Definition of lactose catabolism

GapMind for catabolism of small carbon sources

Definition of lactose catabolism

As rules and steps, or see full text

Rules

Overview: Lactose utilization in GapMind is based on MetaCyc pathway lactose degradation II via 3'-ketolactose (link), pathway III via beta-galactosidase (link), or uptake by a PTS system followed by hydrolysis of lactose 6'-phosphate. (There is no pathway I.)

all:

lactose-transport, beta-galactosidase, galactose-degradation and glk
or lactose-PTS, pbgal, galactose-6-phosphate-degradation and glk
or lacA', lacC', lacB', klh and glucose-utilization
Comment: 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.) Or, a PTS forms lactose 6'-phosphate and phosphogalactosidase (pbgal) forms galactose 6-phosphate and glucose. 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.

beta-galactosidase:

lacZ
or lacL and lacM
Comment: Most lactases are homomeric, but Lactobacillus have a heteromeric enzyme LacLM. (There is also a heteromeric beta-galactosidase in barley, see 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.)

glucose-utilization:

glucose-transport and glk
or glucose-PTS
or gdh, gnl, gadh1, gadh2, gadh3, kguT, kguK, kguD, edd and eda
Comment: Glucose can be taken up and then phosphorylated to glucose 6-phosphate by the kinase glk. Or, both uptake and phosphorylation are catalyzed by a PTS system. Or, glucose is oxidized to glucono-1,5-lactone in the periplasm (by gdh), hydrolyzed to gluconate (by gnl), oxidized to 2-ketogluconate (by gadh123), taken up by kguT, phosphorylated to 2-dehydro-6-phosphogluconate (by kguK), reduced to gluconate 6-phosphate (by kguD), dehydrated by edd to 2-dehydro-3-deoxy-gluconate 6-phosphate, and cleaved by aldolase eda to pyruvate and D-glyceraldehyde 3-phosphate.

glucose-PTS:

ptsG-crr
or bglF
or ptsG and crr
or manX, manY and manZ

glucose-transport:

MFS-glucose
or SSS-glucose
or glcU'
or PAST-A
or SemiSWEET
or SWEET1
or mglA, mglB and mglC
or gtsA, gtsB, gtsC and gtsD
or glcS, glcT, glcU and glcV
or aglE', aglF', aglG' and aglK'
Comment: Transporters and PTS systems were analyzed uzing query: transporter:glucose:D-glucose:D-glucopyranose:ALPHA-GLUCOSE:GLC:CPD-15374

galactose-degradation:

galK, galT, galE and pgmA
or galdh, galactonolactonase, dgoD, dgoK and dgoA
Comment: In the Leloir pathway, galactokinase (galK) forms galactose 1-phosphate, a uridyltransferase (galT) uses glucose 1-phosphate to form UDP-galactose, an epimerase (galE) forms UDP-glucose, and this is converted to glucose 1-phosphate by the same uridyltransferase. (We initially included the 1-epimerase galM, EC 5.1.3.3, in our model of the Leloir pathway, but found that in most bacteria, galM proteins were not important for fitness during growth on galactose; the only exception was Echvi_0697.) The oxidative pathway begins with oxidation to a lactone (by galdh) and hydrolysis to galactonate; galactonate is then dehydrated, phosphorylated, and cleaved by an aldolase.

galactose-6-phosphate-degradation: lacA, lacB, lacC, tag16P-aldolase and tpi

Comment: The tagatose 6-phosphate pathway involves the isomerization of galactose 6-phosphate to tagatose-6-phosphate (by lacAB), phosphorylation to tagatose 1,6-bisphosphate (by lacC), and an aldolase.

tag16P-aldolase:

lacD
or gatY and gatZ
Comment: Two forms of D-tagatose-1,6-phosphate aldolase are known, homomeric (lacD) or heteromeric (gatYZ or kbaYZ)

lactose-PTS:

lacIIA, lacIIB and lacIIC
or lacIIA and lacIICB
Comment: 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-transport:

lacE, lacF, lacG and lacK
or lacP
or lacS
or lacY
Comment: Transporters and PTS systems were identified using query: transporter:lactose:alpha-lactose:CPD-15971

Steps

lacE: lactose ABC transporter, substrate-binding component

Curated sequence P29822: LacE, component of Lactose porter
Curated sequence SM_b21652: ABC transporter for Lactose, periplasmic substrate-binding component
Comment: Agrobacterium radiobacter and Sinorhizobium meliloti have related systems, named lacEFGK in Agrobacterium
Total: 2 characterized proteins

lacF: lactose ABC transporter, permease component 1

Curated sequence P29823: LacF, component of Lactose porter
Curated sequence SM_b21653: ABC transporter for Lactose, permease component 1
Total: 2 characterized proteins

lacG: lactose ABC transporter, permease component 2

Curated sequence P29824: LacG, component of Lactose porter
Curated sequence SM_b21654: ABC transporter for Lactose, permease component 2
Total: 2 characterized proteins

lacK: lactose ABC transporter, ATPase component

Curated sequence Q01937: LacK, component of Lactose porter
Curated sequence SM_b20002: ABC transporter for Lactose, ATPase component
Total: 2 characterized proteins

lacIIA: lactose PTS system, EIIA component

Curated sequence P0A0D6: PTS system lactose-specific EIIA component; EIIA-Lac; EIII-Lac; Lactose-specific phosphotransferase enzyme IIA component. PtlA aka LACF, component of Lactose (Lac) porter, LacEF
Curated sequence P11502: PTS system lactose-specific EIIA component; EIIA-Lac; EIII-Lac; FIII-Lac; Lactose-specific phosphotransferase enzyme IIA component
Curated sequence P23532: PTS system lactose-specific EIIA component; EIIA-Lac; EIII-Lac; Lactose-specific phosphotransferase enzyme IIA component
Curated sequence Q045H4: Cellobiose-specific PTS system IIA component, component of Lactose PTS group translocator #2, IIA/IICB
Curated sequence Q045X4: PTS system lactose-specific IIA component, Lac family, component of Lactose PTS group translocator #1, IIA/IICB
Curated sequence U5MLJ3: PTS lactose transporter subunit IIA, component of PTS-type lactose transporter, IIC-IIB-IIA
Total: 6 characterized proteins

lacIIB: lactose PTS system, EIIB component

Curated sequence U5MIE1: PTS lactose transporter subunit IIB, component of PTS-type lactose transporter, IIC-IIB-IIA
Total: 1 characterized proteins

lacIIC: lactose PTS system, EIIC component

Curated sequence U5MFA1: PTS lactose transporter subunit IIC, component of PTS-type lactose transporter, IIC-IIB-IIA
Total: 1 characterized proteins

lacIICB: lactose PTS system, fused EIIC and EIIB components

Curated sequence P11162: PTS system lactose-specific EIICB component; EIICB-Lac; EII-Lac; EC 2.7.1.207. PtlB aka LACE, component of Lactose (Lac) porter, LacEF
Curated sequence P23531: PTS system lactose-specific EIICB component; EIICB-Lac; EII-Lac; EC 2.7.1.207
Curated sequence P24400: PTS system lactose-specific EIICB component; EIICB-Lac; EII-Lac; EC 2.7.1.207
Curated sequence Q045H3: PTS system lactose-specific IIB component, Lac family / PTS system lactose-specific IIC component, Lac family, component of Lactose PTS group translocator #2, IIA/IICB
Curated sequence Q045X3: PTS system lactose-specific IIB component, Lac family / PTS system lactose-specific IIC component, Lac family, component of Lactose PTS group translocator #1, IIA/IICB
Total: 5 characterized proteins

lacP: lactose permease LacP

Curated sequence CH_124122: lactose permease
Curated sequence CH_124118: lactose permease
Curated sequence CH_124308: lactose permease
Curated sequence CH_124309: lactose permease
Curated sequence P07921: Lactose, galactose:H+ symporter
Total: 5 characterized proteins

lacS: lactose permease LacS

Curated sequence Q7WTB2: Lactose permease; Lactose transport protein; Lactose transporter; Lactose-proton symporter; EC 2.7.1.-
Curated sequence P23936: Lactose permease, LacS. Mediates uptake of β-galactooligosaccharides, lactitol, and a broad range of prebiotic β-galactosides that selectively stimulate beneficial gut microbiota
Total: 2 characterized proteins

lacY: lactose:proton symporter LacY

Curated sequence P02920: Lactose permease; Lactose-proton symport. β- and α-galactopyranoside:H+. lactose permease. lactose permease
Curated sequence P96517: Melibiose permease; Melibiose transporter MelY. Melibiose:H+ symporter, MelY (Shinnick et al., 2003). Transports melibiose and lactose, but not TMG, which does however bind to the transporter
Total: 2 characterized proteins

pbgal: phospho-beta-galactosidase

Curated proteins or TIGRFams with EC 3.2.1.85
Total: 1 HMMs and 13 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

lacD: D-tagatose-1,6-bisphosphate aldolase (monomeric)

