GapMind for catabolism of small carbon sources

 

L-valine catabolism in Saccharomonospora cyanea NA-134

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 (36 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
Bap2 L-valine permease Bap2 SACCYDRAFT_RS20860 SACCYDRAFT_RS13365
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit SACCYDRAFT_RS24865 SACCYDRAFT_RS10835
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit SACCYDRAFT_RS24870 SACCYDRAFT_RS10830
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component SACCYDRAFT_RS24875 SACCYDRAFT_RS10825
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component SACCYDRAFT_RS06380 SACCYDRAFT_RS10840
acdH isobutyryl-CoA dehydrogenase SACCYDRAFT_RS19835 SACCYDRAFT_RS21785
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase SACCYDRAFT_RS18310 SACCYDRAFT_RS19675
bch 3-hydroxyisobutyryl-CoA hydrolase SACCYDRAFT_RS03705 SACCYDRAFT_RS18310
mmsB 3-hydroxyisobutyrate dehydrogenase SACCYDRAFT_RS12710
mmsA methylmalonate-semialdehyde dehydrogenase SACCYDRAFT_RS20580 SACCYDRAFT_RS03230
pccA propionyl-CoA carboxylase, alpha subunit SACCYDRAFT_RS03395 SACCYDRAFT_RS19840
pccB propionyl-CoA carboxylase, beta subunit SACCYDRAFT_RS03415 SACCYDRAFT_RS19845
epi methylmalonyl-CoA epimerase SACCYDRAFT_RS18435
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit SACCYDRAFT_RS03315 SACCYDRAFT_RS16070
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit SACCYDRAFT_RS03315
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase SACCYDRAFT_RS14425
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) SACCYDRAFT_RS14425
bcaP L-valine uptake transporter BcaP/CitA SACCYDRAFT_RS10940
brnQ L-valine:cation symporter BrnQ/BraZ/BraB
dddA 3-hydroxypropionate dehydrogenase SACCYDRAFT_RS20575 SACCYDRAFT_RS15820
hpcD 3-hydroxypropionyl-CoA dehydratase SACCYDRAFT_RS18310 SACCYDRAFT_RS03705
iolA malonate semialdehyde dehydrogenase (CoA-acylating) SACCYDRAFT_RS20580 SACCYDRAFT_RS15225
livF L-valine ABC transporter, ATPase component 1 (LivF/BraG) SACCYDRAFT_RS15020 SACCYDRAFT_RS20255
livG L-valine ABC transporter, ATPase component 2 (LivG/BraF) SACCYDRAFT_RS15025 SACCYDRAFT_RS15380
livH L-valine ABC transporter, permease component 1 (LivH/BraD) SACCYDRAFT_RS15015
livJ L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3)
livM L-valine ABC transporter, permease component 2 (LivM/BraE) SACCYDRAFT_RS15010
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components SACCYDRAFT_RS03315 SACCYDRAFT_RS16070
natA L-valine ABC transporter, ATPase component 1 (NatA) SACCYDRAFT_RS15025 SACCYDRAFT_RS10270
natB L-valine ABC transporter, substrate-binding component NatB SACCYDRAFT_RS18990
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) SACCYDRAFT_RS15020 SACCYDRAFT_RS13560
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 SACCYDRAFT_RS02020
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit SACCYDRAFT_RS03395 SACCYDRAFT_RS19840
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit SACCYDRAFT_RS19840
pco propanyl-CoA oxidase SACCYDRAFT_RS20625 SACCYDRAFT_RS04895
phtJ L-valine uptake permease PhtJ
prpB 2-methylisocitrate lyase SACCYDRAFT_RS18195 SACCYDRAFT_RS18415
prpC 2-methylcitrate synthase SACCYDRAFT_RS21740 SACCYDRAFT_RS21820
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 SACCYDRAFT_RS02025
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 Apr 09 2024. 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