GapMind for catabolism of small carbon sources

 

L-leucine catabolism in Marinobacter guineae M3B

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 (29 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-leucine ABC transporter, ATPase component 1 (LivF/BraG) CLH62_RS07860 CLH62_RS05520
livG L-leucine ABC transporter, ATPase component 2 (LivG/BraF) CLH62_RS07855 CLH62_RS05525
livJ L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) CLH62_RS07840
livH L-leucine ABC transporter, permease component 1 (LivH/BraD) CLH62_RS07845 CLH62_RS05535
livM L-leucine ABC transporter, permease component 2 (LivM/BraE) CLH62_RS07850 CLH62_RS05530
ilvE L-leucine transaminase CLH62_RS19085 CLH62_RS16190
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit CLH62_RS08825
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit CLH62_RS08830
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component CLH62_RS08835 CLH62_RS07790
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component CLH62_RS18585 CLH62_RS03305
liuA isovaleryl-CoA dehydrogenase CLH62_RS15440 CLH62_RS13200
liuB 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit CLH62_RS15455 CLH62_RS04865
liuD 3-methylcrotonyl-CoA carboxylase, beta subunit CLH62_RS15445 CLH62_RS04850
liuC 3-methylglutaconyl-CoA hydratase CLH62_RS15450 CLH62_RS15970
liuE hydroxymethylglutaryl-CoA lyase CLH62_RS15460
atoA acetoacetyl-CoA transferase, A subunit CLH62_RS15680 CLH62_RS11885
atoD acetoacetyl-CoA transferase, B subunit CLH62_RS11890 CLH62_RS15675
atoB acetyl-CoA C-acetyltransferase CLH62_RS07455 CLH62_RS15420
Alternative steps:
aacS acetoacetyl-CoA synthetase CLH62_RS11015 CLH62_RS15470
AAP1 L-leucine permease AAP1
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ CLH62_RS02950
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) CLH62_RS02940
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP CLH62_RS02935 CLH62_RS06600
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) CLH62_RS02945
Bap2 L-leucine permease Bap2
bcaP L-leucine uptake transporter BcaP
brnQ L-leucine:Na+ symporter BrnQ/BraB
leuT L-leucine:Na+ symporter LeuT CLH62_RS16195
natA L-leucine ABC transporter, ATPase component 1 (NatA) CLH62_RS05525 CLH62_RS12085
natB L-leucine ABC transporter, substrate-binding component NatB
natC L-leucine ABC transporter, permease component 1 (NatC) CLH62_RS07850
natD L-leucine ABC transporter, permease component 2 (NatD) CLH62_RS07845 CLH62_RS15915
natE L-leucine ABC transporter, ATPase component 2 (NatE) CLH62_RS05520 CLH62_RS07860
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused CLH62_RS16185
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