GapMind for catabolism of small carbon sources

 

L-valine catabolism in Nautilia profundicola AmH

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 (17 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-valine ABC transporter, ATPase component 1 (LivF/BraG) NAMH_RS01040 NAMH_RS03905
livG L-valine ABC transporter, ATPase component 2 (LivG/BraF) NAMH_RS01035 NAMH_RS03905
livJ L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) NAMH_RS00390
livH L-valine ABC transporter, permease component 1 (LivH/BraD) NAMH_RS00405
livM L-valine ABC transporter, permease component 2 (LivM/BraE) NAMH_RS00410
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
acdH isobutyryl-CoA dehydrogenase
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase
bch 3-hydroxyisobutyryl-CoA hydrolase
mmsB 3-hydroxyisobutyrate dehydrogenase
mmsA methylmalonate-semialdehyde dehydrogenase NAMH_RS07680
prpC 2-methylcitrate synthase
prpD 2-methylcitrate dehydratase
acn (2R,3S)-2-methylcitrate dehydratase NAMH_RS07830
prpB 2-methylisocitrate lyase
Alternative steps:
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming)
Bap2 L-valine permease Bap2
bcaP L-valine uptake transporter BcaP/CitA
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit NAMH_RS03820
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component
brnQ L-valine:cation symporter BrnQ/BraZ/BraB
dddA 3-hydroxypropionate dehydrogenase
epi methylmalonyl-CoA epimerase
hpcD 3-hydroxypropionyl-CoA dehydratase
iolA malonate semialdehyde dehydrogenase (CoA-acylating)
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component NAMH_RS03810
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) NAMH_RS01035 NAMH_RS03905
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) NAMH_RS00405
natE L-valine ABC transporter, ATPase component 2 (NatE) NAMH_RS01040 NAMH_RS03905
ofoA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit OfoA
ofoB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit OfoB NAMH_RS06050
pccA propionyl-CoA carboxylase, alpha subunit NAMH_RS00295
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit NAMH_RS00295
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit
pco propanyl-CoA oxidase NAMH_RS02535
phtJ L-valine uptake permease PhtJ
prpF methylaconitate isomerase
vorA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit VorA
vorB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit VorB NAMH_RS06055 NAMH_RS01200
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