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# 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:
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