As text, or see rules and steps
# Lactose utilization in GapMind is based on # MetaCyc pathway lactose degradation II via 3'-ketolactose (metacyc:LACTOSEUTIL-PWY), # pathway III via beta-galactosidase (metacyc:BGALACT-PWY), # or uptake by a PTS system followed by hydrolysis of lactose 6'-phosphate. # (There is no pathway I.) # ABC transporters: # Agrobacterium radiobacter and Sinorhizobium meliloti have related systems, # named lacEFGK in Agrobacterium lacE lactose ABC transporter, substrate-binding component curated:TCDB::P29822 curated:reanno::Smeli:SM_b21652 lacF lactose ABC transporter, permease component 1 curated:TCDB::P29823 curated:reanno::Smeli:SM_b21653 lacG lactose ABC transporter, permease component 2 curated:TCDB::P29824 curated:reanno::Smeli:SM_b21654 lacK lactose ABC transporter, ATPase component curated:TCDB::Q01937 curated:reanno::Smeli:SM_b20002 # Transporters and PTS systems were identified using # query: transporter:lactose:alpha-lactose:CPD-15971 lactose-transport: lacE lacF lacG lacK # PTS systems: lacIIA lactose PTS system, EIIA component curated:SwissProt::P0A0D6 curated:SwissProt::P11502 curated:SwissProt::P23532 curated:TCDB::Q045H4 curated:TCDB::Q045X4 curated:TCDB::U5MLJ3 lacIIB lactose PTS system, EIIB component curated:TCDB::U5MIE1 lacIIC lactose PTS system, EIIC component curated:TCDB::U5MFA1 lacIICB lactose PTS system, fused EIIC and EIIB components curated:SwissProt::P11162 curated:SwissProt::P23531 curated:SwissProt::P24400 curated:TCDB::Q045H3 curated:TCDB::Q045X3 # PTS systems forming lactose 6'-phosphate. # Klebsiella pneumoniae has a EIIA,B,C in three separate proteins. # The other characterized PTS systems have EIIA and EIICB lactose-PTS: lacIIA lacIIB lacIIC lactose-PTS: lacIIA lacIICB # Homomeric transporters lacP lactose permease LacP curated:CharProtDB::CH_124122 curated:CharProtDB::CH_124118 curated:CharProtDB::CH_124308 curated:CharProtDB::CH_124309 curated:TCDB::P07921 lactose-transport: lacP lacS lactose permease LacS curated:SwissProt::Q7WTB2 curated:TCDB::P23936 lactose-transport: lacS lacY lactose:proton symporter LacY curated:SwissProt::P02920 curated:SwissProt::P96517 lactose-transport: lacY # Ignored sugar exporters such as setA or sotA pbgal phospho-beta-galactosidase EC:3.2.1.85 import fructose.steps:tpi # part of galactose degradation import galactose.steps:galactose-6-phosphate-degradation galactose-degradation # LacACB from Caulobacter is the best studied lactose 3-dehydrogenase, # but a related system from Pedobacter is also required for lactose utilization. # EC:1.1.99.13 includes 3-ketoglycoside dehydrogenases more broadly. # Other types of periplasmic 3-ketoglycoside dehydrogenases have been # reported (ThuAB from Agrobacterium and Sinorhizobium and BT2158 from # Bacteroides thetaiotaomicron) but these do not seem to be involved # in lactose utilization. # To avoid confusion with galactose catabolism genes, these are named # lacA' etc. in GapMind. lacA' periplasmic lactose 3-dehydrogenase, LacA subunit curated:reanno::Caulo:CCNA_01706 curated:reanno::Pedo557:CA265_RS15345 ignore_other: 1.1.99.13 lacC' periplasmic lactose 3-dehydrogenase, LacC subunit curated:reanno::Caulo:CCNA_01707 curated:reanno::Pedo557:CA265_RS15340 ignore_other: 1.1.99.13 lacB' periplasmic lactose 3-dehydrogenase, cytochrome c component (LacB) curated:reanno::Caulo:CCNA_01704 