GapMind for catabolism of small carbon sources

 

L-leucine catabolism in Hydrogenophaga taeniospiralis CCUG 15921 NBRC 102512

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 (27 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-leucine ABC transporter, ATPase component 1 (LivF/BraG) HTA01S_RS16505 HTA01S_RS04375
livG L-leucine ABC transporter, ATPase component 2 (LivG/BraF) HTA01S_RS16510 HTA01S_RS05080
livJ L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) HTA01S_RS07615
livH L-leucine ABC transporter, permease component 1 (LivH/BraD) HTA01S_RS16520 HTA01S_RS04360
livM L-leucine ABC transporter, permease component 2 (LivM/BraE) HTA01S_RS16515 HTA01S_RS08705
ilvE L-leucine transaminase HTA01S_RS23370 HTA01S_RS09175
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused HTA01S_RS23185
liuA isovaleryl-CoA dehydrogenase HTA01S_RS11035 HTA01S_RS14020
liuB 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit HTA01S_RS11160 HTA01S_RS06730
liuD 3-methylcrotonyl-CoA carboxylase, beta subunit HTA01S_RS11130 HTA01S_RS04495
liuC 3-methylglutaconyl-CoA hydratase HTA01S_RS24335 HTA01S_RS11150
liuE hydroxymethylglutaryl-CoA lyase HTA01S_RS11175 HTA01S_RS25890
atoA acetoacetyl-CoA transferase, A subunit HTA01S_RS02180
atoD acetoacetyl-CoA transferase, B subunit HTA01S_RS02175
atoB acetyl-CoA C-acetyltransferase HTA01S_RS02090 HTA01S_RS06660
Alternative steps:
aacS acetoacetyl-CoA synthetase HTA01S_RS11125 HTA01S_RS10250
AAP1 L-leucine permease AAP1
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ HTA01S_RS18560
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) HTA01S_RS18550 HTA01S_RS09505
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP HTA01S_RS18545 HTA01S_RS09510
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) HTA01S_RS18555 HTA01S_RS13175
Bap2 L-leucine permease Bap2
bcaP L-leucine uptake transporter BcaP
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit HTA01S_RS06615
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit HTA01S_RS06620 HTA01S_RS01230
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component HTA01S_RS06625 HTA01S_RS00010
brnQ L-leucine:Na+ symporter BrnQ/BraB
leuT L-leucine:Na+ symporter LeuT
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component HTA01S_RS00005 HTA01S_RS07650
natA L-leucine ABC transporter, ATPase component 1 (NatA) HTA01S_RS16510 HTA01S_RS14295
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) HTA01S_RS16520 HTA01S_RS05630
natE L-leucine ABC transporter, ATPase component 2 (NatE) HTA01S_RS14300 HTA01S_RS16505
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 09 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