GapMind for catabolism of small carbon sources

 

L-leucine catabolism in Marivita geojedonensis DPG-138

Best path

natA, natB, natC, natD, natE, 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 (28 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
natA L-leucine ABC transporter, ATPase component 1 (NatA) MGEO_RS19860 MGEO_RS14455
natB L-leucine ABC transporter, substrate-binding component NatB MGEO_RS14450
natC L-leucine ABC transporter, permease component 1 (NatC) MGEO_RS14470
natD L-leucine ABC transporter, permease component 2 (NatD) MGEO_RS14465 MGEO_RS19850
natE L-leucine ABC transporter, ATPase component 2 (NatE) MGEO_RS14460 MGEO_RS19855
ilvE L-leucine transaminase MGEO_RS04230 MGEO_RS11470
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused MGEO_RS11165
liuA isovaleryl-CoA dehydrogenase MGEO_RS05735 MGEO_RS13880
liuB 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit MGEO_RS05760 MGEO_RS05495
liuD 3-methylcrotonyl-CoA carboxylase, beta subunit MGEO_RS05755 MGEO_RS05475
liuC 3-methylglutaconyl-CoA hydratase MGEO_RS05775 MGEO_RS17480
liuE hydroxymethylglutaryl-CoA lyase MGEO_RS05770
atoA acetoacetyl-CoA transferase, A subunit MGEO_RS07025 MGEO_RS03530
atoD acetoacetyl-CoA transferase, B subunit MGEO_RS07035 MGEO_RS03535
atoB acetyl-CoA C-acetyltransferase MGEO_RS09905 MGEO_RS17560
Alternative steps:
aacS acetoacetyl-CoA synthetase MGEO_RS19425 MGEO_RS05190
AAP1 L-leucine permease AAP1
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ MGEO_RS16990
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) MGEO_RS17000 MGEO_RS10180
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP MGEO_RS17005 MGEO_RS07775
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) MGEO_RS16995
Bap2 L-leucine permease Bap2
bcaP L-leucine uptake transporter BcaP
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit MGEO_RS05650 MGEO_RS04995
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit MGEO_RS04990 MGEO_RS05645
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component MGEO_RS09570 MGEO_RS04975
brnQ L-leucine:Na+ symporter BrnQ/BraB
leuT L-leucine:Na+ symporter LeuT
livF L-leucine ABC transporter, ATPase component 1 (LivF/BraG) MGEO_RS05250 MGEO_RS04030
livG L-leucine ABC transporter, ATPase component 2 (LivG/BraF) MGEO_RS04005 MGEO_RS05255
livH L-leucine ABC transporter, permease component 1 (LivH/BraD) MGEO_RS04010 MGEO_RS10635
livJ L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3)
livM L-leucine ABC transporter, permease component 2 (LivM/BraE) MGEO_RS19845 MGEO_RS14470
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component MGEO_RS09565 MGEO_RS18755
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