curated:reanno::Pedo557:CA265_RS15360 ignore_other: 1.1.99.13 # DUF1080 (PF06439) was recently identified # as a family of 3-ketoglycoside hydrolases, and fitness data identified # CCNA_01705 as the 3'-ketolactose hydrolase (PMID:33657378). klh periplasmic 3'-ketolactose hydrolase curated:reanno::Caulo:CCNA_01705 # glk is glucokinase import glucose.steps:glucose-utilization glk lacL heteromeric lactase, large subunit curated:BRENDA::A0SWS3 curated:CAZy::AAA25267.1 curated:CAZy::AAL09167.1 curated:CAZy::ABF72116.1 curated:CAZy::ABJ65308.1 curated:CAZy::ACC38286.1 curated:CAZy::AEG39988.1 curated:CAZy::AEJ32720.1 curated:CAZy::BAA20536.1 curated:CAZy::CAA57730.1 curated:CAZy::CAD65569.1 curated:CAZy::CAZ66936.1 curated:SwissProt::Q7WTB4 lacM heteromeric lactase, small subunit curated:BRENDA::A0SWS4 curated:BRENDA::Q19R71 curated:SwissProt::Q7WTB3 # Mark the sequences for lacL or lacM as ignore, and also uniprot:BGAL_HORVU. # Also mark some similar enzymes annotated as beta-glycosidases as ignore. lacZ lactase (homomeric) EC:3.2.1.108 EC:3.2.1.23 ignore:BRENDA::A0SWS3 ignore:CAZy::AAA25267.1 ignore:CAZy::AAL09167.1 ignore:CAZy::ABF72116.1 ignore:CAZy::ABJ65308.1 ignore:CAZy::ACC38286.1 ignore:CAZy::AEG39988.1 ignore:CAZy::AEJ32720.1 ignore:CAZy::BAA20536.1 ignore:CAZy::CAA57730.1 ignore:CAZy::CAD65569.1 ignore:CAZy::CAZ66936.1 ignore:SwissProt::Q7WTB4 ignore:BRENDA::A0SWS4 ignore:BRENDA::Q19R71 ignore:SwissProt::Q7WTB3 ignore:SwissProt::P83252 ignore:CAZy::AAA79030.1 ignore:CAZy::AAN05439.1 ignore:CAZy::AAF36392.1 ignore:CAZy::AAN05441.1 ignore:CAZy::ABW87307.1 ignore:CAZy::AAO15361.1 ignore:CAZy::AAN05440.1 ignore:CAZy::ABW01253.1 ignore:CAZy::AAY81155.1 ignore:CAZy::CAA34074.1 ignore:CAZy::ADL19795.1 ignore:CAZy::AEE47485.1 ignore:CAZy::ACK41548.1 ignore:CAZy::ABX04075.1 ignore:CAZy::BAA78713.1 ignore:BRENDA::Q8DR24 # Most lactases are homomeric, but Lactobacillus have a heteromeric enzyme LacLM. # (There is also a heteromeric beta-galactosidase in barley, see uniprot:BGAL_HORVU, but it is not included. # Also, "evolved beta-galactosidase" ebgA from E. coli is more active with its partner ebgC, # but it retains activity on its own, so it is included in step lacZ instead.) beta-galactosidase: lacZ beta-galactosidase: lacL lacM # In pathway III, lactose is taken up and cleaved to galactose and glucose by beta-galactosidase; # the glucose is consumed by kinase glk. # (The galactose 1-epimerase galM, EC:5.1.3.3, is not included in galactose degradation; # it is important for lactose utilization in E. coli (PMID:7966338), but # not in Sinorhizobium meliloti or in Bacteroides thetaiotaomicron, which also # use this pathway.) all: lactose-transport beta-galactosidase galactose-degradation glk # Or, a PTS forms lactose 6'-phosphate and phosphogalactosidase (pbgal) # forms galactose 6-phosphate and glucose. all: lactose-PTS pbgal galactose-6-phosphate-degradation glk # Or, lactose is oxidized to 3'-ketolactose by a periplasmic # 3-component dehydrogenase (lacACB'), and then hydrolyzed by a # periplasmic enzyme (klh) to 3-keto-beta-D-galactose and # D-glucopyranose, and hypothetical reduction of the # 3-ketogalactose. Liberation of glucose is probably sufficient for # growth. all: lacA' lacC' lacB' klh glucose-utilization
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:
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