GapMind for catabolism of small carbon sources

 

L-valine catabolism in Rhodococcus qingshengii djl-6-2

Best path

natA, natB, natC, natD, natE, bkdA, bkdB, bkdC, lpd, 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 (37 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
natA L-valine ABC transporter, ATPase component 1 (NatA) C1M55_RS16610 C1M55_RS22600
natB L-valine ABC transporter, substrate-binding component NatB C1M55_RS16620
natC L-valine ABC transporter, permease component 1 (NatC)
natD L-valine ABC transporter, permease component 2 (NatD) C1M55_RS16600 C1M55_RS07895
natE L-valine ABC transporter, ATPase component 2 (NatE) C1M55_RS16615 C1M55_RS22595
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit C1M55_RS19770 C1M55_RS30500
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit C1M55_RS30495 C1M55_RS19775
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component C1M55_RS30490 C1M55_RS19780
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component C1M55_RS07790 C1M55_RS25440
acdH isobutyryl-CoA dehydrogenase C1M55_RS09270 C1M55_RS19625
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase C1M55_RS19610 C1M55_RS12340
bch 3-hydroxyisobutyryl-CoA hydrolase C1M55_RS19620 C1M55_RS01960
mmsB 3-hydroxyisobutyrate dehydrogenase C1M55_RS19615 C1M55_RS16845
mmsA methylmalonate-semialdehyde dehydrogenase C1M55_RS10170 C1M55_RS19630
prpC 2-methylcitrate synthase C1M55_RS25465 C1M55_RS23230
prpD 2-methylcitrate dehydratase C1M55_RS25475
acn (2R,3S)-2-methylcitrate dehydratase C1M55_RS15295
prpB 2-methylisocitrate lyase C1M55_RS07975 C1M55_RS25470
Alternative steps:
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) C1M55_RS15295
Bap2 L-valine permease Bap2 C1M55_RS20600 C1M55_RS07700
bcaP L-valine uptake transporter BcaP/CitA C1M55_RS10990 C1M55_RS12490
brnQ L-valine:cation symporter BrnQ/BraZ/BraB
dddA 3-hydroxypropionate dehydrogenase C1M55_RS09145
epi methylmalonyl-CoA epimerase C1M55_RS19315 C1M55_RS04095
hpcD 3-hydroxypropionyl-CoA dehydratase C1M55_RS19610 C1M55_RS01960
iolA malonate semialdehyde dehydrogenase (CoA-acylating) C1M55_RS19630 C1M55_RS10170
livF L-valine ABC transporter, ATPase component 1 (LivF/BraG) C1M55_RS22595 C1M55_RS06875
livG L-valine ABC transporter, ATPase component 2 (LivG/BraF) C1M55_RS22600 C1M55_RS16610
livH L-valine ABC transporter, permease component 1 (LivH/BraD) C1M55_RS16600 C1M55_RS06865
livJ L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3)
livM L-valine ABC transporter, permease component 2 (LivM/BraE) C1M55_RS16605 C1M55_RS22585
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit C1M55_RS15405
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit C1M55_RS15405
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components C1M55_RS15405 C1M55_RS15400
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused C1M55_RS23815
ofoA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit OfoA
ofoB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit OfoB
pccA propionyl-CoA carboxylase, alpha subunit C1M55_RS10790 C1M55_RS09265
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit C1M55_RS09265 C1M55_RS10790
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit C1M55_RS09265
pccB propionyl-CoA carboxylase, beta subunit C1M55_RS10840 C1M55_RS01140
pco propanyl-CoA oxidase C1M55_RS08415 C1M55_RS24690
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
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