GapMind for catabolism of small carbon sources

 

L-isoleucine catabolism in Rhodospirillum rubrum ATCC 11170

Best path

livF, livG, livJ, livH, livM, ofo, acdH, ech, ivdG, fadA, prpC, prpD, acn, prpB

Rules

Overview: Isoleucine degradation in GapMind is based on MetaCyc pathway L-isoleucine degradation I (link). The other pathways are fermentative and do not lead to carbon incorporation (link, link).

45 steps (38 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-isoleucine ABC transporter, ATPase component 1 (LivF/BraG) Rru_A1748 Rru_A3725
livG L-isoleucine ABC transporter, ATPase component 2 (LivG/BraF) Rru_A1749 Rru_A3724
livJ L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) Rru_A2171 Rru_A1746
livH L-isoleucine ABC transporter, permease component 1 (LivH/BraD) Rru_A1751 Rru_A3726
livM L-isoleucine ABC transporter, permease component 2 (LivM/BraE) Rru_A1750 Rru_A3727
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused Rru_A2185
acdH (2S)-2-methylbutanoyl-CoA dehydrogenase Rru_A1835 Rru_A1948
ech 2-methyl-3-hydroxybutyryl-CoA hydro-lyase Rru_A3801 Rru_A1309
ivdG 3-hydroxy-2-methylbutyryl-CoA dehydrogenase Rru_A1507 Rru_A0273
fadA 2-methylacetoacetyl-CoA thiolase Rru_A1380 Rru_A0274
prpC 2-methylcitrate synthase Rru_A2319 Rru_A1600
prpD 2-methylcitrate dehydratase Rru_A2318
acn (2R,3S)-2-methylcitrate dehydratase Rru_A3511
prpB 2-methylisocitrate lyase Rru_A2320
Alternative steps:
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) Rru_A3511
Bap2 L-isoleucine permease Bap2
bcaP L-isoleucine uptake transporter BcaP/CitA
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit Rru_A1881
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit Rru_A1880
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component Rru_A1214 Rru_A1879
brnQ L-isoleucine:cation symporter BrnQ/BraZ/BraB
dddA 3-hydroxypropionate dehydrogenase
epi methylmalonyl-CoA epimerase Rru_A1572
hpcD 3-hydroxypropionyl-CoA dehydratase Rru_A3801 Rru_A2506
iolA malonate semialdehyde dehydrogenase (CoA-acylating) Rru_A2071 Rru_A1542
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component Rru_A1878 Rru_A1215
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit Rru_A2479 Rru_A3062
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit Rru_A3062 Rru_A2479
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components Rru_A2479 Rru_A2480
natA L-isoleucine ABC transporter, ATPase component 1 (NatA) Rru_A3414 Rru_A3724
natB L-isoleucine ABC transporter, substrate-binding component NatB Rru_A1746
natC L-isoleucine ABC transporter, permease component 1 (NatC) Rru_A3415
natD L-isoleucine ABC transporter, permease component 2 (NatD) Rru_A3416 Rru_A3306
natE L-isoleucine ABC transporter, ATPase component 2 (NatE) Rru_A3413 Rru_A1748
ofoA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit OfoA Rru_A2721
ofoB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit OfoB Rru_A2722
pccA propionyl-CoA carboxylase, alpha subunit Rru_A0052 Rru_A1941
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit Rru_A0052 Rru_A2435
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit Rru_A1941
pccB propionyl-CoA carboxylase, beta subunit Rru_A0053 Rru_A1943
pco propanyl-CoA oxidase Rru_A2005
prpF methylaconitate isomerase
vorA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit VorA
vorB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit VorB Rru_A2721
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