As text, or see rules and steps
# Maltose utilization in GapMind is based on the MetaCyc pathway # via maltose phosphorylase (metacyc:MALTOSECAT-PWY), # or a phosphotransferase system followed by 6-phospho-alphaglucosidase, # or a phosphotransferase system followed by a phosphatase back to maltose followed by maltose phosphorylase, # or hydrolysis by alpha-glucosidase after uptake, # or periplasmic hydrolysis by alpha-glucosidase followed by glucose utilization. # ABC transporters: # E. coli has malEFGK. In Salmonella typhimurium, malK only is listed. # Related systems are found in Klebsiella michiganensis and Pseudomonas stutzeri RCH2. malE maltose ABC transporter, substrate-binding component MalE curated:BRENDA::P0AEX9 curated:reanno::Koxy:BWI76_RS01830 curated:reanno::psRCH2:GFF849 malF maltose ABC transporter, permease component 1 (MalF) curated:BRENDA::P02916 curated:reanno::Koxy:BWI76_RS01825 curated:reanno::psRCH2:GFF850 malG maltose ABC transporter, permease component 2 (MalG) curated:BRENDA::P68183 curated:reanno::Koxy:BWI76_RS01820 curated:reanno::psRCH2:GFF851 malK maltose ABC transporter, ATPase component MalK curated:BRENDA::P68187 curated:SwissProt::P19566 curated:reanno::psRCH2:GFF857 # Transporters and PTS systems identified using: # query: transporter:maltose:ALPHA-MALTOSE:CPD-15717 maltose-transport: malE malF malG malK # Sinorhizobium meliloti has thuEFGK; similar systems are found in # Thermus thermophilus, Thermococcus literalis, and Streptomyces coelicolor. thuE maltose ABC transporter, substrate-binding component ThuE curated:TCDB::Q9R9Q7 curated:TCDB::O51923 curated:TCDB::Q72H68 curated:TCDB::Q7AKP1 curated:SwissProt::Q7LYW7 thuF maltose ABC transporter, permease component 1 (ThuF) curated:TCDB::Q72H67 curated:SwissProt::O51924 curated:TCDB::O51924 curated:TCDB::Q9KZ07 curated:reanno::Smeli:SM_b20326 thuG maltose ABC transporter, permease component 2 (ThuG) curated:SwissProt::Q7LYX6 curated:TCDB::Q72H66 curated:TCDB::Q9KZ08 curated:reanno::Smeli:SM_b20327 thuK maltose ABC transporter, ATPase component ThuK curated:SwissProt::Q9YGA6 curated:TCDB::Q9R9Q4 curated:reanno::Smeli:SMc03065 curated:TCDB::Q72L52 maltose-transport: thuE thuF thuG thuK # Thermotoga maritima has malE1E2F1F2G1G2K; both SBPs bind maltose, so require only one to be present. malE1 maltose ABC transporter, substrate-binding component (MalE1/MalE2) curated:TCDB::Q9S5Y1 curated:TCDB::Q9X0T1 malF1 maltose ABC transporter, permease component 1 (MalF1) curated:TCDB::Q9X0T0 malG1 maltose ABC transporter, permease component 2 (MalG1/MalG2) curated:BRENDA::Q9X0S9 curated:BRENDA::Q9X2F5 malK1 maltose ABC transporter, ATPase component curated:TCDB::Q9X103 maltose-transport: malE1 malF1 malG1 malK1 # Streptococcus mutans has malXFGK, distantly related to these other systems malX_Sm maltose ABC transporter, substrate-binding component curated:TCDB::Q8DT28 malF_Sm maltose ABC transporter, permease component 1 curated:TCDB::Q8DT27 malG_Sm maltose ABC transporter, permease component 2 curated:TCDB::Q8DT26 malK_Sm maltose ABC transporter, ATPase component curated:TCDB::Q8DT25 maltose-transport: malX_Sm malF_Sm malG_Sm malK_Sm # Corynebacterium glutamicum has musEFGKI (cg2705,cg2704,cg2703,cg2708,cg2701) musE maltose ABC transporter, substrate-binding component MusE curated:TCDB::Q8NMV3 musF maltose ABC transporter, permease component 