GapMind for catabolism of small carbon sources

 

L-valine catabolism in Mucilaginibacter mallensis MP1X4

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 (25 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 BLU33_RS24660 BLU33_RS19455
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit BLU33_RS24660 BLU33_RS18750
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component BLU33_RS10760 BLU33_RS18030
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component BLU33_RS07565 BLU33_RS18175
acdH isobutyryl-CoA dehydrogenase BLU33_RS24850 BLU33_RS17775
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase BLU33_RS22635
bch 3-hydroxyisobutyryl-CoA hydrolase
mmsB 3-hydroxyisobutyrate dehydrogenase BLU33_RS24355 BLU33_RS13615
mmsA methylmalonate-semialdehyde dehydrogenase BLU33_RS14055 BLU33_RS06915
pccA propionyl-CoA carboxylase, alpha subunit BLU33_RS09750 BLU33_RS23025
pccB propionyl-CoA carboxylase, beta subunit BLU33_RS16640 BLU33_RS08985
epi methylmalonyl-CoA epimerase BLU33_RS16180
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit BLU33_RS21780 BLU33_RS16615
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit BLU33_RS22630
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase BLU33_RS00830
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming)
bcaP L-valine uptake transporter BcaP/CitA BLU33_RS17855
brnQ L-valine:cation symporter BrnQ/BraZ/BraB
dddA 3-hydroxypropionate dehydrogenase
hpcD 3-hydroxypropionyl-CoA dehydratase BLU33_RS22635
iolA malonate semialdehyde dehydrogenase (CoA-acylating) BLU33_RS14055 BLU33_RS06915
livF L-valine ABC transporter, ATPase component 1 (LivF/BraG) BLU33_RS23120 BLU33_RS15970
livG L-valine ABC transporter, ATPase component 2 (LivG/BraF) BLU33_RS23120 BLU33_RS00530
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 BLU33_RS16615 BLU33_RS21780
natA L-valine ABC transporter, ATPase component 1 (NatA) BLU33_RS23120 BLU33_RS00530
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) BLU33_RS23120 BLU33_RS17430
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 BLU33_RS09750 BLU33_RS23025
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pco propanyl-CoA oxidase BLU33_RS08585 BLU33_RS17775
phtJ L-valine uptake permease PhtJ
prpB 2-methylisocitrate lyase
prpC 2-methylcitrate synthase BLU33_RS14570
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