GapMind for catabolism of small carbon sources

 

L-leucine catabolism in Rhizorhabdus wittichii RW1

Best path

leuT, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB

Rules

Overview: Leucine degradation in GapMind is based on MetaCyc pathway L-leucine degradation I, via branched alpha-keto acid dehydrogenase (link). Other pathways for are not included here because they are not linked to sequence (link) or do not result in carbon incorporation.

39 steps (27 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
leuT L-leucine:Na+ symporter LeuT
ilvE L-leucine transaminase SWIT_RS03965 SWIT_RS20630
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit SWIT_RS10830 SWIT_RS03985
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit SWIT_RS10825 SWIT_RS03980
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component SWIT_RS03975 SWIT_RS10820
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component SWIT_RS06910 SWIT_RS24900
liuA isovaleryl-CoA dehydrogenase SWIT_RS10910 SWIT_RS10095
liuB 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit SWIT_RS10920 SWIT_RS14620
liuD 3-methylcrotonyl-CoA carboxylase, beta subunit SWIT_RS10915 SWIT_RS14645
liuC 3-methylglutaconyl-CoA hydratase SWIT_RS11725 SWIT_RS03865
liuE hydroxymethylglutaryl-CoA lyase SWIT_RS11725
atoA acetoacetyl-CoA transferase, A subunit SWIT_RS04890 SWIT_RS26985
atoD acetoacetyl-CoA transferase, B subunit SWIT_RS26190 SWIT_RS04885
atoB acetyl-CoA C-acetyltransferase SWIT_RS03220 SWIT_RS10105
Alternative steps:
aacS acetoacetyl-CoA synthetase SWIT_RS07325 SWIT_RS22105
AAP1 L-leucine permease AAP1
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ SWIT_RS13335
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) SWIT_RS13325 SWIT_RS13330
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP SWIT_RS13320 SWIT_RS04010
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) SWIT_RS13330 SWIT_RS13325
Bap2 L-leucine permease Bap2 SWIT_RS03485
bcaP L-leucine uptake transporter BcaP SWIT_RS22305 SWIT_RS13040
brnQ L-leucine:Na+ symporter BrnQ/BraB
livF L-leucine ABC transporter, ATPase component 1 (LivF/BraG) SWIT_RS14705 SWIT_RS04010
livG L-leucine ABC transporter, ATPase component 2 (LivG/BraF) SWIT_RS14705 SWIT_RS13320
livH L-leucine ABC transporter, permease component 1 (LivH/BraD)
livJ L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3)
livM L-leucine ABC transporter, permease component 2 (LivM/BraE)
natA L-leucine ABC transporter, ATPase component 1 (NatA) SWIT_RS14705 SWIT_RS18740
natB L-leucine ABC transporter, substrate-binding component NatB
natC L-leucine ABC transporter, permease component 1 (NatC)
natD L-leucine ABC transporter, permease component 2 (NatD)
natE L-leucine ABC transporter, ATPase component 2 (NatE) SWIT_RS14705 SWIT_RS18740
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused SWIT_RS09265 SWIT_RS05980
ofoA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit OfoA
ofoB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit OfoB SWIT_RS16345
vorA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit VorA
vorB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit VorB SWIT_RS16340
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 09 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