GapMind for catabolism of small carbon sources

 

L-leucine catabolism in Bacillus altitudinis 41KF2b

Best path

brnQ, 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 (24 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
brnQ L-leucine:Na+ symporter BrnQ/BraB BA79_RS07760 BA79_RS07765
ilvE L-leucine transaminase BA79_RS09645 BA79_RS06860
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit BA79_RS11115 BA79_RS01950
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit BA79_RS11120 BA79_RS01105
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component BA79_RS11125 BA79_RS01960
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component BA79_RS01965 BA79_RS11110
liuA isovaleryl-CoA dehydrogenase BA79_RS18235 BA79_RS09030
liuB 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit BA79_RS02075 BA79_RS11005
liuD 3-methylcrotonyl-CoA carboxylase, beta subunit BA79_RS18205 BA79_RS11175
liuC 3-methylglutaconyl-CoA hydratase BA79_RS18210 BA79_RS07305
liuE hydroxymethylglutaryl-CoA lyase BA79_RS18215
atoA acetoacetyl-CoA transferase, A subunit BA79_RS14645
atoD acetoacetyl-CoA transferase, B subunit BA79_RS14650
atoB acetyl-CoA C-acetyltransferase BA79_RS09045 BA79_RS04980
Alternative steps:
aacS acetoacetyl-CoA synthetase BA79_RS18230 BA79_RS07315
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) BA79_RS09605 BA79_RS06425
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP BA79_RS06410 BA79_RS09600
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) BA79_RS06420
Bap2 L-leucine permease Bap2 BA79_RS05520 BA79_RS14470
bcaP L-leucine uptake transporter BcaP BA79_RS14915 BA79_RS12440
leuT L-leucine:Na+ symporter LeuT
livF L-leucine ABC transporter, ATPase component 1 (LivF/BraG) BA79_RS06410 BA79_RS08570
livG L-leucine ABC transporter, ATPase component 2 (LivG/BraF) BA79_RS12885 BA79_RS05440
livH L-leucine ABC transporter, permease component 1 (LivH/BraD)
livJ L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3)
livM L-leucine ABC transporter, permease component 2 (LivM/BraE)
natA L-leucine ABC transporter, ATPase component 1 (NatA) BA79_RS08110 BA79_RS05190
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)
natE L-leucine ABC transporter, ATPase component 2 (NatE) BA79_RS08570 BA79_RS11155
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
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