GapMind for catabolism of small carbon sources

 

L-leucine catabolism in Lacinutrix himadriensis E4-9a

Best path

brnQ, 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 (20 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
brnQ L-leucine:Na+ symporter BrnQ/BraB AMD28_RS00295
ilvE L-leucine transaminase AMD28_RS17735 AMD28_RS17125
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit AMD28_RS14910 AMD28_RS04760
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit AMD28_RS14910 AMD28_RS08345
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component AMD28_RS16375 AMD28_RS04765
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component AMD28_RS05465 AMD28_RS06695
liuA isovaleryl-CoA dehydrogenase AMD28_RS04680 AMD28_RS05185
liuB 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit AMD28_RS05795 AMD28_RS11080
liuD 3-methylcrotonyl-CoA carboxylase, beta subunit AMD28_RS13295 AMD28_RS05800
liuC 3-methylglutaconyl-CoA hydratase AMD28_RS12825
liuE hydroxymethylglutaryl-CoA lyase AMD28_RS01735
atoA acetoacetyl-CoA transferase, A subunit AMD28_RS10385
atoD acetoacetyl-CoA transferase, B subunit AMD28_RS10380
atoB acetyl-CoA C-acetyltransferase AMD28_RS15255 AMD28_RS12845
Alternative steps:
aacS acetoacetyl-CoA synthetase AMD28_RS03415
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 AMD28_RS08690 AMD28_RS03840
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
leuT L-leucine:Na+ symporter LeuT
livF L-leucine ABC transporter, ATPase component 1 (LivF/BraG) AMD28_RS16880 AMD28_RS06200
livG L-leucine ABC transporter, ATPase component 2 (LivG/BraF) AMD28_RS16880 AMD28_RS03840
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) AMD28_RS16880 AMD28_RS17695
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) AMD28_RS16880 AMD28_RS01550
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
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