As text, or see rules and steps
# Leucine degradation in GapMind is based on MetaCyc pathway L-leucine degradation I, # via branched alpha-keto acid dehydrogenase (metacyc:LEU-DEG2-PWY). # Other pathways for are not included here because they are not linked to sequence # (metacyc:PWY-5075) or do not result in carbon incorporation. # ABC transporters: # E. coli livFGHMJ or livFGHMK (livK and livJ are alternate SBPs); # and livJFGHM from Streptococcus pneumoniae; # and braCDEFG from Pseudomonas aeruginosa (braC is the SBP); # and braDEFG/braC3 from R. leguminosarum; braC3 (RL3540; Q1MDE9) is a secondary # SBP that transports leucine/isoleucine/valine/alanine (PMID:19597156); the # proximal braC (Q9L3M3) is also thought to be involved in leucine transport (PMC135202); # LivH/BraD = RL3750/Q1MCU0; LivM/BraE = RL3749/Q1MCU1; # LivG/BraF = RL3748/Q1MCU2; LivF/BraG = RL3747/Q1MCU3; # and in Acidovorax sp. GW101-3H11: # LivF = Ac3H11_1692 (A0A165KC78), LivG = Ac3H11_1693 (A0A165KC86), # LivJ = Ac3H11_2396 (A0A165KTD4; not near the other components, but strong phenotype on leucine and cofitness), # LivH = Ac3H11_1695 (A0A165KC95), LivM = Ac3H11_1694 (A0A165KER0); livF L-leucine ABC transporter, ATPase component 1 (LivF/BraG) curated:CharProtDB::CH_003736 curated:TCDB::P21630 curated:TCDB::Q8DQH7 uniprot:Q1MCU3 uniprot:A0A165KC78 livG L-leucine ABC transporter, ATPase component 2 (LivG/BraF) curated:TCDB::P0A9S7 curated:TCDB::P21629 curated:TCDB::Q8DQH8 uniprot:Q1MCU2 uniprot:A0A165KC86 livJ L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) curated:SwissProt::P21175 curated:CharProtDB::CH_107418 curated:TCDB::P0AD96 curated:TCDB::Q8DQI1 uniprot:Q1MDE9 curated:TCDB::Q9L3M3 uniprot:A0A165KTD4 livH L-leucine ABC transporter, permease component 1 (LivH/BraD) curated:TCDB::P21627 curated:TCDB::Q8DQI0 curated:ecocyc::LIVH-MONOMER uniprot:Q1MCU0 uniprot:A0A165KC95 # LivM from Streptococcus pneumoniae lacks an N-terminal domain of unknown # function (DUF3382) that is found in E.coli and P. aeruginosa livM L-leucine ABC transporter, permease component 2 (LivM/BraE) curated:SwissProt::P22729 curated:TCDB::P21628 curated:TCDB::Q8DQH9 uniprot:Q1MCU1 uniprot:A0A165KER0 # Transporters were identified using # query: transporter:leucine:L-leucine leucine-transport: livF livG livJ livH livM # Synechocystis natABCDE and a related system in Anabaena (annotated with "leu" not leucine as the substrate) natA L-leucine ABC transporter, ATPase component 1 (NatA) curated:TCDB::Q55164 curated:TCDB::Q7A2H0 natB L-leucine ABC transporter, substrate-binding component NatB curated:TCDB::Q55387 curated:TCDB::Q8YVY4 natC L-leucine ABC transporter, permease component 1 (NatC) curated:TCDB::P74455 curated:TCDB::Q8YY08 natD L-leucine ABC transporter, permease component 2 (NatD) curated:TCDB::P74318 curated:TCDB::Q8YXD0 natE L-leucine ABC transporter, ATPase component 2 (NatE) curated:TCDB::P73650 curated:TCDB::Q8YT15 leucine-transport: natA natB natC natD natE # AapJQMP from Rhizobium leguminosarum is described in glutamate.steps import glutamate.steps:aapJ aapQ aapM aapP leucine-transport: aapJ aapQ aapM aapP # Homomeric transporters: leuT L-leucine:Na+ symporter LeuT curated:TCDB::O67854 leucine-transport: leuT brnQ L-leucine:Na+ symporter BrnQ/BraB curated:TCDB::P0AD99 curated:TCDB::P19072 leucine-transport: brnQ bcaP L-leucine uptake transporter BcaP curated:TCDB::S6EX81 leucine-transport: bcaP Bap2 L-leucine permease Bap2 curated:CharProtDB::CH_091448 curated:TCDB::Q2VQZ4 leucine-transport: Bap2 