Curated sequence Q5HE13: tagatose-bisphosphate aldolase (EC 4.1.2.40). D-tagatose-1,6-diphosphate aldolase (EC 4.1.2.40)
Curated sequence P26593: Tagatose 1,6-diphosphate aldolase; D-tagatose-1,6-bisphosphate aldolase; Tagatose-bisphosphate aldolase; EC 4.1.2.40
Total: 2 characterized proteins

gatY: D-tagatose-1,6-bisphosphate aldolase, catalytic subunit (GatY/KbaY)

Curated sequence CH_024465: tagatose-bisphosphate aldolase; EC 4.1.2.40. D-tagatose-1,6-bisphosphate aldolase subunit KbaY; TBPA; TagBP aldolase; D-tagatose-bisphosphate aldolase class II; Ketose 1,6-bisphosphate aldolase class II; Tagatose-bisphosphate aldolase; EC 4.1.2.40. tagatose-1,6-bisphosphate aldolase 1 subunit KbaY (EC 4.1.2.40). D-tagatose-1,6-bisphosphate aldolase subunit KbaY (EC 4.1.2.40). tagatose-1,6-bisphosphate aldolase 1 subunit KbaY (EC 4.1.2.40)
Curated sequence P0C8J6: D-tagatose-1,6-bisphosphate aldolase subunit GatY; TBPA; TagBP aldolase; D-tagatose-bisphosphate aldolase class II; Tagatose-bisphosphate aldolase; EC 4.1.2.40. tagatose-1,6-bisphosphate aldolase 2 subunit GatY (EC 4.1.2.40). tagatose-1,6-bisphosphate aldolase 2 subunit GatY (EC 4.1.2.40)
Curated sequence P0C8J7: D-tagatose-1,6-bisphosphate aldolase subunit GatY; TBPA; TagBP aldolase; D-tagatose-bisphosphate aldolase class II; Tagatose-bisphosphate aldolase; EC 4.1.2.40
Curated sequence Q8VS16: D-tagatose-1,6-bisphosphate aldolase subunit GatY; TBPA; TagBP aldolase; D-tagatose-bisphosphate aldolase class II; Tagatose-bisphosphate aldolase; EC 4.1.2.40. tagatose-bisphosphate aldolase (EC 4.1.2.40)
Curated sequence Q9KIP8: D-tagatose-1,6-bisphosphate aldolase subunit KbaY; TBPA; TagBP aldolase; D-tagatose-bisphosphate aldolase class II; Ketose 1,6-bisphosphate aldolase class II; Tagatose-bisphosphate aldolase; EC 4.1.2.40
Total: 5 characterized proteins

gatZ: D-tagatose-1,6-bisphosphate aldolase, chaperone subunit (GatZ/KbaZ)

Curated sequence P0C8J8: D-tagatose-1,6-bisphosphate aldolase subunit GatZ. tagatose-1,6-bisphosphate aldolase 2 subunit GatZ (EC 4.1.2.40). tagatose-1,6-bisphosphate aldolase 2 subunit GatZ (EC 4.1.2.40)
Curated sequence P0C8J9: D-tagatose-1,6-bisphosphate aldolase subunit GatZ
Curated sequence P0C8K0: D-tagatose-1,6-bisphosphate aldolase subunit KbaZ. D-tagatose-1,6-bisphosphate aldolase subunit KbaZ. tagatose-1,6-bisphosphate aldolase 1 subunit KbaZ (EC 4.1.2.40). tagatose-1,6-bisphosphate aldolase 1 subunit KbaZ (EC 4.1.2.40)
Curated sequence MONOMER-18280: D-tagatose-1,6-bisphosphate aldolase subunit KbaZ (EC 4.1.2.40)
Curated sequence Q8VS12: D-tagatose-1,6-bisphosphate aldolase subunit GatZ
Total: 5 characterized proteins

lacA: galactose-6-phosphate isomerase, lacA subunit

Curated sequence P23494: Galactose-6-phosphate isomerase subunit LacA; EC 5.3.1.26
Curated sequence MONOMER-2781: galactose-6-phosphate isomerase lacA subunit (EC 5.3.1.26)
Comment: EC 5.3.1.26; only a few characterized members, all heterodimeric
Total: 2 characterized proteins

lacB: galactose-6-phosphate isomerase, lacB subunit

Curated sequence P23495: Galactose-6-phosphate isomerase subunit LacB; EC 5.3.1.26
Curated sequence MONOMER-2782: galactose-6-phosphate isomerase lacB subunit (EC 5.3.1.26)
Total: 2 characterized proteins

lacC: D-tagatose-6-phosphate kinase

Curated proteins or TIGRFams with EC 2.7.1.144
Total: 1 HMMs and 4 characterized proteins

galK: galactokinase (-1-phosphate forming)

Curated proteins or TIGRFams with EC 2.7.1.6
Ignore hits to items matching galactokinase when looking for 'other' hits
Comment: Some curated sequences match an HMM and are annotated as galactokinases, but without the EC number.
Total: 1 HMMs and 10 characterized proteins

galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase

Curated proteins or TIGRFams with EC 2.7.7.12
Curated sequence Echvi_0695: UTP--hexose-1-phosphate uridylyltransferase (EC 2.7.7.10)
Curated sequence CA265_RS06120: UTP--hexose-1-phosphate uridylyltransferase (EC 2.7.7.10)
Comment: In the reannotations, galT is often misannotated as 2.7.7.10 (using UTP rather than UDP-glucose as the substrate)
Total: 1 HMMs and 13 characterized proteins

galE: UDP-glucose 4-epimerase

Curated proteins or TIGRFams with EC 5.1.3.2
UniProt sequence L0FXG3: RecName: Full=UDP-glucose 4-epimerase {ECO:0000256|ARBA:ARBA00018569, ECO:0000256|RuleBase:RU366046}; EC=5.1.3.2 {ECO:0000256|ARBA:ARBA00013189, ECO:0000256|RuleBase:RU366046};
Comment: Echvi_1472 (L0FXG3) is important for galactose utilization and similar to E. coli galE
Total: 1 HMMs and 41 characterized proteins

pgmA: alpha-phosphoglucomutase

Curated proteins or TIGRFams with EC 5.4.2.2
Curated sequence MONOMER-13382: phosphomannose mutase (EC 5.4.2.8)
Comment: PH0923 (MONOMER-13382) is both phosphomannomutase and phosphoglucomutase (PMID:16091590)
Total: 1 HMMs and 34 characterized proteins

galdh: D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones)

Curated proteins or TIGRFams with EC 1.1.1.48
Curated proteins or TIGRFams with EC 1.1.1.360
Ignore hits to items matching 1.1.1.46 when looking for 'other' hits
Curated sequence Q92RN6: Probable galactose dehydrogenase GalD; EC 1.1.1.-
Comment: Some L-arabinose dehydrogenases (EC 1.1.1.46) are bifunctional. Q92RN6 is annotated as a probable galactose dehydrogenase, and mutants are defective in utilization, but was not given this EC number.
Total: 13 characterized proteins

galactonolactonase: galactonolactonase (either 1,4- or 1,5-lactone)