1 (MusF) curated:TCDB::Q8NMV4 musG maltose ABC transporter, permease component 2 (MusG) curated:TCDB::Q8NMV5 musK maltose ABC transporter, ATPase component MusK curated:BRENDA::Q8NMV1 musI maltose ABC transporter, uncharacterized membrane component MusI curated:TCDB::Q6M306 maltose-transport: musE musF musG musK musI # Alicyclobacillus acidocaldarius: malK only is curated, but PMID:15136159 lists malEFG as well. # malE = Aaci_2873 = Q9RHZ6, see PDB 1urg. # malFG are presumably the adjacent proteins Aaci_2872 (uniprot:C8WUR0) and Aaci_2871 (uniprot:C8WUQ9). malE_Aa maltose ABC transporter, substrate-binding component uniprot:Q9RHZ6 malF_Aa maltose ABC transporter, permease component 1 uniprot:C8WUR0 malG_Aa maltose ABC transporter, permease component 2 uniprot:C8WUQ9 malK_Aa maltose ABC transporter, ATPase component curated:BRENDA::Q70HW1 maltose-transport: malE_Aa malF_Aa malG_Aa malK_Aa # Sinorhizobium meliloti has a second system, algEFGK. # A similar system from Dinoroseobacter shibae, Dshi_1652:Dshi_1648, is involved in maltose uptake. # Dinoroseobacter shibae aglE = Dshi_1652 = A8LLL6. aglE maltose ABC transporter, substrate-binding component AglK curated:TCDB::Q9Z3R5 uniprot:A8LLL6 # Dinoroseobacter shibae aglF = Dshi_1651 = A8LLL5. aglF maltose ABC transporter, permease component 1 (AglF) curated:reanno::Smeli:SMc03062 uniprot:A8LLL5 # Dinoroseobacter shibae aglG = Dshi_1650 = A8LLL4. aglG maltose ABC transporter, permease component 2 (AglG) curated:reanno::Smeli:SMc03063 uniprot:A8LLL4 # Dinoroseobacter shibae aglK = Dshi_1648 = A8LLL2. aglK maltose ABC transporter, ATPase component AglK curated:reanno::Smeli:SMc03065 uniprot:A8LLL2 maltose-transport: aglE aglF aglG aglK # Bdellovibrio bacteriovorus has fused malEF (Bd1227, uniprot:Q6MNM0) # and also malG, malK. # malG must be Bd1226 (uniprot:Q6MNM1) and malK must be Bd1225 (uniprot:Q6MNM2). malEF_Bb maltose ABC transporter, fused substrate-binding and permease component 1 curated:TCDB::Q6MNM0 malG_Bb maltose ABC transporter, permease component 2 uniprot:Q6MNM1 malK_Bb maltose ABC transporter, ATPase component uniprot:Q6MNM2 maltose-transport: malEF_Bb malG_Bb malK_Bb # Sulfolobus solfataricus has malEFGK. malE_Ss maltose ABC transporter, substrate-binding component curated:TCDB::Q97UG7 malF_Ss maltose ABC transporter, permease component 1 curated:TCDB::Q97UG4 malG_Ss maltose ABC transporter, permease component 2 curated:TCDB::Q97UG3 malK_Ss maltose ABC transporter, ATPase component curated:TCDB::Q97UG5 maltose-transport: malE_Ss malF_Ss malG_Ss malK_Ss # PTS systems: # Ignore E. coli malX, which can apparently facilitate diffusion of maltose, # because its physiological role is unclear # Streptococcus mutans and Streptococcus pyogenes have a EII-CBA system malT. # A related system in Enterococcus faecalis (EF0958 = uniprot:Q836Y6) was also shown to # be a PTS sytem for maltose (PMID:15752325). # The EII-CB portion of these proteins is similar to the EII-CB portion of B. subtilis, so that # is marked ignore. malEIICBA maltose phosphotransferase system, EII-CBA components curated:TCDB::Q48WG5 curated:TCDB::Q8DS05 uniprot:Q836Y6 ignore:TCDB::Q63GK8 # PTS systems form maltose 6'-phosphate maltose-PTS: malEIICBA # Bacillus subtilis has a EII-CB system malP. # PMID:30038046 showed that ptsG (P20166), YpqE (P50829) or GamP (P39816) provide the EII-A