GapMind for catabolism of small carbon sources

 

L-leucine catabolism in Collimonas arenae Ter10

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 (26 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-leucine ABC transporter, ATPase component 1 (LivF/BraG) CAter10_RS06900 CAter10_RS12275
livG L-leucine ABC transporter, ATPase component 2 (LivG/BraF) CAter10_RS15135 CAter10_RS06905
livJ L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) CAter10_RS04195 CAter10_RS04200
livH L-leucine ABC transporter, permease component 1 (LivH/BraD) CAter10_RS15145 CAter10_RS06915
livM L-leucine ABC transporter, permease component 2 (LivM/BraE) CAter10_RS15140 CAter10_RS06910
ilvE L-leucine transaminase CAter10_RS18075 CAter10_RS08670
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit CAter10_RS11335
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit CAter10_RS11330
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component CAter10_RS11325 CAter10_RS12510
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component CAter10_RS16765 CAter10_RS12505
liuA isovaleryl-CoA dehydrogenase CAter10_RS07495 CAter10_RS02405
liuB 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit CAter10_RS20935
liuD 3-methylcrotonyl-CoA carboxylase, beta subunit CAter10_RS20990
liuC 3-methylglutaconyl-CoA hydratase CAter10_RS20965 CAter10_RS20925
liuE hydroxymethylglutaryl-CoA lyase CAter10_RS20925
atoA acetoacetyl-CoA transferase, A subunit CAter10_RS13190
atoD acetoacetyl-CoA transferase, B subunit CAter10_RS13185 CAter10_RS02130
atoB acetyl-CoA C-acetyltransferase CAter10_RS02100 CAter10_RS21010
Alternative steps:
aacS acetoacetyl-CoA synthetase CAter10_RS19070
AAP1 L-leucine permease AAP1
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ CAter10_RS01915
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) CAter10_RS01925 CAter10_RS14305
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP CAter10_RS19005 CAter10_RS10285
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ)
Bap2 L-leucine permease Bap2
bcaP L-leucine uptake transporter BcaP
brnQ L-leucine:Na+ symporter BrnQ/BraB
leuT L-leucine:Na+ symporter LeuT
natA L-leucine ABC transporter, ATPase component 1 (NatA) CAter10_RS06905 CAter10_RS12280
natB L-leucine ABC transporter, substrate-binding component NatB
natC L-leucine ABC transporter, permease component 1 (NatC) CAter10_RS06910
natD L-leucine ABC transporter, permease component 2 (NatD) CAter10_RS15145 CAter10_RS12285
natE L-leucine ABC transporter, ATPase component 2 (NatE) CAter10_RS19520 CAter10_RS12275
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