GapMind for catabolism of small carbon sources

 

L-valine catabolism in Algoriphagus machipongonensis PR1

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 ALPR1_RS18330 ALPR1_RS02675
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit ALPR1_RS18330 ALPR1_RS06440
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component ALPR1_RS14510 ALPR1_RS12815
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component ALPR1_RS03970 ALPR1_RS17920
acdH isobutyryl-CoA dehydrogenase ALPR1_RS02465 ALPR1_RS19205
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase ALPR1_RS16285 ALPR1_RS07745
bch 3-hydroxyisobutyryl-CoA hydrolase
mmsB 3-hydroxyisobutyrate dehydrogenase
mmsA methylmalonate-semialdehyde dehydrogenase ALPR1_RS01205 ALPR1_RS06860
pccA propionyl-CoA carboxylase, alpha subunit ALPR1_RS12520 ALPR1_RS12915
pccB propionyl-CoA carboxylase, beta subunit ALPR1_RS04635 ALPR1_RS14955
epi methylmalonyl-CoA epimerase ALPR1_RS14785
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit ALPR1_RS17365 ALPR1_RS12840
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit ALPR1_RS17365
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase ALPR1_RS07835
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) ALPR1_RS07835
bcaP L-valine uptake transporter BcaP/CitA
brnQ L-valine:cation symporter BrnQ/BraZ/BraB
dddA 3-hydroxypropionate dehydrogenase ALPR1_RS01365
hpcD 3-hydroxypropionyl-CoA dehydratase ALPR1_RS16285 ALPR1_RS05015
iolA malonate semialdehyde dehydrogenase (CoA-acylating) ALPR1_RS01205 ALPR1_RS06860
livF L-valine ABC transporter, ATPase component 1 (LivF/BraG) ALPR1_RS03040 ALPR1_RS06390
livG L-valine ABC transporter, ATPase component 2 (LivG/BraF) ALPR1_RS03040 ALPR1_RS06225
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 ALPR1_RS12840 ALPR1_RS17365
natA L-valine ABC transporter, ATPase component 1 (NatA) ALPR1_RS03040
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) ALPR1_RS03040 ALPR1_RS17310
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 ALPR1_RS12520 ALPR1_RS12915
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pco propanyl-CoA oxidase ALPR1_RS19490 ALPR1_RS12195
phtJ L-valine uptake permease PhtJ
prpB 2-methylisocitrate lyase
prpC 2-methylcitrate synthase ALPR1_RS08615
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