Definition of D-fructose catabolism
As rules and steps, or see full text
Rules
Overview: Many bacteria take up fructose by a phosphotransferase (PTS) system that forms fructose 1-phosphate; this can be consumed via 1-phosphofructokinase and glycolysis (link). Alternatively, some PTS systems form fructose 6-phosphate, which is a central metabolic intermediate. Fructose can also be taken up directly and then phosphorylated to fructose 6-phosphate, a central metabolic intermediate. Another path is known in Aeromonas hydrophila -- phosphofructomutase converts fructose 1-phosphate (formed by a PTS system) to fructose 6-phosphate (PMID:9579084). This path is not included in GapMind because phosphofructomutase has not been linked to sequence. Also, in eukaryotes, fructose-1,6-bisphosphate aldolase is reported to cleave fructose 1-phosphate to glycerone phosphate and glyceraldehyde (link). This would make 1-phosphofructokinase unnececessary. It's not clear that this occurs in prokaryotes, so this is not listed.
- all: fructose-utilization
- fructose-utilization:
- fructose-PTS-6-phosphate
- or fructose-transport and scrK
- or fructose-PTS-1-phosphate, 1pfk, fba and tpi
- Comment: For a PTS forming fructose 6-phosphate, no further steps are needed to reach central metabolism. For direct transport, the usual pathway is fructokinase (scrK), forming fructose 6-phosphate. For PTS forming fructose 1-phosphate, the usual path is phosphorylation (1pfk) and cleavage by fructose 1,6-bisphosphate aldolase (fba); triose-phosphate isomerase (tpi) converts the glycerone phosphate to D-glyceraldehyde 3-phosphate, which is a central metabolic intermediate.
- fructose-transport:
- fructose-PTS-6-phosphate:
- fructose-PTS-1-phosphate:
- fruA and fruB
- or fruA and fruI
- or fruA and fruD
- or fruII-A, fruII-B and fruII-C
- or fruII-ABC
- Comment: Fructose 1-phosphate forming PTS systems contain FruA with either FruB, FruI, or FruD. FruA has EII-B'BC components; the other genes all have E-IIA but their domain content varies. FruB has E-IIA and Hpr components; FruI has EI-Hpr-IIA components; and FruD has E-IIA only.
Steps
fruA: fructose-specific PTS system (fructose 1-phosphate forming), EII-B'BC components
- Curated sequence Q8DWE7: protein-Npi-phosphohistidine-D-fructose phosphotransferase (subunit 2/2) (EC 2.7.1.202). Putative PTS system, fructose-specific IIBC component aka FruC, component of The constitutive fructose porter FruC/FruD
- Curated sequence P20966: PTS system fructose-specific EIIB'BC component; EIIB'BC-Fru; EC 2.7.1.202. PTFB aka FRUA aka PTSF aka B2167, component of Fructose porter (FruAB) (fructose-1-P forming). fructose-specific PTS multiphosphoryl transfer protein FruA. fructose-specific PTS multiphosphoryl transfer protein FruA
- Curated sequence P23355: PTS system fructose-specific EIIB'BC component; EIIB'BC-Fru; EC 2.7.1.202
- Ignore hits to P32154 when looking for 'other' hits (Fructose-like PTS system EIIBC component, component of Fructose-like PTS Enzyme II complex, FrvA (IIA of 148 aas) - FrvB (IIBC of 483 aas and 9 predicted TMSs). putative PTS enzyme IIBC component FrvB)
- Curated sequence Q9HY57: Phosphotransferase system transporter fructose-specific IIBC component, FruA, component of Fructose-specific PTS permease, FruIIBC/FruI-HPr-IIA
- Curated sequence Q9RZP7: Fructose PTS Enzyme IIBC, FruA
- UniProt sequence G8B0J2: SubName: Full=Fructose phosphotransferase system, IIB/IIC components {ECO:0000313|EMBL:CCD03701.1};
- Total: 6 characterized proteins
fruB: fructose-specific PTS system (fructose 1-phosphate forming), Hpr and EII-A components
- Curated sequence P69811: Multiphosphoryl transfer protein; MTP; Diphosphoryl transfer protein; DTP; Phosphotransferase FPr protein; Pseudo-HPr. PTFA aka FRUB aka FRUF aka FPR aka B2169, component of Fructose porter (FruAB) (fructose-1-P forming). fructose-specific PTS multiphosphoryl transfer protein FruB. fructose-specific PTS multiphosphoryl transfer protein FruB
- Ignore hits to P17127 when looking for 'other' hits (Multiphosphoryl transfer protein; MTP; Diphosphoryl transfer protein; DTP; Phosphotransferase FPr protein; Pseudo-HPr)
- Ignore hits to P44715 when looking for 'other' hits (Multiphosphoryl transfer protein; MTP; Diphosphoryl transfer protein; DTP; Phosphotransferase FPr protein; Pseudo-HPr)
- Comment: Homologs of fruB from Salmonella typhimurium and Haemophilus influenzae probably have the same function, but are annotated differently in SwissProt.