Curated proteins or TIGRFams with EC 3.1.1.25
Ignore hits to A3FJ64 when looking for 'other' hits (N-acyl homoserine lactonase AiiA; AHL-lactonase AiiA; EC 3.1.1.81. quorum-quenching N-acyl-homoserine lactonase (EC 3.1.1.81). 1,4-lactonase (EC 3.1.1.25). quorum-quenching N-acyl-homoserine lactonase (EC 3.1.1.81). quorum-quenching N-acyl-homoserine lactonase (EC 3.1.1.81). N-acyl homoserine lactonase; AHL-lactonase; Homoserine lactone lactonase; EC 3.1.1.81)
Curated sequence BPHYT_RS16915: L-arabinolactonase (EC 3.1.1.15)
UniProt sequence A0A1I2AUG6: SubName: Full=L-arabinonolactonase {ECO:0000313|EMBL:SFE46663.1};
Curated sequence GFF3393: galactaro-1,5-lactonase
Curated sequence PfGW456L13_3314: D-galactono-lactonase (EC 3.1.1.-)
UniProt sequence A0A165IRV8: SubName: Full=Gluconolactonase {ECO:0000313|EMBL:KZT13455.1};
UniProt sequence Q92RN9: RecName: Full=Putative sugar lactone lactonase; EC=3.1.1.-;
Ignore hits to Q92RN9 when looking for 'other' hits (Putative sugar lactone lactonase; EC 3.1.1.-)
Ignore hits to items matching 3.1.1.15 when looking for 'other' hits
Comment: This step includes both galactono-1,4-lactonases (EC 3.1.1.25) and galactono-1-5-lactonases. Some galactonolactonases are also L-arabinolactonases (EC 3.1.1.15), so those are ignored. BRENDA annotates A3FJ64 (from Bacillus thuringensis) as this, which seems questionable. Fitness data confirms diverged lactonases N515DRAFT_1229 (A0A1I2AUG6) and BPHYT_RS16915. PS417_17365 from P. simiae WCS417 (GFF3393) is a galactono-1,5-lactonase, so is not given the EC number. Similarly for PfGW456L13_3314. In Acidovorax sp. GW101-3H11, fitness data suggests that the lactonase is Ac3H11_615 (A0A165IRV8). And fitness data suggests that SMc00883 (Q92RN9) is a galactonolactonase and an arabinonolaconase (it has a vague annotation in SwissProt).
Total: 20 characterized proteins

dgoD: D-galactonate dehydratase

Curated proteins or TIGRFams with EC 4.2.1.6
Curated proteins or TIGRFams with EC 4.2.1.140
Total: 7 characterized proteins

dgoK: 2-dehydro-3-deoxygalactonokinase

Curated proteins or TIGRFams with EC 2.7.1.58
Curated proteins or TIGRFams with EC 2.7.1.178
Ignore hits to Q9ZU29 when looking for 'other' hits (2-dehydro-3-deoxyglucono/galactono-kinase (EC 2.7.1.178))
UniProt sequence B2SYR9: SubName: Full=2-keto-3-deoxy-galactonokinase {ECO:0000313|EMBL:ACD17804.1};
UniProt sequence A0A1I2AR49: SubName: Full=2-dehydro-3-deoxygalactonokinase {ECO:0000313|EMBL:SFE46505.1};
UniProt sequence D8J0Z3: SubName: Full=2-keto-3-deoxygalactonate kinase protein {ECO:0000313|EMBL:ADJ62548.1}; EC=2.7.1.58 {ECO:0000313|EMBL:ADJ62548.1};
Comment: BRENDA misannotates Q9zU29 as dgoK. Fitness data confirms diverged dgoK proteins BPHYT_RS16950 (B2SYR9), N515DRAFT_1233 (A0A1I2AR49), and HSERO_RS05160 (D8J0Z3).
Total: 12 characterized proteins

dgoA: 2-dehydro-3-deoxy-6-phosphogalactonate aldolase

Curated proteins or TIGRFams with EC 4.1.2.21
Curated proteins or TIGRFams with EC 4.1.2.55
Total: 11 characterized proteins

lacA': periplasmic lactose 3-dehydrogenase, LacA subunit

Curated sequence CCNA_01706: lactose 3-dehydrogenase flavin subunit (EC 1.1.99.13). lacA: subunit of periplasmic glucoside 3-dehydrogenase (EC 1.1.99.13)
Curated sequence CA265_RS15345: periplasmic glucoside 3-dehydrogenase (lacA subunit) (EC 1.1.99.13)
Ignore hits to items matching 1.1.99.13 when looking for 'other' hits
Comment: 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.
Total: 2 characterized proteins

lacC': periplasmic lactose 3-dehydrogenase, LacC subunit

Curated sequence CCNA_01707: lactose 3-dehydrogenase γ subunit (EC 1.1.99.13). lacC: subunit of periplasmic glucoside 3-dehydrogenase (EC 1.1.99.13)
Curated sequence CA265_RS15340: periplasmic glucoside 3-dehydrogenase (lacC subunit) (EC 1.1.99.13)
Ignore hits to items matching 1.1.99.13 when looking for 'other' hits
Total: 2 characterized proteins

lacB': periplasmic lactose 3-dehydrogenase, cytochrome c component (LacB)

Curated sequence CCNA_01704: lacB: cytochrome c2 component of periplasmic glucoside 3-dehydrogenase (EC 1.1.99.13)
Curated sequence CA265_RS15360: predicted cytochrome c component of periplasmic glucoside 3-dehydrogenase (EC 1.1.99.13)
Ignore hits to items matching 1.1.99.13 when looking for 'other' hits
Total: 2 characterized proteins

klh: periplasmic 3'-ketolactose hydrolase

Curated sequence CCNA_01705: predicted periplasmic 3-ketoglycoside hydrolase (DUF1080)
Comment: 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).
Total: 1 characterized proteins

