS01935
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component BLR02_RS22480 BLR02_RS01940
brnQ L-valine:cation symporter BrnQ/BraZ/BraB
dddA 3-hydroxypropionate dehydrogenase BLR02_RS18510 BLR02_RS02205
epi methylmalonyl-CoA epimerase
hpcD 3-hydroxypropionyl-CoA dehydratase BLR02_RS23955 BLR02_RS08090
iolA malonate semialdehyde dehydrogenase (CoA-acylating) BLR02_RS18460 BLR02_RS07320
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component BLR02_RS01950 BLR02_RS16900
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components
natA L-valine ABC transporter, ATPase component 1 (NatA) BLR02_RS12515 BLR02_RS02515
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) BLR02_RS10285 BLR02_RS21770
natE L-valine ABC transporter, ATPase component 2 (NatE) BLR02_RS00885 BLR02_RS12510
ofoA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit OfoA
ofoB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit OfoB BLR02_RS12565
pccA propionyl-CoA carboxylase, alpha subunit BLR02_RS03535 BLR02_RS01010
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit BLR02_RS01010 BLR02_RS23135
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit BLR02_RS03535
pccB propionyl-CoA carboxylase, beta subunit BLR02_RS03530 BLR02_RS23125
pco propanyl-CoA oxidase BLR02_RS06730
phtJ L-valine uptake permease PhtJ
prpF methylaconitate isomerase BLR02_RS04850 BLR02_RS20970
vorA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit VorA
vorB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit VorB BLR02_RS12570
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