- Total: 1 characterized proteins
fruI: fructose-specific PTS system (fructose 1-phosphate forming), EI, Hpr, and EII-A components
- Curated sequence Q9HY55: Phosphotransferase system transporter enzyme I, FruI, component of Fructose-specific PTS permease, FruIIBC/FruI-HPr-IIA
- Curated sequence AZOBR_RS32325: Fructose PTS system (E-I, HPr, and E-IIA components)
- Curated sequence AO353_05485: Fructose-specific PTS system, I, HPr, and IIA components
- Curated sequence P45597: Multiphosphoryl transfer protein; MTP; Triphosphoryl transfer protein; TTP; EC 2.7.3.9
- Curated sequence Pf1N1B4_1146: Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9)
- Curated sequence AO356_07335: Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9)
- Curated sequence GFF780: Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9)
- Curated sequence GFF3291: Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9)
- Comment: Homologs of fruI in other Pseudomonas fluorescens are annotated differently, but are important for fructose utilization, so probably have the same function.
- Total: 8 characterized proteins
fruD: fructose-specific PTS system (fructose 1-phosphate forming), EII-A component
- Curated sequence Q8DWE6: protein-Npi-phosphohistidine-D-fructose phosphotransferase (subunit 1/2) (EC 2.7.1.202). Constitutive fructose permease aka FruD, component of The constitutive fructose porter FruC/FruD
- Comment: Streptococcus mutans has FruA-like "FruC" plus "FruD" with EII-A only.
- Total: 1 characterized proteins
fruII-A: fructose-specific PTS system (fructose 1-phosphate forming), EII-A component
- Curated sequence D2RXA7: Putative PTS IIA-like nitrogen-regulatory protein PtsN, component of Fructose Enzyme II complex (IIAFru - IIBFru - IICFru) (based on homology)
- Curated sequence D4GYE4: PTS system fructose-specific EIIA component; EIIA-Fru; Fructose-specific phosphotransferase enzyme IIA component. Sugar phosphotransferase system IIA component, component of Fructose-specific PTS, PtfABC
- Curated sequence Q5V5X4: Sugar hosphotransferase system IIA component, component of Fructose-specific Enzyme I-HPr-Enzyme IIABC complex, all encoded within a single operon with genes in the order: ptsC (IIC), ptsA (IIA), ptsH (HPr), ptsI (Enzyme I) and ptsB (IIB)
- Comment: 3-part PTS system (fructose 1-phosphate forming) in Haloferax volcanii, Haloterrigena turkmenica, Haloarcula marismortui. The Haloarcula gene cluster also includes enzyme I (ptsI, Q5V5X2) and HPr (ptsH, Q5V5X3), which is not represented here
- Total: 3 characterized proteins
fruII-B: fructose-specific PTS system (fructose 1-phosphate forming), EII-B component
- Curated sequence D4GYE1: PTS system fructose-specific EIIB component; EIIB-Fru; Fructose-specific phosphotransferase enzyme IIB component; EC 2.7.1.202. Phosphotransferase system IIB component, component of Fructose-specific PTS, PtfABC
- Curated sequence D2RXA4: PTS system, fructose-specific, IIB subunnit, component of Fructose Enzyme II complex (IIAFru - IIBFru - IICFru) (based on homology)
- Curated sequence Q5V5X1: Phosphotransferase system IIB component, component of Fructose-specific Enzyme I-HPr-Enzyme IIABC complex, all encoded within a single operon with genes in the order: ptsC (IIC), ptsA (IIA), ptsH (HPr), ptsI (Enzyme I) and ptsB (IIB)
- Total: 3 characterized proteins
fruII-C: fructose-specific PTS system (fructose 1-phosphate forming), EII-C component
- Curated sequence D4GYE5: PTS system fructose-specific EIIC component; EIIC-Fru; Fructose permease IIC. Phosphotransferase system, EIIC, putative, component of Fructose-specific PTS, PtfABC
- Curated sequence D2RXA8: PTS system, fructose subfamily, IIC subunit, component of Fructose Enzyme II complex (IIAFru - IIBFru - IICFru) (based on homology)