MFS-glucose: glucose transporter, MFS superfamily

Curated sequence A0A0H2VG78: Glucose transporter GlcP; Glucose/H(+) symporter
Curated sequence CH_091029: galactose transporter. Galactose, glucose uniporter, Gal2. Also transports xylose
Curated sequence CH_091305: solute carrier family 2, facilitated glucose transporter member 8. The blastocyst/testis glucose transporter, Glut8 (Doege et al., 2000) (insulin stimulated in blastocysts)
Curated sequence CH_091400: low-affinity glucose transporter HXT4. Low-affinity glucose transporter HXT4; Low-affinity glucose transporter LGT1. Low affinity, constitutive, glucose (hexose; xylose) uniporter, Hxt4 (LGT1; Rag1) (also transports arsenic trioxide [As(OH)3] as do Hxtl, 3, 5, 7 and 9)
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 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.
Curated sequence CH_091695: sugar transport protein 1. Sugar transport protein 1; Glucose transporter; Hexose transporter 1. The major hexose transporter, Htr1 (mediates the active uptake of hexoses by sugar:H+ symport. Can transport glucose, 3-O-methylglucose, fructose, xylose, mannose, galactose, fucose, 2-deoxyglucose and arabinose. Confers sensitivity to galactose in seedlings. Km=20 uM for glucose)
Curated sequence CH_122958: high affinity glucose transporter
Curated sequence CH_124310: high-affinity glucose transporter ght2
Curated sequence A0A1D8PCL1: High-affinity glucose transporter 1
Curated sequence F1R0H0: Solute carrier family 2, facilitated glucose transporter member 10; Glucose transporter type 10; GLUT-10
Curated sequence O44616: Facilitated glucose transporter homolog
Curated sequence O44827: Facilitated glucose transporter protein 1
Curated sequence P0AEP1: Galactose-proton symporter; Galactose transporter. Galactose:H+ symporter, GalP. Also transports glucose, xylose, fucose (6-deoxygalactose), 2-deoxygalactose and 2-deoxyglucose) (Henderson and Giddens 1977. ; galactose:H⁺ symporter. galactose:H⁺ symporter. galactose:H+ symporter (galP)
Curated sequence P11166: Solute carrier family 2, facilitated glucose transporter member 1; Glucose transporter type 1, erythrocyte/brain; GLUT-1; HepG2 glucose transporter. The erythrocyte/brain hexose facilitator, glucose transporter-1, Gtr1 or Glut1. Transports D-glucose, dehydroascorbate, arsenite and the flavonone, quercetin, via one pathway and water via a distinct channel. Sugar transport has been suggested to function via a sliding mechanism involving several sugar binding sites (Cunningham et al., 2006). Glut1 is the receptor for human T-cell leukemia virus (HTLV)) (Manel et al., 2003). It is regulated by stomatin (TC# 8.A.21) to take up dehydroascorbate (Montel-Hagen et al., 2008). Mutations cause Glut1 deficiency syndrome, a human encephalopathy that results from decreased glucose flux through the blood brain barrier
Curated sequence P11167: Solute carrier family 2, facilitated glucose transporter member 1; Glucose transporter type 1, erythrocyte/brain; GLUT-1
Curated sequence P11168: Solute carrier family 2, facilitated glucose transporter member 2; Glucose transporter type 2, liver; GLUT-2. Glucosamine/glucose uniporter, Glut-2; it may also transport dehydroascorbate (Mardones et al., 2011;
Curated sequence P11169: Solute carrier family 2, facilitated glucose transporter member 3; Glucose transporter type 3, brain; GLUT-3. Solute carrier family 2, facilitated glucose transporter member 3 (Glucose transporter type 3, brain) (GLUT-3 or GLUT3). It mediates the facilitative uptake of glucose, 2-deoxyglucose, galactose, mannose, xylose and fucose, and probably dehydroascorbate, but not fructose
Curated sequence P12336: Solute carrier family 2, facilitated glucose transporter member 2; Glucose transporter type 2, liver; GLUT-2
Curated sequence P14142: Solute carrier family 2, facilitated glucose transporter member 4; GT2; Glucose transporter type 4, insulin-responsive; GLUT-4
Curated sequence P14246: Solute carrier family 2, facilitated glucose transporter member 2; Glucose transporter type 2, liver; GLUT-2
Curated sequence P14672: Solute carrier family 2, facilitated glucose transporter member 4; Glucose transporter type 4, insulin-responsive; GLUT-4. Insulin-responsive facilitative glucose transporter in skeletal and cardiac muscle, adipose, and other tissues, Glut4 (GTR4; SLC2A4; 509aas). Defects in Glut4 cause noninsulin-dependent diabetes mellitus (NIDDM)
Curated sequence P17809: Solute carrier family 2, facilitated glucose transporter member 1; Glucose transporter type 1, erythrocyte/brain; GLUT-1; GT1
Curated sequence P19357: Solute carrier family 2, facilitated glucose transporter member 4; Glucose transporter type 4, insulin-responsive; GLUT-4
Curated sequence P27674: Solute carrier family 2, facilitated glucose transporter member 1; Glucose transporter type 1, erythrocyte/brain; GLUT-1
Curated sequence P32037: Solute carrier family 2, facilitated glucose transporter member 3; Glucose transporter type 3, brain; GLUT-3
Curated sequence P47843: Solute carrier family 2, facilitated glucose transporter member 3; Glucose transporter type 3, brain; GLUT-3
Curated sequence P58353: Solute carrier family 2, facilitated glucose transporter member 5; Fructose transporter; Glucose transporter type 5, small intestine; GLUT-5
Curated sequence P58354: Solute carrier family 2, facilitated glucose transporter member 8; Glucose transporter type 8; GLUT-8; Glucose transporter type X1
Curated sequence Q07647: Solute carrier family 2, facilitated glucose transporter member 3; Glucose transporter type 3, brain; GLUT-3. Glucose uniporter, Glut3 (also transports dehydro-ascorbate; Maulén et al., 2003). Down-regulated in the brains of Alzheimer's disease patients (Liu et al., 2008b)
Curated sequence Q56ZZ7: Plastidic glucose transporter 4; AtpGlcT. Plastidic glucose transporter 4 (AtpGlcT). glucose transporter
Curated sequence Q9JIF3: Solute carrier family 2, facilitated glucose transporter member 8; Glucose transporter type 8; GLUT-8; Glucose transporter type X1
Curated sequence Q9JJZ1: Solute carrier family 2, facilitated glucose transporter member 8; Glucose transporter type 8; GLUT-8; Glucose transporter type X1
Curated sequence Q9NY64: Solute carrier family 2, facilitated glucose transporter member 8; Glucose transporter type 8; GLUT-8; Glucose transporter type X1. Solute carrier family 2, facilitated glucose transporter member 8 (Glucose transporter type 8) (GLUT-8) (Glucose transporter type X1)
Curated sequence Q9WV38: Solute carrier family 2, facilitated glucose transporter member 5; Fructose transporter; Glucose transporter type 5, small intestine; GLUT-5
Curated sequence Q9XSC2: Solute carrier family 2, facilitated glucose transporter member 3; Glucose transporter type 3, brain; GLUT-3
Curated sequence A0QZX3: Glucose permease GlcP (Pimentel-Schmitt et al., 2008) (most similar to 2.A.1.1.32)
Curated sequence A0ZXK6: The monosaccharide (MST) (glucose > mannose > galactose > fructose):H+ symporter, MST1
Curated sequence A1Z264: Sugar & polyol transporter 1 (SPT1): broad specificity; takes up glucose (Schilling and Oesterhelt, 2007). Loss of the first 3 TMSs of the 12 TMSs does not prevent sugar uptake or sugar recognition but lowers substrate affinity & transport rate, and abolished H+ symport
Curated sequence G4N740: Glucose transporter Rco-3 or MoST1. MoST1 plays a specific role in conidiation and mycelial melanization which is not shared by other hexose transporter family members in M. oryzae
Curated sequence H9BPB6: The sea bream facilitative glucose transporter 1 (GLUT1)
Curated sequence P15729: Glucose/fructose:H+ symporter, GlcP
Curated sequence P23585: High-affinity glucose transporter HXT2
Curated sequence P49374: The high affinity glucose transporter, Hgt1
Curated sequence Q0SE66: The glucose uptake porter, GluP
Curated sequence Q2MDH1: Glucose/xylose facilitator-1, GXF1 (functions by sugar uniport; low affinity
Curated sequence Q2MEV7: Glucose/xylose: H+ symporter, Gsx1
Curated sequence Q63ZP5: Glucose transporter 1, GLUT1 or Slc2A1 of 491 aas and 12 TMSs
Curated sequence Q7BEC4: The major glucose (or 2-deoxyglucose) uptake transporter, GlcP
Curated sequence Q8G3X1: The D-glucose:H+ symporter, GlcP (glucose uptake is inhibited by 2-deoxyglucose, mannose and galactose)
Curated sequence Q8J0U9: Low affinity glucose:H+ symporter, MstC
Curated sequence Q8NTX0: Myo-Inositol uptake porter, IolT1 (Km=0.2mM)
