GapMind for catabolism of small carbon sources

 

L-valine catabolism in Brucella inopinata BO1

Best path

livF, livG, livJ, livH, livM, 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 (34 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-valine ABC transporter, ATPase component 1 (LivF/BraG) BIBO1_RS12235 BIBO1_RS14990
livG L-valine ABC transporter, ATPase component 2 (LivG/BraF) BIBO1_RS12240 BIBO1_RS14985
livJ L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) BIBO1_RS12225 BIBO1_RS06815
livH L-valine ABC transporter, permease component 1 (LivH/BraD) BIBO1_RS12250 BIBO1_RS19000
livM L-valine ABC transporter, permease component 2 (LivM/BraE) BIBO1_RS12245 BIBO1_RS0105460
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit BIBO1_RS17495 BIBO1_RS08625
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit BIBO1_RS17500 BIBO1_RS08620
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component BIBO1_RS17505 BIBO1_RS05695
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component BIBO1_RS17510 BIBO1_RS08610
acdH isobutyryl-CoA dehydrogenase BIBO1_RS17185 BIBO1_RS09650
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase BIBO1_RS06755 BIBO1_RS15870
bch 3-hydroxyisobutyryl-CoA hydrolase BIBO1_RS07240 BIBO1_RS06755
mmsB 3-hydroxyisobutyrate dehydrogenase BIBO1_RS09655 BIBO1_RS07930
mmsA methylmalonate-semialdehyde dehydrogenase BIBO1_RS12430 BIBO1_RS15435
pccA propionyl-CoA carboxylase, alpha subunit BIBO1_RS09065 BIBO1_RS06830
pccB propionyl-CoA carboxylase, beta subunit BIBO1_RS09060 BIBO1_RS06835
epi methylmalonyl-CoA epimerase BIBO1_RS07490
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit BIBO1_RS09070
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit BIBO1_RS09070
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase BIBO1_RS10365
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) BIBO1_RS10365
Bap2 L-valine permease Bap2 BIBO1_RS14845
bcaP L-valine uptake transporter BcaP/CitA
brnQ L-valine:cation symporter BrnQ/BraZ/BraB
dddA 3-hydroxypropionate dehydrogenase BIBO1_RS19010 BIBO1_RS15375
hpcD 3-hydroxypropionyl-CoA dehydratase BIBO1_RS06755 BIBO1_RS15870
iolA malonate semialdehyde dehydrogenase (CoA-acylating) BIBO1_RS12430 BIBO1_RS10860
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components BIBO1_RS09070
natA L-valine ABC transporter, ATPase component 1 (NatA) BIBO1_RS19765 BIBO1_RS18990
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) BIBO1_RS19000
natE L-valine ABC transporter, ATPase component 2 (NatE) BIBO1_RS12235 BIBO1_RS19760
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 BIBO1_RS09065 BIBO1_RS07715
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit BIBO1_RS12215
pco propanyl-CoA oxidase BIBO1_RS08430 BIBO1_RS17185
phtJ L-valine uptake permease PhtJ
prpB 2-methylisocitrate lyase BIBO1_RS11515
prpC 2-methylcitrate synthase BIBO1_RS08705
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