- Curated sequence Q5V5X5: Sugar phosphotransferase system IIC component, component of Fructose-specific Enzyme I-HPr-Enzyme IIABC complex, all encoded within a single operon with genes in the order: ptsC (IIC), ptsA (IIA), ptsH (HPr), ptsI (Enzyme I) and ptsB (IIB)
- Total: 3 characterized proteins
fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components
- Curated sequence Q9RMF5: Fructose-specific Enzyme IIABC
- Curated sequence Q3K0G6: Chromosomal fructose Enzyme IIABC (Fru1) of 654 aas; in an operon with fructose-1-P kinase
- Curated sequence P71012: The fructose porter, FruA (fructose-1-P forming IIABC) (Delobbe et al. 1975) FruA is 39% identical to 4.A.2.1.1). fructose can be metabolized to Fru-1-P via this system as well as Fru-6-P by another PTS system
- Curated sequence Q0S1N2: The fructose-specific PTS Enzyme IIABC FruA
- Curated sequence Q1LZ59: The fructose inducible fructose/xylitol porter, FruI
- Comment: Spiroplasma citri has a unified PTS system E-IIABC which clustered with fruA above but is distantly related The others were in cluster 4
- Total: 5 characterized proteins
levD: fructose PTS system (fructose 6-phosphate forming), EII-A component
- Curated sequence P26379: PTS system fructose-specific EIIA component; EIIA-Fru; Fructose-specific phosphotransferase enzyme IIA component; lev-PTS; p16. PTFA aka LEVD aka SACL, component of Fructose group translocator, LevDEFG
- Total: 1 characterized proteins
levE: fructose PTS system (fructose 6-phosphate forming), EII-B component
- Curated sequence P26380: PTS system fructose-specific EIIB component; EIIB-Fru; Fructose-specific phosphotransferase enzyme IIB component; lev-PTS; p18; EC 2.7.1.202. PTFB aka LEVE aka SACL, component of Fructose group translocator, LevDEFG
- Total: 1 characterized proteins
levDE: fructose PTS system (fructose 6-phosphate forming), EII-AB component
- Curated sequence CH_088329: PTS system mannose-specific EIIAB component; EC 2.7.1.-; EC 2.7.1.69. PTS system mannose-specific EIIAB component; EIIAB-Man; EIII-Man; EC 2.7.1.191. PTNA aka MANX aka PTSL aka GPTB aka B1817, component of The mannose (glucose, 2-deoxyglucose, glucosamine, N-acetylglucosamine, N-acetylmannosamine, mannosamine and fructose) PTS porter/group translocator, ManXYZ (Rephaeli and Saier 1980; Plumbridge 2015). Catalyzes xylose facilitated diffusion in lactobacilli. The order of D-sugar substrate affinities is: glucose > mannose > 2-deoxyglucose > N-acetylglucosamine > glucosamine > N-acetylmannosamine > mannosamine > fructose. mannose-specific PTS enzyme IIAB component (EC 2.7.1.191; EC 2.7.1.199; EC 2.7.1.193). mannose-specific PTS enzyme IIAB component
- Curated sequence Q04GK1: Phosphotransferase system, mannose/fructose-specific component IIA, component of The hexose (glucose and fructose demonstrated) PTS uptake system
- Curated sequence Q5M5W6: ManL, component of The glucose/mannose/2-deoxyglucose/fructose phosphotransferase systems (phosphorylates without transport), ManLMN
- Ignore hits to Q9S4L5 when looking for 'other' hits (protein-Npi-phosphohistidine-D-mannose phosphotransferase (EC 2.7.1.191))
- Ignore hits to D2BKY7 when looking for 'other' hits (Mannose-specificPTS system, IIAB component, component of Mannose enzyme II complex, IIAB, IIC, IID. IIC/IID serve allows entry of some bacteriocins including pediocin (class IIa) and lactococcin A (class IIc) (Kjos et al., 2011). Transports and phosphorylates Glucose, Mannose and Glucosamine)
- Comment: Q9S4L5 is nearly identical to Q5M5W6; not sure if it acts on fructose or not. D2BKY7 is very similar to Q5M5W6 and has been studied mostly as a receptor to bacteriocins; not sure if it acts on fructose or not.
