GapMind for catabolism of small carbon sources

 

L-valine catabolism in Cereibacter sphaeroides ATCC 17029

Best path

livF, livG, livJ, livH, livM, ofo, 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 (35 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-valine ABC transporter, ATPase component 1 (LivF/BraG) RSPH17029_RS04835 RSPH17029_RS07940
livG L-valine ABC transporter, ATPase component 2 (LivG/BraF) RSPH17029_RS04855 RSPH17029_RS20335
livJ L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) RSPH17029_RS17965
livH L-valine ABC transporter, permease component 1 (LivH/BraD) RSPH17029_RS17970 RSPH17029_RS20325
livM L-valine ABC transporter, permease component 2 (LivM/BraE) RSPH17029_RS04845 RSPH17029_RS17975
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused RSPH17029_RS08070 RSPH17029_RS18350
acdH isobutyryl-CoA dehydrogenase RSPH17029_RS19795 RSPH17029_RS09050
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase RSPH17029_RS00050 RSPH17029_RS17990
bch 3-hydroxyisobutyryl-CoA hydrolase RSPH17029_RS09045 RSPH17029_RS17990
mmsB 3-hydroxyisobutyrate dehydrogenase RSPH17029_RS09040 RSPH17029_RS07320
mmsA methylmalonate-semialdehyde dehydrogenase RSPH17029_RS08140 RSPH17029_RS04350
pccA propionyl-CoA carboxylase, alpha subunit RSPH17029_RS04405 RSPH17029_RS05950
pccB propionyl-CoA carboxylase, beta subunit RSPH17029_RS04380 RSPH17029_RS05945
epi methylmalonyl-CoA epimerase RSPH17029_RS12460
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit RSPH17029_RS04415 RSPH17029_RS18485
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit RSPH17029_RS04415 RSPH17029_RS18470
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase RSPH17029_RS02300
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) RSPH17029_RS02300
Bap2 L-valine permease Bap2
bcaP L-valine uptake transporter BcaP/CitA
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit RSPH17029_RS05845
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit RSPH17029_RS05840 RSPH17029_RS14900
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component RSPH17029_RS13235 RSPH17029_RS05835
brnQ L-valine:cation symporter BrnQ/BraZ/BraB
dddA 3-hydroxypropionate dehydrogenase RSPH17029_RS20315 RSPH17029_RS04355
hpcD 3-hydroxypropionyl-CoA dehydratase RSPH17029_RS00050 RSPH17029_RS06550
iolA malonate semialdehyde dehydrogenase (CoA-acylating) RSPH17029_RS08140 RSPH17029_RS04350
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component RSPH17029_RS08165 RSPH17029_RS13225
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components RSPH17029_RS04415 RSPH17029_RS18485
natA L-valine ABC transporter, ATPase component 1 (NatA) RSPH17029_RS07935 RSPH17029_RS04855
natB L-valine ABC transporter, substrate-binding component NatB RSPH17029_RS07930
natC L-valine ABC transporter, permease component 1 (NatC)
natD L-valine ABC transporter, permease component 2 (NatD) RSPH17029_RS07945 RSPH17029_RS17970
natE L-valine ABC transporter, ATPase component 2 (NatE) RSPH17029_RS07940 RSPH17029_RS04835
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 RSPH17029_RS04405 RSPH17029_RS09225
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit RSPH17029_RS09220
pco propanyl-CoA oxidase RSPH17029_RS14905
phtJ L-valine uptake permease PhtJ
prpB 2-methylisocitrate lyase
prpC 2-methylcitrate synthase RSPH17029_RS03595
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase RSPH17029_RS18095 RSPH17029_RS18235
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 Apr 10 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