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:
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