- Total: 3 characterized proteins
levF: fructose PTS system (fructose 6-phosphate forming), EII-C component
- Curated sequence CH_088330: mannose permease IIC component. PTS system mannose-specific EIIC component; EII-P-Man; EIIC-Man; Mannose permease IIC component. PTNC aka MANY aka PTSP aka PEL aka B1818, component of The mannose (glucose, 2-deoxyglucose, glucosamine, N-acetylglucosamine, N-acetylmannosamine, mannosamine and fructose) PTS porter/group translocator, ManXYZ (Rephaeli and Saier 1980; Plumbridge 2015). Catalyzes xylose facilitated diffusion in lactobacilli. The order of D-sugar substrate affinities is: glucose > mannose > 2-deoxyglucose > N-acetylglucosamine > glucosamine > N-acetylmannosamine > mannosamine > fructose. mannose-specific PTS enzyme IIC component (EC 2.7.1.191; EC 2.7.1.199; EC 2.7.1.193). mannose-specific PTS enzyme IIC component (EC 2.7.1.191; EC 2.7.1.199; EC 2.7.1.193)
- Curated sequence P26381: PTFC aka LEVF, component of Fructose group translocator, LevDEFG
- Curated sequence Q04GK0: Mannose-specific PTS system component IIC, component of The hexose (glucose and fructose demonstrated) PTS uptake system
- Curated sequence Q5M5W7: ManM, component of The glucose/mannose/2-deoxyglucose/fructose phosphotransferase systems (phosphorylates without transport), ManLMN
- Total: 4 characterized proteins
levG: fructose PTS system (fructose 6-phosphate forming), EII-D component
- Curated sequence P26382: PTFD aka LEVG, component of Fructose group translocator, LevDEFG
- Curated sequence P69805: PTND aka MANZ aka PTSM aka GPTB aka B1819, component of The mannose (glucose, 2-deoxyglucose, glucosamine, N-acetylglucosamine, N-acetylmannosamine, mannosamine and fructose) PTS porter/group translocator, ManXYZ (Rephaeli and Saier 1980; Plumbridge 2015). Catalyzes xylose facilitated diffusion in lactobacilli. The order of D-sugar substrate affinities is: glucose > mannose > 2-deoxyglucose > N-acetylglucosamine > glucosamine > N-acetylmannosamine > mannosamine > fructose
- Curated sequence Q04GJ9: PTS system IID component, Man family, component of The hexose (glucose and fructose demonstrated) PTS uptake system
- Curated sequence Q5M5W8: ManN, component of The glucose/mannose/2-deoxyglucose/fructose phosphotransferase systems (phosphorylates without transport), ManLMN
- Ignore hits to P69805 when looking for 'other' hits (PTS system mannose-specific EIID component; EII-M-Man; EIID-Man; Mannose permease IID component. mannose-specific PTS enzyme IID component (EC 2.7.1.191; EC 2.7.1.199; EC 2.7.1.193). mannose-specific PTS enzyme IID component (EC 2.7.1.191; EC 2.7.1.199; EC 2.7.1.193))
- Ignore hits to Q5IRC0 when looking for 'other' hits (protein-Npi-phosphohistidine-D-mannose phosphotransferase (EC 2.7.1.191))
- Comment: Ignore SwissProt::P69805 which is nearly identical to P69805. Ignore Q5IRC0, whose specificity is unknown.
