GapMind for catabolism of small carbon sources

 

L-valine catabolism in Pontibacter ramchanderi LP43

Best path

brnQ, 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 (25 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
brnQ L-valine:cation symporter BrnQ/BraZ/BraB BD749_RS18850
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit BD749_RS12665 BD749_RS11405
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit BD749_RS12665 BD749_RS17720
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component BD749_RS07170 BD749_RS18710
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component BD749_RS18705 BD749_RS14590
acdH isobutyryl-CoA dehydrogenase BD749_RS11220 BD749_RS09460
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase BD749_RS07655 BD749_RS17005
bch 3-hydroxyisobutyryl-CoA hydrolase BD749_RS17005 BD749_RS10710
mmsB 3-hydroxyisobutyrate dehydrogenase
mmsA methylmalonate-semialdehyde dehydrogenase BD749_RS05780 BD749_RS10835
pccA propionyl-CoA carboxylase, alpha subunit BD749_RS02955 BD749_RS03880
pccB propionyl-CoA carboxylase, beta subunit BD749_RS15550 BD749_RS08175
epi methylmalonyl-CoA epimerase BD749_RS06500
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit BD749_RS08120 BD749_RS03410
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit BD749_RS08120
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming)
Bap2 L-valine permease Bap2
bcaP L-valine uptake transporter BcaP/CitA
dddA 3-hydroxypropionate dehydrogenase
hpcD 3-hydroxypropionyl-CoA dehydratase BD749_RS17005 BD749_RS07655
iolA malonate semialdehyde dehydrogenase (CoA-acylating) BD749_RS10835
livF L-valine ABC transporter, ATPase component 1 (LivF/BraG) BD749_RS11320 BD749_RS14880
livG L-valine ABC transporter, ATPase component 2 (LivG/BraF) BD749_RS11320 BD749_RS02395
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 BD749_RS03410 BD749_RS08120
natA L-valine ABC transporter, ATPase component 1 (NatA) BD749_RS11320
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) BD749_RS11320 BD749_RS12890
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 BD749_RS02955 BD749_RS03880
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pco propanyl-CoA oxidase BD749_RS08765 BD749_RS11220
phtJ L-valine uptake permease PhtJ
prpB 2-methylisocitrate lyase BD749_RS13120
prpC 2-methylcitrate synthase BD749_RS03380
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