GapMind for catabolism of small carbon sources

 

L-leucine catabolism in Cloacibacillus porcorum CL-84

Best path

livF, livG, livJ, livH, livM, ilvE, ofo, 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 (24 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-leucine ABC transporter, ATPase component 1 (LivF/BraG) BED41_RS01985 BED41_RS03710
livG L-leucine ABC transporter, ATPase component 2 (LivG/BraF) BED41_RS01990 BED41_RS13925
livJ L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) BED41_RS04590 BED41_RS03690
livH L-leucine ABC transporter, permease component 1 (LivH/BraD) BED41_RS03695 BED41_RS12755
livM L-leucine ABC transporter, permease component 2 (LivM/BraE) BED41_RS03700 BED41_RS12750
ilvE L-leucine transaminase BED41_RS03640 BED41_RS05005
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
liuA isovaleryl-CoA dehydrogenase
liuB 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit
liuD 3-methylcrotonyl-CoA carboxylase, beta subunit BED41_RS04295 BED41_RS10175
liuC 3-methylglutaconyl-CoA hydratase BED41_RS02945 BED41_RS10185
liuE hydroxymethylglutaryl-CoA lyase BED41_RS01685
atoA acetoacetyl-CoA transferase, A subunit BED41_RS01550 BED41_RS12320
atoD acetoacetyl-CoA transferase, B subunit BED41_RS01555 BED41_RS12325
atoB acetyl-CoA C-acetyltransferase BED41_RS01560 BED41_RS10190
Alternative steps:
aacS acetoacetyl-CoA synthetase BED41_RS01515 BED41_RS14140
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) BED41_RS04025
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP BED41_RS04030 BED41_RS14585
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) BED41_RS04025
Bap2 L-leucine permease Bap2
bcaP L-leucine uptake transporter BcaP
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component
brnQ L-leucine:Na+ symporter BrnQ/BraB
leuT L-leucine:Na+ symporter LeuT BED41_RS11455
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component BED41_RS02590 BED41_RS03525
natA L-leucine ABC transporter, ATPase component 1 (NatA) BED41_RS12745 BED41_RS14290
natB L-leucine ABC transporter, substrate-binding component NatB
natC L-leucine ABC transporter, permease component 1 (NatC) BED41_RS03700
natD L-leucine ABC transporter, permease component 2 (NatD) BED41_RS01975 BED41_RS12755
natE L-leucine ABC transporter, ATPase component 2 (NatE) BED41_RS03710 BED41_RS12740
ofoA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit OfoA
ofoB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit OfoB BED41_RS08355
vorA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit VorA
vorB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit VorB BED41_RS08360
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