component. # Bacillus cereus has a EII-CB system, also named malT. The EII-A component is not known but # crosstalk as in B. subtilis seems likely, even though the EII-CB proteins are distantly related # (27% identity). malEIICB maltose phosphotransferase system, EII-CB components curated:SwissProt::P54715 curated:TCDB::Q63GK8 ignore:TCDB::Q8DS05 ignore:TCDB::Q48WG5 malEIIA maltose phosphotransferase system, EII-A component (PtsG/YpqE/GamP) curated:TCDB::P20166 uniprot:P50829 curated:SwissProt::P39816 maltose-PTS: malEIICB malEIIA MAL11 maltose permease curated:CharProtDB::CH_091394 curated:SwissProt::P0CD99 curated:SwissProt::P0CE00 curated:SwissProt::P38156 curated:TCDB::P15685 maltose-transport: MAL11 SUC2 maltose:H+ symporter curated:CharProtDB::CH_091608 curated:SwissProt::Q39231 curated:metacyc::MONOMER-18237 maltose-transport: SUC2 SUT1 maltose:H+ symporter curated:CharProtDB::CH_091204 maltose-transport: SUT1 cscB maltose permease curated:SwissProt::P30000 maltose-transport: cscB malAP maltose permease curated:TCDB::Q45632 maltose-transport: malAP # Caulobacter malI; also CA265_RS24665 (A0A1X9ZCC9) is specifically important for maltose utilization # and is related. malI maltose transporter curated:TCDB::Q9A612 uniprot:A0A1X9ZCC9 maltose-transport: malI # Ignore chloroplast maltose exporters and outer membrane porins # glk is glucokinase import glucose.steps:glucose-utilization glk malP maltose phosphorylase EC:2.4.1.8 pgmB beta-phosphoglucomutase EC:5.4.2.6 # In the phosphorylase pathway, malP forms beta-glucose-1-phosphate and glucose, # and beta-phosphoglucomutase forms glucose-6-phosphate, a central metabolite; # glucokinase (glk) is also needed to feed the released glucose into # central metabolism. all: maltose-transport malP pgmB glk malA 6-phospho-alphaglucosidase EC:3.2.1.122 # Alternatively, PTS systems produce maltose 6'-phosphate, which can be cleaved by # 6-phospho-alpha-glucosidase to glucose and glucose-6-phosphate. all: maltose-PTS malA glk # Alternatively, maltose 6'-phosphate can be converted back to maltose # by a phosphatase, followed by the phosphorylase pathway. mapP maltose 6'-phosphate phosphatase EC:3.1.3.90 all: maltose-PTS mapP malP pgmB glk # Close homologs are sometimes annotated as maltases (which should be included) # or isomaltase (which should not; that refers to hydrolyzing an alpha-1,6 linkage, # whereas maltose has an alpha-1,4 linkage). # BRENDA::Q2PCE2 seems surprising but is supported by the underlying paper. # susB from Bacteroides thetaiotaomicron (G8JZS4, CAZy::AAC44671.1) is a periplasmic maltase (PMID:18981178) # (it also active on longer substrates) and is important for maltose utilization. # Dshi_1649 from Dinoroseobacter shibae (A8LLL3) is important for maltose utilization and is 60% identical to # the alpha-glucosidase HaG from Halomonas (PMC3298133). susB alpha-glucosidase (maltase) EC:3.2.1.20 curated:CAZy::AAC44671.1 uniprot:A8LLL3 ignore_other:maltase # Alternatively, maltose can be hydrolyzed by alpha-glucosidase (EC:3.2.1.20) in the cytoplasm. all: maltose-transport susB glk # Alternatively, maltose can be hydrolyzed by alpha-glucosidase (EC:3.2.1.20) in the periplasm, # as in Bacteroides thetaiotaomicron, followed by glucose utilization. all: susB 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 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