GapMind for catabolism of small carbon sources

 

L-leucine catabolism in Cereibacter sphaeroides ATCC 17029

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 (28 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-leucine ABC transporter, ATPase component 1 (LivF/BraG) RSPH17029_RS04835 RSPH17029_RS07940
livG L-leucine ABC transporter, ATPase component 2 (LivG/BraF) RSPH17029_RS04855 RSPH17029_RS20335
livJ L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) RSPH17029_RS17965
livH L-leucine ABC transporter, permease component 1 (LivH/BraD) RSPH17029_RS17970 RSPH17029_RS20325
livM L-leucine ABC transporter, permease component 2 (LivM/BraE) RSPH17029_RS04845 RSPH17029_RS17975
ilvE L-leucine transaminase RSPH17029_RS14130 RSPH17029_RS14500
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused RSPH17029_RS08070 RSPH17029_RS18350
liuA isovaleryl-CoA dehydrogenase RSPH17029_RS05935 RSPH17029_RS09050
liuB 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit RSPH17029_RS05950 RSPH17029_RS04405
liuD 3-methylcrotonyl-CoA carboxylase, beta subunit RSPH17029_RS05945 RSPH17029_RS04380
liuC 3-methylglutaconyl-CoA hydratase RSPH17029_RS05960 RSPH17029_RS00050
liuE hydroxymethylglutaryl-CoA lyase RSPH17029_RS05955
atoA acetoacetyl-CoA transferase, A subunit RSPH17029_RS02855
atoD acetoacetyl-CoA transferase, B subunit RSPH17029_RS02850
atoB acetyl-CoA C-acetyltransferase RSPH17029_RS12120 RSPH17029_RS19805
Alternative steps:
aacS acetoacetyl-CoA synthetase RSPH17029_RS17960 RSPH17029_RS13630
AAP1 L-leucine permease AAP1
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ RSPH17029_RS18145 RSPH17029_RS02000
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) RSPH17029_RS18135 RSPH17029_RS02010
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP RSPH17029_RS02015 RSPH17029_RS18130
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) RSPH17029_RS18140 RSPH17029_RS02005
Bap2 L-leucine permease Bap2
bcaP L-leucine uptake transporter BcaP
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit RSPH17029_RS05845
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit RSPH17029_RS05840 RSPH17029_RS14900
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component RSPH17029_RS13235 RSPH17029_RS05835
brnQ L-leucine:Na+ symporter BrnQ/BraB
leuT L-leucine:Na+ symporter LeuT
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component RSPH17029_RS08165 RSPH17029_RS13225
natA L-leucine ABC transporter, ATPase component 1 (NatA) RSPH17029_RS07935 RSPH17029_RS14865
natB L-leucine ABC transporter, substrate-binding component NatB RSPH17029_RS07930
natC L-leucine ABC transporter, permease component 1 (NatC)
natD L-leucine ABC transporter, permease component 2 (NatD) RSPH17029_RS07945 RSPH17029_RS17970
natE L-leucine ABC transporter, ATPase component 2 (NatE) RSPH17029_RS07940 RSPH17029_RS04835
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 Apr 10 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