Curated sequence Q9LT15: The high affinity sugar:H+ symporter (sugar uptake) porter of 514 aas and 12 TMSs, STP10. It transports glucose, galactose and mannose, and is therefore a hexose transporter (Rottmann et al. 2016). The 2.4
Curated sequence O07563: Glucose/mannose transporter GlcP; Glucose/mannose:H(+) symporter. Glucose/Mannose/Xylose: H+ symporter (Paulsen et al., 1998; G.Gosset, personal communication)
Curated sequence Q8TDB8: Solute carrier family 2, facilitated glucose transporter member 14; Glucose transporter type 14; GLUT-14. Solute carrier family 2, facilitated glucose transporter member 14 (Glucose transporter type 14) (GLUT-14)
Curated sequence CH_091552: glucose transporter 9b. The embryonic liver, kidney, and other tissue uric acid (urate) transporter, Glut9 (SLC2A9) (Wright et al. 2010). Mutations in this transporter cause severe renal hyperuricemia
Curated sequence CH_121984: low affinity glucose transporter MstE. The low affinity, glucose-inducible glucose transporter, MstE
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 Q3T9X0: Solute carrier family 2, facilitated glucose transporter member 9; Glucose transporter type 9; GLUT-9; Urate transporter
Curated sequence Q6PXP3: 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 Q9BYW1: Solute carrier family 2, facilitated glucose transporter member 11; Glucose transporter type 11; GLUT-11. The hexose (glucose and fructose but not galactose) transporter (Glut11; SLC2A11)
Curated sequence Q9NRM0: Solute carrier family 2, facilitated glucose transporter member 9; Glucose transporter type 9; GLUT-9; Urate transporter
Curated sequence Q26579: The glucose transport protein, GTP1
Curated sequence A3M0N3: The Glucose Transporter/Sensor Rgt2
Curated sequence CH_091058: high-affinity glucose transporter ght2. Hexose:H+ symporter, Ght2 (Glucose > Fructose)
Curated sequence CH_123257: potential high affinity glucose transporter
Curated sequence B8MYS7: MFS glucose transporter mfs1; Asparasone A synthesis protein mfs1
Curated sequence P32465: Low-affinity glucose transporter HXT1. Low-affinity glucose transporter HXT1
Curated sequence P32466: Low-affinity glucose transporter HXT3
Curated sequence Q9P3U6: High-affinity glucose transporter Ght1 (Hexose transporter 1)
Curated sequence O95528: Solute carrier family 2, facilitated glucose transporter member 10; Glucose transporter type 10; GLUT-10. The glucose transporter, GLUT10, was originally believed to be responsible for Type 2 diabetes. It is now believed to be responsible for arterial tortuosity, a rare autosomal recessive connective tissue disease (Callewaert et al., 2007). GLUT10 transports glucose and 2-deoxy glucose (Km=0.3 mM), and is inhibited by galactose and phloretin
Curated sequence Q5J316: Solute carrier family 2, facilitated glucose transporter member 12; Glucose transporter type 12; GLUT-12
Curated sequence Q6NWF1: Solute carrier family 2, facilitated glucose transporter member 12; Glucose transporter type 12; GLUT-12
Curated sequence Q8BFW9: Solute carrier family 2, facilitated glucose transporter member 12; Glucose transporter type 12; GLUT-12
Curated sequence Q8TD20: Solute carrier family 2, facilitated glucose transporter member 12; Glucose transporter type 12; GLUT-12. solute carrier family 2, member 12, Glut12 of 617 aas and 12 TMSs
Curated sequence B1PLM1: Hexose (glucose) transporter, GT4 (D2) (almost identical to 2.A.1.1.16)
Curated sequence O61059: The D-glucose/D-ribose transporter, LmGT2 (Most similar to 1.A.1.1.18)
Curated sequence O61060: The glucose transporter, LmGT3 (homologous to LmGT2 (1.A.1.1.75)). Two threonine residues located in the hydrophilic loops connecting TMSs 3 & 4 and 7 & 8 of GT3 prevent transport of D-ribose. Changing these two residues to alanine (as in GT2) allows transport of ribose. Thus, loops 3-4 and 7-8 partially determine substrate specificity
Curated sequence O76486: Glucose transporter, GT1. GT1, 2, and 3 are homologues. GT2 and GT3 transport ribose as well as glucose at different rates. GT3 transports ribose with 6-fold lower efficiency due to two threonines in GT3 that are alanines in GT2. They are in two loops between TMSs 3, 4, and 7, 8 (Naula et al., 2010). GT1 is expressed in the flagellar membrane and may be both a glucose transporter and sensor, allowing the parasites to enter the stationary phase when they deplete glucose although in the absence of the sensor, they lose viability
Curated sequence Q06222: Glucose/mannose/fructose transporter and high affinity sensor, Snf3p (regulates glucose transport via other systems)
Curated sequence A5Y0C3: Facilitative (Na+-independent) glucose-specific transporter (Km = 3 mM) of 486 aas and 12 TMSs, HT1; inhibited by cytochalasin B and localized to the midgut
Curated sequence Q3UDF0: Solute carrier family 2, facilitated glucose transporter member 6; Glucose transporter type 6; GLUT-6
Curated sequence Q9UGQ3: Solute carrier family 2, facilitated glucose transporter member 6; Glucose transporter type 6; GLUT-6. solute carrier family 2 (facilitated glucose transporter), member 6
Curated sequence O25788: The Na+-dependent sugar transporter, HP1174 (transports glucose, galactose, mannose and 2-deoxyglucose (Psakis et al. 2009)). (most similar to 2.A.1.7.2; 49% identity)
Curated sequence P0C105: Glucose/galactose porter
Curated sequence Q04DP6: The glucose transporter, OEOE_1574; does not transport fructose
Curated sequence Q04FN1: Glucose transporter, OEOE_0819. Does not transport fructose
Curated sequence CH_091224: D-xylose-proton symporter-like 1. Vacuolar (tonoplast) glucose transporter1, Vgt1 (important for seed germination and flowering)
Curated sequence CH_091141: sodium-dependent glucose transporter 1. Sodium-dependent glucose transporter 1; rNaGLT1; Major facilitator superfamily domain-containing protein 4B. Rat kidney Na+-dependent glucose (methyl α-glucoside) transporter, NaGLT1 (glucose:Na+:Na+=1:1)
Curated sequence P21906: Glucose facilitated diffusion protein. Glucose uniporter
Curated sequence Q8IRI6: Glucose transporter type 1
Curated sequence C5DX43: The fructose/glucose uniporter, Ffz2 (64% identical to 2.A.1.2.23)
Curated sequence P39004: High-affinity hexose transporter HXT7. High affinity, glucose-repressible, glucose (hexose) uniporter (Hxt6/Hxt7). Asn331 and hydrophobic residue side chains in TMS5 determine substrate affinity
Curated sequence CH_091031: high-affinity hexose transporter HXT6
Ignore hits to CH_091031 when looking for 'other' hits (high-affinity hexose transporter HXT6)
Curated sequence P43581: hexose transporter HXT10. Hexose uniporter
Ignore hits to CH_122303 when looking for 'other' hits (high-affinity hexose transporter)
Ignore hits to P40886 when looking for 'other' hits (Hexose transporter HXT8)
Ignore hits to P54862 when looking for 'other' hits (Hexose transporter HXT11 (Low-affinity glucose transporter LGT3))
Ignore hits to Q9P3U7 when looking for 'other' hits (Probable high-affinity hexose transporter ght8, mitochondrial; Hexose transporter 8)
Ignore hits to C5E4Z7 when looking for 'other' hits (The fructose-specific uniporter, Ffz1 (69% identical to Ffz2)
Ignore hits to CH_123252 when looking for 'other' hits (potential hexose transporter)
Ignore hits to CH_123250 when looking for 'other' hits (potential hexose transporter)
Ignore hits to CH_122864 when looking for 'other' hits (potential sugar sensor or transporter)
Ignore hits to P39924 when looking for 'other' hits (Hexose transporter HXT13)
Ignore hits to CH_124796 when looking for 'other' hits (hexose transporter Ght4)
Ignore hits to P54854 when looking for 'other' hits (Hexose transporter HXT15)
UniProt sequence A0KXM0: SubName: Full=Glucose/galactose transporter {ECO:0000313|EMBL:ABK48539.1};
Comment: MFS superfamily glucose transporters include: glcP, O07563 (glcP from B. subtilis), SLCA14/Q8TDB8, ght/rgt, SLC2A10, GT4, GTR6, gluP, and singletons Q04DP6 Q04FN1 CH_091224 CH_091141 P21906 Q8IRI6 C5DX43. Also add the hexose transporters HXT7_YEAST / P39004, CharProtDB::CH_091031 (nearly identical). Ignore CharProtDB::CH_091031 which is nearly identical to G4N740. Add P43581, yet another yeast glucose transporter. Ignore CH_122303, yet another hexose transporter. Ignore yet more yeast hexose transporters P40886, P54862, GHT8_SCHPO / Q9P3U7, C5E4Z7, CH_123252, CH_123250, CH_122864, P39924, CH_124796, P54854. Shewana3_2310 = glcP(Mal) = A0KXM0 was shown to be a glucose transporter (PMID:20836887).
Total: 97 characterized proteins

