GapMind for catabolism of small carbon sources

 

L-leucine catabolism in Geotalea uraniireducens Rf4

Best path

livF, livG, livJ, livH, livM, 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 (23 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-leucine ABC transporter, ATPase component 1 (LivF/BraG) GURA_RS10775 GURA_RS00570
livG L-leucine ABC transporter, ATPase component 2 (LivG/BraF) GURA_RS10785 GURA_RS00575
livJ L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) GURA_RS10805
livH L-leucine ABC transporter, permease component 1 (LivH/BraD) GURA_RS10795
livM L-leucine ABC transporter, permease component 2 (LivM/BraE) GURA_RS10790
ilvE L-leucine transaminase GURA_RS20105 GURA_RS03090
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit GURA_RS14760 GURA_RS06460
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit GURA_RS14755 GURA_RS06465
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component GURA_RS14750 GURA_RS08200
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component GURA_RS06450 GURA_RS04270
liuA isovaleryl-CoA dehydrogenase GURA_RS15475 GURA_RS16870
liuB 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit GURA_RS14795 GURA_RS09260
liuD 3-methylcrotonyl-CoA carboxylase, beta subunit
liuC 3-methylglutaconyl-CoA hydratase GURA_RS15480 GURA_RS08130
liuE hydroxymethylglutaryl-CoA lyase
atoA acetoacetyl-CoA transferase, A subunit GURA_RS22155
atoD acetoacetyl-CoA transferase, B subunit GURA_RS22150
atoB acetyl-CoA C-acetyltransferase GURA_RS15490 GURA_RS08100
Alternative steps:
aacS acetoacetyl-CoA synthetase GURA_RS08015
AAP1 L-leucine permease AAP1
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM)
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP GURA_RS11650 GURA_RS19800
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ)
Bap2 L-leucine permease Bap2
bcaP L-leucine uptake transporter BcaP
brnQ L-leucine:Na+ symporter BrnQ/BraB
leuT L-leucine:Na+ symporter LeuT
natA L-leucine ABC transporter, ATPase component 1 (NatA) GURA_RS00575 GURA_RS10785
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) GURA_RS10775 GURA_RS00570
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 GURA_RS11110
vorA* branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit VorA GURA_RS11365 with GURA_RS11360
vorB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit VorB GURA_RS11370 GURA_RS11115
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