- Total: 4 characterized proteins
araV: fructose ABC transporter, ATPase component AraV
- Curated sequence Q97UF2: AraV, component of Arabinose, fructose, xylose porter
- Comment: AraSUTV from Sulfolobus solfataricus
- Total: 1 characterized proteins
araU: fructose ABC transporter, permease component 1 (AraU)
araT: fructose ABC transporter, permease component 2 (AraT)
araS: fructose ABC transporter, substrate-binding component AraS
fruE: fructose ABC transporter, substrate-binding component FruE
- Curated sequence Q8G848: Fructose import binding protein FruE
- Comment: FruEFGK from Bifidobacterium longum. (FruF is distantly related to frcC, which is described separately)
- Total: 1 characterized proteins
fruF: fructose ABC transporter, permease component 1 (FruF)
fruG: fructose ABC transporter, permease component 2 (FruG)
fruK: fructose ABC transporter, ATPase component FruK
frcA: fructose ABC transporter, ATPase component FrcA
- Curated sequence Q9F9B0: Fructose import ATP-binding protein FrcA; EC 7.5.2.-. FrcA, component of Fructose/mannose/ribose porter
- UniProt sequence A0A0C4Y5F6: SubName: Full=ABC-type sugar transport system, ATP-binding protein {ECO:0000313|EMBL:AJG18103.1}; EC=3.6.3.17 {ECO:0000313|EMBL:AJG18103.1};
- Comment: FrcABC from Rhizobium meliloti. A distantly related system in Ralstonia eutropha H16 is required for fructose utilization (PMID:21478317), and fitness data confirms that the homologs in Cupriavidus basilensis 4G11 are important during growth on fructose (frcA = RR42_RS03360 = A0A0C4Y5F6; frcC = RR42_RS03365 = A0A0C4Y7K0; frcB = RR42_RS03370 = A0A0C4Y591)
- Total: 2 characterized proteins
frcB: fructose ABC transporter, substrate-binding component FrcB
- Curated sequence Q9F9B2: Fructose import binding protein FrcB. FrcB, component of Fructose/mannose/ribose porter
- UniProt sequence A0A0C4Y591: SubName: Full=Xylose ABC transporter, periplasmic xylose-binding protein XylF {ECO:0000313|EMBL:AJG18105.1};
- Total: 2 characterized proteins
frcC: fructose ABC transporter, permease component FrcC
- Curated sequence Q9F9B1: Fructose import permease protein FrcC. FrcC, component of Fructose/mannose/ribose porter
- UniProt sequence A0A0C4Y7K0: SubName: Full=Ribose ABC transport system, permease protein RbsC {ECO:0000313|EMBL:AJG18104.1};
- Total: 2 characterized proteins
Slc2a5: fructose:H+ symporter
- Curated sequence A0ZXK6: The monosaccharide (MST) (glucose > mannose > galactose > fructose):H+ symporter, MST1
- Curated sequence CH_091463: sugar transport protein 13. The glucose/fructose:H+ symporter, STP13 (sugar transport protein 13). Expressed in vascular tissues and induced during programmed cell death
- Curated sequence P22732: Solute carrier family 2, facilitated glucose transporter member 5; Fructose transporter; Glucose transporter type 5, small intestine; GLUT-5. Fructose uniporter, GLUT5
- Curated sequence P43427: Solute carrier family 2, facilitated glucose transporter member 5; Fructose transporter; Glucose transporter type 5, small intestine; GLUT-5
- Curated sequence P46408: Solute carrier family 2, facilitated glucose transporter member 5; Fructose transporter; Glucose transporter type 5, small intestine; GLUT-5
- Curated sequence P58353: Solute carrier family 2, facilitated glucose transporter member 5; Fructose transporter; Glucose transporter type 5, small intestine; GLUT-5
- Ignore hits to Q6PXP3 when looking for 'other' hits (Solute carrier family 2, facilitated glucose transporter member 7; Glucose transporter type 7; GLUT-7; hGLUT7. The glucose/fructose facilitator, Glut7 (SLC2A7) (a single mutation, I314V, results in loss of fructose transport but retention of glucose transport)
- Curated sequence Q9WV38: Solute carrier family 2, facilitated glucose transporter member 5; Fructose transporter; Glucose transporter type 5, small intestine; GLUT-5
- Curated sequence Q9XIH7: The fructose/xylose:H+ symporter, PMT1 (polyol monosaccharide transporter-1). Also transports other substrates at lower rates. PMT2 is largely of the same sequence and function. Both are present in pollen and young xylem cells (Klepek et al., 2005). A similar ortholog has been identifed in pollen grains of Petunia hybrida
- Comment: Ignore Q6PXP3 (GTR7_HUMAN) as there is debate as to its activity
- Total: 8 characterized proteins
ffz: fructose facilitator (uniporter)
- Curated sequence C5DX43: The fructose/glucose uniporter, Ffz2 (64% identical to 2.A.1.2.23)
- Curated sequence C5E4Z7: The fructose-specific uniporter, Ffz1 (69% identical to Ffz2
- Curated sequence Q70WR7: The fructose-specific facilitator (uniporter), Ffz1
- Total: 3 characterized proteins
glcP: fructose:H+ symporter GlcP
ght6: high-affinity fructose transporter ght6
STP6: sugar transport protein 6
- Curated sequence CH_091493: sugar transport protein 6. Sugar transport protein 6; Hexose transporter 6. High affinity monosaccharide (KM ≈ 20 µM):H+ symporter, Stp6 (takes up glucose, 3-O-methylglucose, mannose, fructose, galactose and to a lesser extent, xylose and ribulose.