SSS-glucose: Sodium/glucose cotransporter

Curated sequence A0PJK1: Sodium/glucose cotransporter 5; Na(+)/glucose cotransporter 5; Solute carrier family 5 member 10. Sodium/glucose cotransporter 5 (Na+/glucose cotransporter 5) (Solute carrier family 5 member 10)
Curated sequence CH_091086: sodium/glucose cotransporter 1. Sodium/glucose cotransporter 1; Na(+)/glucose cotransporter 1; High affinity sodium-glucose cotransporter; Solute carrier family 5 member 1. Glucose or galactose:Na+ symporter, SGLT1 (galactose > glucose > fucose). Cotransports water against an osmotic gradient (Naftalin, 2008). TMS IV of the high-affinity sodium-glucose cotransporter participates in sugar binding
Curated sequence P11170: Sodium/glucose cotransporter 1; Na(+)/glucose cotransporter 1; High affinity sodium-glucose cotransporter; Solute carrier family 5 member 1
Curated sequence P31636: Solute carrier family 5 member 4; Low affinity sodium-glucose cotransporter. Glucose:Na+ symporter 3 (low affinity)
Curated sequence P31639: Sodium/glucose cotransporter 2; Na(+)/glucose cotransporter 2; Low affinity sodium-glucose cotransporter; Solute carrier family 5 member 2. Sodium/glucose cotransporter 2 (Na+/glucose cotransporter 2) (Low affinity sodium-glucose cotransporter) (Solute carrier family 5 member 2) of 672 aas and 14 TMSs
Curated sequence P96169: Sodium/glucose cotransporter; Na(+)/glucose symporter. Glucose or galactose:Na+ symporter, SglS or SglT of 543 aas and 14 TMSs (Turk et al. 2006). The 3.0 Å structure is known (Faham et al., 2008). Sodium exit causes a reorientation of transmembrane helix 1 that opens an inner gate required for substrate exit (Watanabe et al., 2010). The involvement of aromatic residue pi interactions, especially with Na+ binding, has been examined
Curated sequence Q28610: Sodium/glucose cotransporter 5; Na(+)/glucose cotransporter 5; RK-D; Solute carrier family 5 member 10
Curated sequence Q28728: Sodium/myo-inositol cotransporter 2; Na(+)/myo-inositol cotransporter 2; Sodium-dependent glucose cotransporter; Sodium/glucose cotransporter KST1; rKST1; Sodium/myo-inositol transporter 2; SMIT2; Solute carrier family 5 member 11
Curated sequence Q2M3M2: Sodium/glucose cotransporter 4; Na(+)/glucose cotransporter 4; hSGLT4; Solute carrier family 5 member 9. Sodium/glucose cotransporter 4 (Na+/glucose cotransporter 4) (hSGLT4) (Solute carrier family 5 member 9)
Curated sequence Q6R4Q5: Sodium/glucose cotransporter 5; Na(+)/glucose cotransporter 5; Solute carrier family 5 member 10
Curated sequence Q8K0E3: Sodium/myo-inositol cotransporter 2; Na(+)/myo-inositol cotransporter 2; Sodium-dependent glucose cotransporter; Sodium/glucose cotransporter KST1; Sodium/myo-inositol transporter 2; SMIT2; Solute carrier family 5 member 11
Curated sequence Q8WWX8: Sodium/myo-inositol cotransporter 2; Na(+)/myo-inositol cotransporter 2; Sodium-dependent glucose cotransporter; Sodium/glucose cotransporter KST1; Sodium/myo-inositol transporter 2; SMIT2; Solute carrier family 5 member 11. Myoinositol:Na+ symporter, SMIT2 (also transports D-chiro-inositol, D-glucose and D-xylose)
Curated sequence Q9NY91: Solute carrier family 5 member 4. Low affinity sodium-glucose cotransporter (Sodium/glucose cotransporter 3) (Na+/glucose cotransporter 3) (Solute carrier family 5 member 4)
Curated sequence Q9Z1F2: Sodium/myo-inositol cotransporter 2; Na(+)/myo-inositol cotransporter 2; Sodium-dependent glucose cotransporter; Sodium/glucose cotransporter KST1; rkST1; Sodium/myo-inositol transporter 2; SMIT2; Solute carrier family 5 member 11
Curated sequence P26430: Nucleoside or glucose(?):Na+ symporter
Curated sequence Q2A687: Renal Na+:D-glucose symporter type 1 (Sglt1; Slc5a1) of 662 aas and 14 TMSs
Comment: solute_symporter (SSS) family transpoters
Total: 16 characterized proteins

glcU': Glucose uptake protein GlcU

Curated sequence O07881: Glucose uptake protein GlcU. Glucose uptake permease, GlcU
Curated sequence P40420: Glucose uptake protein GlcU. Glucose permease, GlcU (also called YcxE). (Fiegler et al., 1999) (similar to 2.A.7.5.1)
Curated sequence L8DP77: The glucose uptake porter of 285 aas, GlcU
Curated sequence Q9CDF7: Glucose:H+ symporter, GlcU (YxfA) (high specificity, low affinity)
Comment: Named glcU' in GapMind to distinguish from an ABC transporter component named glcU
Total: 4 characterized proteins

PAST-A: proton-associated sugar transporter A

Curated sequence Q8K4S3: Proton-associated sugar transporter A; PAST-A; Solute carrier family 45 member 1. The brain proton:associated sugar (glucose) transporter, PAST-A
Curated sequence Q9Y2W3: Proton:glucose symporter A; proton-associated sugar transporter A
Total: 2 characterized proteins

SemiSWEET: Sugar transporter SemiSWEET

Curated sequence B0SR19: Sugar transporter SemiSWEET. SemiSWEET half glucose transporter of 93 aas and 3 TMSs with an N-terminal amphipathic α-helix
Ignore hits to Q8F4F7 when looking for 'other' hits (3 TMS bacterial MtN3 homologue (96aas))
Ignore hits to P0DMV3 when looking for 'other' hits (Sugar transporter SemiSWEET)
Ignore hits to A2BS89 when looking for 'other' hits (3 TMS MtN3 homologue (85aas))
Ignore hits to Q57574 when looking for 'other' hits (3 TMS Sweet homologue, MJ_0110 (93aas))
Comment: Ignore some uncharacterized homologs: SwissProt::B0SR19, TCDB::Q8F4F7, SwissProt::P0DMV3 (structure is known; transports sucrose poorly; physiological substrate unclear), TCDB::A2BS89, TCDB::Q57574 ("LbSemiSWEET"; has glucose transport activity, but not clear if it is the physiological substrate).
Total: 1 characterized proteins

SWEET1: bidirectional sugar transporter SWEET1

Curated sequence Q8L9J7: Bidirectional sugar transporter SWEET1; AtSWEET1; Protein SUGARS WILL EVENTUALLY BE EXPORTED TRANSPORTERS 1. Sweet1: bidirectional low affinity
Total: 1 characterized proteins

mglA: glucose ABC transporter, ATP-binding component (MglA)

Ignore hits to D4GPW3 when looking for 'other' hits (Glucose import ATP-binding protein TsgD13; EC 7.5.2.-)
Curated sequence G4FGN3: Monosaccharide-transporting ATPase, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR
Curated sequence O05176: GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter
Curated sequence P0AAG8: Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter. D-galactose/methyl-galactoside ABC transporter ATP binding subunit. D-galactose/methyl-galactoside ABC transporter ATP binding subunit
Curated sequence GFF3641: glucose transporter, ATPase component
Ignore hits to P23924 when looking for 'other' hits (Galactose/methyl galactoside import ATP-binding protein MglA; EC 7.5.2.11)
Comment: mglABC-like ABC transporters, from E. coli, Haloferax, Thermotoga, Agrobacterium, and Phaeobacter. But in Haloferax, only two components are known; there is a SBP nearby but also a second permease. So mark TSGDD_HALVD / D4GPW3 and D4GPW2 as ignore. Also, there is one paper about the Salmonella ortholog of mglABC; not clear if that transports glucose or not, so ignore that as well (P23924).
Total: 4 characterized proteins

mglB: glucose ABC transporter, substrate-binding component

Curated sequence P0AEE5: D-galactose-binding periplasmic protein DGAL aka MglB aka B2150, component of Galactose/glucose (methyl galactoside) porter. D-galactose/methyl-galactoside ABC transporter periplasmic binding protein. D-galactose/methyl-galactoside ABC transporter periplasmic binding protein
Curated sequence P25548: CVE1 aka ChvE aka ATU2348 aka AGR_C_4267, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter
Curated sequence GFF3639: glucose transporter, periplasmic substrate-binding component
Curated sequence G4FGN5: LacI family transcriptional regulator, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR
Ignore hits to P54083 when looking for 'other' hits (Multiple sugar-binding periplasmic protein SbpA; Sugar-binding protein A)
Comment: mglB (b2150) from E. coli (P0AEE5; 332 a.a.), chvE, or TC 3.A.1.2.20 / G4FGN5 in Thermotoga (343 a.a.) [absent from Haloferax]. Ignore SBPA_AZOBR / P54083 from Azospirillum, whose substrate specificity is uncertain.
Total: 4 characterized proteins

mglC: glucose ABC transporter, permease component (MglC)

Curated sequence G4FGN4: Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR
Curated sequence P23200: MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter. D-galactose/methyl-galactoside ABC transporter membrane subunit. D-galactose/methyl-galactoside ABC transporter membrane subunit
Curated sequence O05177: GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter
Curated sequence GFF3640: glucose transporter, permease component
Ignore hits to D4GPW2 when looking for 'other' hits (Glucose ABC transporter permease protein TsgB13)
Comment: mglC (b2148) and related proteins, and a protein from Haloferax (TSGBD_HALVD / D4GPW2; TSGDD_HALVD / D4GPW3)
Total: 4 characterized proteins

gtsA: glucose ABC transporter, substrate-binding component (GtsA)