AAP1 L-leucine permease AAP1 curated:CharProtDB::CH_091601 leucine-transport: AAP1 # Ignore heteromeric systems found only in animals (i.e., TC 2.A.3.8.25) # Ignore regulatory proteins such as SC16B_HUMAN, SSY1_YEAST # Ignore amino acid exporters such as leuE, yjeH, brnEF # These enzymes transfer the amino group to 2-oxoglutarate to form # glutamate; glutamate dehydrogenase (not included in the pathway # definition) can then release the ammonia. Many other paths are # possible but do not seem to be known (i.e., transfer to oxaloacetate # followed by aspartate-ammonia lyase). ilvE L-leucine transaminase EC:2.6.1.6 EC:2.6.1.42 bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit curated:SwissProt::P12694 curated:BRENDA::Q72GU1 curated:CharProtDB::CH_121278 curated:SwissProt::O45924 curated:SwissProt::P11178 curated:SwissProt::P9WIS3 curated:SwissProt::Q5SLR4 curated:SwissProt::Q84JL2 curated:SwissProt::Q9LPL5 curated:reanno::Smeli:SMc03201 curated:reanno::pseudo13_GW456_L13:PfGW456L13_3540 curated:reanno::pseudo3_N2E3:AO353_26635 curated:reanno::pseudo5_N2C3_1:AO356_22990 curated:reanno::pseudo6_N2E2:Pf6N2E2_481 curated:metacyc::MONOMER-11683 bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit curated:CharProtDB::CH_121283 curated:SwissProt::P21953 curated:SwissProt::P9WIS1 curated:SwissProt::Q5SLR3 curated:SwissProt::Q9LDY2 curated:metacyc::MONOMER-11684 curated:reanno::Smeli:SMc03202 curated:reanno::WCS417:GFF3430 curated:reanno::pseudo13_GW456_L13:PfGW456L13_3541 curated:reanno::pseudo5_N2C3_1:AO356_22985 curated:reanno::pseudo6_N2E2:Pf6N2E2_480 curated:BRENDA::Q9HIA4 bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component EC:2.3.1.168 lpd branched-chain alpha-ketoacid dehydrogenase, E3 component EC:1.8.1.4 vorA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit VorA curated:SwissProt::P80907 ignore_other:1.2.7.7 vorB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit VorB curated:SwissProt::P80908 ignore_other:1.2.7.7 vorC branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC curated:SwissProt::P80909 ignore_other:1.2.7.7 # ofoAB is similar to low-specificity 2-oxoacid oxidoreductases (EC:1.2.7.11); it is generally # not certain if these act on 4-methyl-2-oxopentanoate or not, but they probably do. ofoA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit OfoA curated:SwissProt::P72578 ignore_other:1.2.7.7 ignore_other:1.2.7.11 ofoB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit OfoB curated:SwissProt::P72579 ignore_other:1.2.7.7 ignore_other:1.2.7.11 ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused curated:reanno::Cup4G11:RR42_RS19540 curated:reanno::psRCH2:GFF3452 ignore_other:1.2.7.7 ignore_other:1.2.7.11 # These decarboxylating dehydrogenases act on # 4-methyl-2-oxopentanoate, # 3-methyl-2-oxobutanoate (2-oxoisovalerate) # and (S)-3-methyl-2-oxopentanoate and are known as the branched-chain # alpha-ketoacid dehydrogenases. # They can pass electrons to NAD (EC:1.2.1.25) or to ferredoxin (EC:1.2.7.7). # The NAD-dependent enzyme is the sum of three activities: # EC:1.2.4.4 (the 4-methyl-2-oxopentanoate dehydrogenase, with transfer to the lipopoyllysine residue of 2.3.1.168) # which is itself heteromeric, with alpha and beta subunits; # EC:2.3.1.168 (dihydrolipoyllysine-residue (3-methylbutanoyl)transferase); # and EC:1.8.1.4 (dihydrolipoyl dehydrogenase, transferring electrons to NAD). BKD: bkdA bkdB bkdC lpd # The well-characterized ferredoxin-dependent enzymes have 3 subunits (vorABC) or 2 subunits (ofoAB). BKD: vorA vorB vorC BKD: ofoA ofoB # Genetic data identified a fused ferredoxin-dependent enzyme with just 1 subunit (ofo). BKD: ofo liuA isovaleryl-CoA dehydrogenase EC:1.3.8.4 EC:1.3.99.10 # 3-methylcrotonyl-CoA carboxylase has 2 subunits liuB 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit curated:CharProtDB::CH_122249 curated:BRENDA::Q42523 curated:BRENDA::Q9I299 curated:SwissProt::Q2QMG2 curated:SwissProt::Q96RQ3 curated:SwissProt::Q99MR8 curated:reanno::SB2B:6937189 curated:reanno::Smeli:SM_b21124 curated:reanno::pseudo1_N1B4:Pf1N1B4_3984 curated:reanno::pseudo5_N2C3_1:AO356_01595 curated:reanno::pseudo6_N2E2:Pf6N2E2_2194 ignore_other:6.4.1.4 liuD 3-methylcrotonyl-CoA carboxylase, beta subunit curated:BRENDA::Q9I297 curated:BRENDA::Q9LDD8 curated:CharProtDB::CH_122289 curated:SwissProt::Q9HCC0 curated:SwissProt::Q9V9A7 curated:reanno::SB2B:6937191 curated:reanno::Smeli:SM_b21122 curated:reanno::psRCH2:GFF1050 curated:reanno::pseudo5_N2C3_1:AO356_01585 curated:reanno::pseudo6_N2E2:Pf6N2E2_2192 ignore_other:6.4.1.4 # SM_b21126 (Q92VJ6) is a bit diverged and is confirmed by fitness data liuC 3-methylglutaconyl-CoA hydratase EC:4.2.1.18 uniprot:Q92VJ6 liuE hydroxymethylglutaryl-CoA lyase EC:4.1.3.4 atoA acetoacetyl-CoA transferase, A subunit curated:ecocyc::ATOD-MONOMER curated:metacyc::HP0691-MONOMER curated:reanno::psRCH2:GFF1045 curated:reanno::pseudo6_N2E2:Pf6N2E2_2111 ignore_other:2.8.3.5 atoD acetoacetyl-CoA transferase, B subunit curated:ecocyc::ATOA-MONOMER curated:metacyc::HP0692-MONOMER curated:reanno::psRCH2:GFF1044 curated:reanno::pseudo6_N2E2:Pf6N2E2_2112 ignore_other:2.8.3.5 aacS acetoacetyl-CoA synthetase EC:6.2.1.16 # acetyl-CoA:acetoacetyl-CoA transferase (sometimes given EC:2.8.3.9 or EC:2.8.3.8) # or succinyl-CoA:acetoacetyl-CoA transferase (EC:2.8.3.5, also known as 3-oxoacid CoA-transferase) # can activate acetoacetate. # These have an A and B subunit. acetoacetate-activation: atoA atoD # Alternatively, an ATP-dependent ligase (aacS) can activate acetoacetate (EC:6.2.1.16). acetoacetate-activation: aacS # Produces two acetyl-CoA from acetoacetyl-CoA and CoA. # EC:2.3.1.16 describes a broader range of beta-ketothiolases. # This enzyme is usually homomeric, but uniprot:I3R3D0 and uniprot:I3RA71 are non-catalytic subunits # of an enzyme from Haloferax mediterranei that also contains a # "normal" catalytic subunit (uniprot:I3R3D1, uniprot:I3RA72). # Inclusion of uniprot:P07256 was an error in BRENDA. # And CharProtDB includes an odd annotation of the form "similar to acetyl-CoA acetyltransferase" atoB acetyl-CoA C-acetyltransferase EC:2.3.1.9 ignore_other:2.3.1.16 ignore:BRENDA::P07256 ignore:BRENDA::I3R3D0 ignore:BRENDA::I3RA71 ignore_other:similar to acetyl-CoA acetyltransferase # The acetoacetate is activated to acetoacetyl-CoA, # and cleaved by acetyl-CoA acetyltransferase, # giving two acetyl-CoA. acetoacetate-degradation: acetoacetate-activation atoB # After transamination to 4-methyl-2-oxopentanoate by ilvE, # kbd oxidatively decarboxylates it to isovaleryl-CoA (also known as 3-methylbutanoyl-CoA), # liuA oxidizes it to 3-methylcrotonyl-CoA, # liuBD carboxylates it to 3-methylglutaconyl-CoA, # liuC hydrates it to hydroxymethylglutaryl-CoA, # and liuE hydrolyzes it to acetoacetate and acetyl-CoA. all: leucine-transport ilvE BKD liuA liuB liuD liuC liuE acetoacetate-degradation
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:
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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