- Total: 1 characterized proteins
THT2A: fructose THT2A
- Curated sequence Q06222: Glucose/mannose/fructose transporter and high affinity sensor, Snf3p (regulates glucose transport via other systems)
- Total: 1 characterized proteins
frt1: fructose:H+ symporter Frt1
fruP: fructose porter FruP
- UniProt sequence A0A1I2JXG1: SubName: Full=MFS transporter, FHS family, L-fucose permease {ECO:0000313|EMBL:SFF59552.1};
- Comment: N515DRAFT_1918 (A0A1I2JXG1) from Dyella japonica UNC79MFTsu3.2 is an MFS-type transporter that is specifically important for growth on fructose.
- Total: 1 characterized proteins
BT1758: fructose transporter
- UniProt sequence Q8A6W8: SubName: Full=Glucose/galactose transporter {ECO:0000313|EMBL:AAO76865.1};
- Comment: The putative hexose transporter BT1758 (Q8A6W8) is important for fructose and levan utilization It is in a fructan utilization cluster, so was propsoed to be the fructose transporter (see PMC3225772)
- Total: 1 characterized proteins
scrK: fructokinase
- Curated proteins or TIGRFams with EC 2.7.1.4
- Ignore hits to Q09123 when looking for 'other' hits (Fructokinase; EC 2.7.1.4)
- Comment: ignore fragmentary sequence of Q09123
- Total: 36 characterized proteins
1pfk: 1-phosphofructokinase
fba: fructose 1,6-bisphosphate aldolase
- Curated proteins or TIGRFams with EC 4.1.2.13
- Ignore hits to P84722 when looking for 'other' hits (Putative fructose-bisphosphate aldolase, chloroplastic; PS6; EC 4.1.2.13)
- Ignore hits to P86979 when looking for 'other' hits (Fructose-bisphosphate aldolase A; Muscle-type aldolase; Allergen Thu a 3.0101; EC 4.1.2.13)
- Ignore hits to P86980 when looking for 'other' hits (Fructose-bisphosphate aldolase A; Muscle-type aldolase; Allergen Gad m 3.0101; EC 4.1.2.13)
- Ignore hits to CH_091808 when looking for 'other' hits (fructose-1,6-bisphosphate aldolase; EC 5.3.1.9)
- Ignore hits to Q5SJM8 when looking for 'other' hits (fructose-bisphosphatase (EC 3.1.3.11))
- Comment: Ignore several fragmentary sequences, and CH_091808 seems to be misannotated with another EC number Q5SJM8 is nearly identical to Q72K02, a bifunctional aldolase/phosphatase, but is annotated only as phosphatase
- Total: 3 HMMs and 73 characterized proteins
tpi: triose-phosphate isomerase
- Curated proteins or TIGRFams with EC 5.3.1.1
- Ignore hits to P85814 when looking for 'other' hits (Triosephosphate isomerase; TIM; Triose-phosphate isomerase; Allergen Pla o 4; EC 5.3.1.1)
- Comment: Ignore a fragmentary (allergen) sequence
- Total: 1 HMMs and 55 characterized proteins
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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:
- ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
- HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.
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:
- ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
- ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
- HMMer finds a hit (regardless of coverage or other bits).
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:
- our ignorance of proteins' functions,
- omissions in the gene models,
- frame-shift errors in the genome sequence, or
- the organism lacks the pathway.
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