Curated sequence Q88P38: GtsA (GLcE), component of Glucose porter, GtsABCD
Curated sequence Q72KX2: Glucose-binding protein aka TT_C0328, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25)
Curated sequence PfGW456L13_1894: ABC transporter for D-Galactose and D-Glucose, periplasmic substrate-binding component
Curated sequence GFF4324: ABC transporter for D-Glucose-6-Phosphate, periplasmic substrate-binding component
UniProt sequence A0A165KPY4: SubName: Full=Sugar ABC transporter substrate-binding protein {ECO:0000313|EMBL:KZT15782.1};
Comment: gtsABCD-like ABC transporters, from Thermus, Pseudomonas putida, and Pseudomonas fluorescens GW456-L13. (Some components cluster with glcSTUV from Saccharolobus, which is described separately; those are marked ignore here.) The system in P. fluorescens is very similar (~90% a.a. identity) to PS417_22145:PS417_22130 (GFF4324:GFF4321), which is involved in glucose-6-phosphate utilization, probably as a glucose transporter. Fitness data also identified a gtsABCD-like glucose transporter in Acidovorax sp. GW101-3H11 (Ac3H11_2062:Ac3H11_2064:Ac3H11_2065:Ac3H11_2066; A0A165KPY4, A0A165KPZ4, A0A165KQ00, A0A165KQ08).
Total: 5 characterized proteins

gtsB: glucose ABC transporter, permease component 1 (GtsB)

Curated sequence Q88P37: GtsB (GLcF), component of Glucose porter, GtsABCD
Curated sequence PfGW456L13_1895: ABC transporter for D-Galactose and D-Glucose, permease component 1
Curated sequence Q72KX3: Glucose transport system permease protein aka TT_C0327, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25)
Curated sequence GFF4323: ABC transporter for D-Glucose-6-Phosphate, permease component 2
UniProt sequence A0A165KPZ4: SubName: Full=ABC transporter permease {ECO:0000313|EMBL:KZT15783.1};
Total: 5 characterized proteins

gtsC: glucose ABC transporter, permease component 2 (GtsC)

Curated sequence Q72KX4: Sugar transport system permease protein aka TT_C0326, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25)
Curated sequence Q88P36: GtsC (GLcG), component of Glucose porter, GtsABCD
Curated sequence PfGW456L13_1896: ABC transporter for D-Galactose and D-Glucose, permease component 2
Curated sequence GFF4322: ABC transporter for D-Glucose-6-Phosphate, permease component 1
UniProt sequence A0A165KQ00: SubName: Full=Sugar ABC transporter permease {ECO:0000313|EMBL:KZT15784.1};
Total: 5 characterized proteins

gtsD: glucose ABC transporter, ATPase component (GtsD)

Curated sequence Q72L52: Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose
Ignore hits to Q97UY8 when looking for 'other' hits (monosaccharide-transporting ATPase (EC 3.6.3.17). Glucose import ATP-binding protein GlcV; EC 7.5.2.-. GlcV, component of Glucose, mannose, galactose porter)
Curated sequence Q88P35: GtsD (GLcK), component of Glucose porter, GtsABCD
Curated sequence PfGW456L13_1897: ABC transporter for D-Galactose and D-Glucose, ATPase component
Curated sequence GFF4321: ABC transporter for D-Glucose-6-Phosphate, ATPase component
UniProt sequence A0A165KQ08: SubName: Full=Sugar ABC transporter ATP-binding protein {ECO:0000313|EMBL:KZT15785.1};
Total: 5 characterized proteins

glcS: glucose ABC transporter, substrate-binding component (GlcS)

Curated sequence Q97UZ1: Glucose-binding protein GlcS; GBP. GlcS, component of Glucose, mannose, galactose porter
Comment: ABC transporter glcSTUV from Saccharolobus/Sulfolobus
Total: 1 characterized proteins

glcT: glucose ABC transporter, permease component 1 (GlcT)

Curated sequence Q97UZ0: GlcT, component of Glucose, mannose, galactose porter
Total: 1 characterized proteins

glcU: glucose ABC transporter, permease component 2 (GlcU)

Curated sequence Q97UY9: GlcU, component of Glucose, mannose, galactose porter
Total: 1 characterized proteins

glcV: glucose ABC transporter, ATPase component (GclV)

Curated sequence Q97UY8: monosaccharide-transporting ATPase (EC 3.6.3.17). Glucose import ATP-binding protein GlcV; EC 7.5.2.-. GlcV, component of Glucose, mannose, galactose porter
Total: 1 characterized proteins

aglE': glucose ABC transporter, substrate-binding component (AglE)

UniProt sequence A8LLL6: SubName: Full=Putative bacterial solute-binding protein 1 family {ECO:0000313|EMBL:ABV93394.1};
Ignore hits to SMc03061 when looking for 'other' hits (AglE aka R00695 aka SMC03061, component of Sucrose/maltose/trehalose porter (sucrose-inducible). ABC transporter for D-Maltose and D-Trehalose, ATPase component)
Comment: ABC transporter aglEFGK (Dshi_1652:Dshi_1648) from Dinoroseobacter shibae. The gene names are from the related system aglEFGK of Sinorhizobium meliloti, which are involved in uptake of sucrose and some other disaccharides (PMID:10400573). In fitness data, S. meliloti aglEFGK are important for maltose & trehalose utilization (see SMc03061 = aglE); they are not important on glucose but S. meliloti also has SM_b20894, which is similar to gguA/mglA O05176. It is uncertain whether aglEFGK from S. meliloti can transport glucose or not, so it is ignored. Dshi_1652 = A8LLL6.
Total: 1 characterized proteins

aglF': glucose ABC transporter, permease component 1 (AglF)

UniProt sequence A8LLL5: SubName: Full=Inner membrane ABC transporter permease protein {ECO:0000313|EMBL:ABV93393.1};
Ignore hits to SMc03062 when looking for 'other' hits (ABC transporter for D-Maltose and D-Trehalose, permease component 1. AglF aka R00696 aka SMC03062, component of Sucrose/maltose/trehalose porter (sucrose-inducible))
Comment: Dshi_1651 = A8LLL5.
Total: 1 characterized proteins

aglG': glucose ABC transporter, permease component 2 (AglG)

UniProt sequence A8LLL4: SubName: Full=Inner membrane ABC transporter permease protein {ECO:0000313|EMBL:ABV93392.1};
Ignore hits to SMc03063 when looking for 'other' hits (ABC transporter for D-Maltose and D-Trehalose, permease component 2. glucosyl-dolichyl phosphate glucuronosyltransferase (EC 2.4.1.356). AglG aka R00697 aka SMC03063, component of Sucrose/maltose/trehalose porter (sucrose-inducible))
Comment: Dshi_1650 = A8LLL4.
Total: 1 characterized proteins

aglK': glucose ABC transporter, ATPase component (AglK)

UniProt sequence A8LLL2: SubName: Full=Maltose/maltodextrin import ATP-binding protein {ECO:0000313|EMBL:ABV93390.1}; EC=3.6.3.19 {ECO:0000313|EMBL:ABV93390.1};
Ignore hits to SMc03065 when looking for 'other' hits (ABC transporter for D-Maltose and D-Trehalose, ATPase component. AglK aka R00699 aka SMC03065, component of Sucrose/maltose/trehalose porter (sucrose-inducible))
Comment: Dshi_1648 = A8LLL2.
Total: 1 characterized proteins

ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG)

Curated sequence CH_001857: PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69. The glucose IICBA porter (PtsG) 44% identical to 4.A.1.1.1)
Curated sequence Q53922: PTS system glucoside-specific EIICBA component; EIICBA-Glc 2; EC 2.7.1.-. Glucose porter GlcB (IICBA). Glucose uptake is inhibited by methyl-α-D-glucoside, methyl-β-D-glucoside, p-nitrophenyl-α-D-glucoside, o-nitrophenyl-β-D-glucoside and salicin, but not by 2-deoxyglucose. Mannose and N-acetylglucosamine are not transported
Curated sequence Q57071: PTS system glucose-specific EIICBA component; EIICBA-Glc; EII-Glc; EIICBA-Glc 1; EC 2.7.1.199. Glucose porter, GlcA (IICBA). Glucose uptake is inhibited by 2-deoxyglucose and methyl-β-D-glucoside
Comment: Fused (one-component) PTS system, EIICBA (ptsG in B. subtilis; two systems from Staphylococcus)
Total: 3 characterized proteins

bglF: glucose PTS, enzyme II (BCA components, BglF)

