GapMind for catabolism of small carbon sources

 

L-valine catabolism in Halomonas titanicae BH1

Best path

natA, natB, natC, natD, natE, bkdA, bkdB, bkdC, lpd, acdH, ech, bch, mmsB, mmsA, prpC, acnD, prpF, 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 (33 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
natA L-valine ABC transporter, ATPase component 1 (NatA) HALTITAN_RS19870 HALTITAN_RS05165
natB L-valine ABC transporter, substrate-binding component NatB HALTITAN_RS19895
natC L-valine ABC transporter, permease component 1 (NatC)
natD L-valine ABC transporter, permease component 2 (NatD) HALTITAN_RS19880 HALTITAN_RS02320
natE L-valine ABC transporter, ATPase component 2 (NatE) HALTITAN_RS19875 HALTITAN_RS05170
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit HALTITAN_RS16760
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit HALTITAN_RS16765
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component HALTITAN_RS16770 HALTITAN_RS13360
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component HALTITAN_RS12210 HALTITAN_RS09625
acdH isobutyryl-CoA dehydrogenase HALTITAN_RS05190 HALTITAN_RS16815
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase HALTITAN_RS11900 HALTITAN_RS16865
bch 3-hydroxyisobutyryl-CoA hydrolase HALTITAN_RS05195 HALTITAN_RS11900
mmsB 3-hydroxyisobutyrate dehydrogenase HALTITAN_RS05200 HALTITAN_RS00920
mmsA methylmalonate-semialdehyde dehydrogenase HALTITAN_RS01125 HALTITAN_RS20310
prpC 2-methylcitrate synthase HALTITAN_RS18470 HALTITAN_RS12175
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) HALTITAN_RS18475 HALTITAN_RS14545
prpF methylaconitate isomerase HALTITAN_RS18480
acn (2R,3S)-2-methylcitrate dehydratase HALTITAN_RS18475 HALTITAN_RS09135
prpB 2-methylisocitrate lyase HALTITAN_RS18465
Alternative steps:
Bap2 L-valine permease Bap2
bcaP L-valine uptake transporter BcaP/CitA
brnQ L-valine:cation symporter BrnQ/BraZ/BraB
dddA 3-hydroxypropionate dehydrogenase HALTITAN_RS21330 HALTITAN_RS05605
epi methylmalonyl-CoA epimerase
hpcD 3-hydroxypropionyl-CoA dehydratase HALTITAN_RS11900 HALTITAN_RS01660
iolA malonate semialdehyde dehydrogenase (CoA-acylating) HALTITAN_RS21335 HALTITAN_RS00495
livF L-valine ABC transporter, ATPase component 1 (LivF/BraG) HALTITAN_RS02305 HALTITAN_RS22535
livG L-valine ABC transporter, ATPase component 2 (LivG/BraF) HALTITAN_RS02310 HALTITAN_RS03355
livH L-valine ABC transporter, permease component 1 (LivH/BraD) HALTITAN_RS02320 HALTITAN_RS05180
livJ L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) HALTITAN_RS19895
livM L-valine ABC transporter, permease component 2 (LivM/BraE) HALTITAN_RS02315
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused HALTITAN_RS01790
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 HALTITAN_RS05140 HALTITAN_RS06100
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit HALTITAN_RS06100 HALTITAN_RS02185
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit HALTITAN_RS07915
pccB propionyl-CoA carboxylase, beta subunit HALTITAN_RS05150
pco propanyl-CoA oxidase HALTITAN_RS07760 HALTITAN_RS16815
phtJ L-valine uptake permease PhtJ
prpD 2-methylcitrate dehydratase HALTITAN_RS18485
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