GapMind for catabolism of small carbon sources

 

L-leucine catabolism in Algoriphagus machipongonensis PR1

Best path

leuT, 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 (19 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
leuT L-leucine:Na+ symporter LeuT
ilvE L-leucine transaminase ALPR1_RS13420 ALPR1_RS17415
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit ALPR1_RS18330 ALPR1_RS02675
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit ALPR1_RS18330 ALPR1_RS06440
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component ALPR1_RS14510 ALPR1_RS12815
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component ALPR1_RS03970 ALPR1_RS17920
liuA isovaleryl-CoA dehydrogenase ALPR1_RS19205 ALPR1_RS02465
liuB 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit ALPR1_RS12520 ALPR1_RS12915
liuD 3-methylcrotonyl-CoA carboxylase, beta subunit ALPR1_RS14955 ALPR1_RS04635
liuC 3-methylglutaconyl-CoA hydratase ALPR1_RS05015 ALPR1_RS16285
liuE hydroxymethylglutaryl-CoA lyase ALPR1_RS13305
atoA acetoacetyl-CoA transferase, A subunit ALPR1_RS11165
atoD acetoacetyl-CoA transferase, B subunit ALPR1_RS11160
atoB acetyl-CoA C-acetyltransferase ALPR1_RS13240 ALPR1_RS01085
Alternative steps:
aacS acetoacetyl-CoA synthetase ALPR1_RS09835 ALPR1_RS10080
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)
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP ALPR1_RS13410 ALPR1_RS08010
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
livF L-leucine ABC transporter, ATPase component 1 (LivF/BraG) ALPR1_RS03040 ALPR1_RS06390
livG L-leucine ABC transporter, ATPase component 2 (LivG/BraF) ALPR1_RS03040 ALPR1_RS06225
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) ALPR1_RS03040
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) ALPR1_RS03040 ALPR1_RS17310
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