Curated sequence P08722: β-Glucoside (salicin, arbutin, cellobiose, etc) group translocator, BglF. β-glucoside specific PTS enzyme II / BglG kinase / BglG phosphatase (EC 2.7.1.199). β-glucoside specific PTS enzyme II / BglG kinase / BglG phosphatase (EC 2.7.1.199)
Comment: Another one-component PTS system, bglF from E. coli
Total: 1 characterized proteins

ptsG: glucose PTS, enzyme IICB

Ignore hits to Q9AGA7 when looking for 'other' hits (PTS system alpha-glucoside-specific EIICB component; EC 2.7.1.-. The α-glucoside-specific IICB, AglB (transports glucose, methyl-α-glucoside, maltitol, isomaltose, trehalulose α(1→1), turanose α(1→3), maltulose α(1→4), leucrose α(1→5), and palatinose α(1→6), but not sucrose (most resembles 4.A.1.1.4 and 4.A.1.1.8))
Curated sequence P69786: protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199). PTS system glucose-specific EIICB component; EC 2.7.1.69. PTS system glucose-specific EIICB component; EIICB-Glc; EII-Glc; EC 2.7.1.199. PTS system glucose-specific EIICB component PTGB aka PTSG aka GLCA aka UMG aka B1101, component of Glucose porter (PtsG; GlcA; Umg) (transports D-glucose and α-methyl-D-glucopyranoside). glucose-specific PTS enzyme IIBC component (EC 2.7.1.199). glucose-specific PTS enzyme IIBC component (EC 2.7.1.199)
Curated sequence P37439: PTS system glucose-specific EIICB component; EIICB-Glc; EII-Glc; EC 2.7.1.199
Ignore hits to O51590 when looking for 'other' hits (Glucose-specific Enzyme IIBC of the PTS, PtsG)
Ignore hits to P19642 when looking for 'other' hits (PTS system maltose- and glucose-specific EIICB component; EC 2.7.1.69. PTS system maltose-specific EIICB component; EC 2.7.1.208. Maltose porter (MalX). PTS enzyme IIBC component MalX. PTS enzyme IIBC component MalX)
Comment: EII-CB proteins. Ignore O51590 (4.A.1.1.18) from Borrelia burgdorferi, which is not characterized and the EIIA component is uncertain. Ignore E. coli malX (P19642), which facilitates diffusion of glucose (no phosphorylation); its physiological function is unclear so it is not listed as a sole glucose transporter. Ignore PTUCB_KLEPN / Q9AGA7 from Klebsiella, as the EII-A component was not described
Total: 2 characterized proteins

crr: glucose PTS, enzyme IIA

Curated sequence CH_088352: glucose-specific phosphotransferase enzyme IIA component; EC 2.7.1.-. PTS system glucose-specific EIIA component; EIIA-Glc; EIII-Glc; Glucose-specific phosphotransferase enzyme IIA component. Glucose-specific phosphotransferase enzyme IIA component PTGA aka CRR aka GSR aka IEX aka TGS aka TRED aka B2417, component of Glucose porter (PtsG; GlcA; Umg) (transports D-glucose and α-methyl-D-glucopyranoside). Enzyme IIA^Glc (EC 2.7.1.199; EC 2.7.1.201; EC 2.7.1.192). Enzyme IIA^Glc (EC 2.7.1.199)
Curated sequence P0A283: PTS system glucose-specific EIIA component; EIIA-Glc; EIII-Glc; Glucose-specific phosphotransferase enzyme IIA component
Ignore hits to Q8L3C4 when looking for 'other' hits (IIA aka Crr, component of The N,N' -diacetylchitobiose Enzyme II (Toratani et al., 2008) (>80% identical to the E. coli enzyme (4.A.3.2.1)))
Comment: Ignore a close homlog in Serratia (TC 4.A.3.2.5 / Q8L3C4) which is reported to be the II-A component for N,N' -diacetylchitobiose (probably shared with other sugars).
Total: 2 characterized proteins

manX: glucose PTS, enzyme EIIAB

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 E1UCI0: PTS system, mannose-specific, IIAB component, component of The primary glucose /mannose uptake transporter, ManLMN
Curated sequence Q04GK1: Phosphotransferase system, mannose/fructose-specific component IIA, component of The hexose (glucose and fructose demonstrated) PTS uptake system
Curated sequence Q2QKM4: ManL aka EIIAB, component of Glucose porter, ManLMN
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: PTS system manXYZ (manX is EIIAB; manY is EIIC; manZ is EIID) from E. coli, Listeria, Oenococcus, Lactobacillus, and Streptococcus. Systems related to manXYZ in Streptococcus salivarius and Lactococcus lactis subsp. lactis are reported to act on glucose, but are listed with other preferred substrates; ignore these.
Total: 5 characterized proteins

manY: glucose PTS, enzyme EIIC

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 E1UCI1: PTS system, mannose/fructose/sorbose family, IIC component, component of The primary glucose /mannose uptake transporter, ManLMN
Curated sequence Q04GK0: Mannose-specific PTS system component IIC, component of The hexose (glucose and fructose demonstrated) PTS uptake system
Curated sequence Q2QKM3: ManM aka EIIC, component of Glucose porter, ManLMN
Curated sequence Q5M5W7: ManM, component of The glucose/mannose/2-deoxyglucose/fructose phosphotransferase systems (phosphorylates without transport), ManLMN
Comment: Also similar is Lmo0782 (TC 4.A.6.1.16 / Q8Y8W0) from MpoABCD, a PTS-like glucose sensor; this is not ignored but possibly should be.
Total: 5 characterized proteins

manZ: glucose PTS, enzyme EIID

Curated sequence P69805: 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)
Curated sequence E1UCI2: PTS system, mannose/fructose/sorbose family, IID component, component of The primary glucose /mannose uptake transporter, ManLMN
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 Q2QKM2: ManN aka EIID, component of Glucose porter, ManLMN
Curated sequence Q5M5W8: ManN, component of The glucose/mannose/2-deoxyglucose/fructose phosphotransferase systems (phosphorylates without transport), ManLMN
Ignore hits to Q5IRC0 when looking for 'other' hits (protein-Npi-phosphohistidine-D-mannose phosphotransferase (EC 2.7.1.191))
Ignore hits to D2BKY9 when looking for 'other' hits (Mannose-specific PTS system, IID 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: (The E. coli entry, P69805, is listed twice, because the sequence in TCDB has 3 extra N-terminal residues.) Also similar is Lmo0781 (TC 4.A.6.1.16 / Q8Y8W1) from MpoABCD; should perhaps be ignored.
Total: 6 characterized proteins

gdh: quinoprotein glucose dehydrogenase

Curated proteins or TIGRFams with EC 1.1.5.2
Total: 5 characterized proteins

gnl: gluconolactonase

Curated proteins or TIGRFams with EC 3.1.1.17
UniProt sequence Q9HWH7: SubName: Full=Periplasmic gluconolactonase, PpgL {ECO:0000313|EMBL:AAG07591.1};
Comment: Add Pseudomonas ppgL (PA4204 = Q9HWH7; see PMID:18832304)
Total: 7 characterized proteins

gadh1: gluconate 2-dehydrogenase flavoprotein subunit

Curated sequence O34214: Gluconate 2-dehydrogenase flavoprotein; GA 2-DH dehydrogenase subunit; GADH dehydrogenase subunit; EC 1.1.99.3. gluconate 2-dehydrogenase dehydrogenase subunit (EC 1.1.99.3)
Curated sequence MONOMER-12745: D-gluconate dehydrogenase dehydrogenase subunit (EC 1.1.99.3)
Curated sequence A4PIB0: gluconate 2-dehydrogenase (EC 1.1.1.215)
UniProt sequence G5EBD9: SubName: Full=Gluconate 2-dehydrogenase alpha chain {ECO:0000313|EMBL:AAW60992.1}; EC=1.1.99.3 {ECO:0000313|EMBL:AAW60992.1};
Curated sequence C0LE03: gluconate 2-dehydrogenase (EC 1.1.1.215)
Comment: gluconate 2-dehydrogenase has three subunits; known in Pseudomonas fluorescens and Pantoea/Pectobacterium cypripedii. There's also papers about two different enzymes in Gluconobacter. PMID:17720837 describes A4PIA9 = gndS = gadh3; A4PIB0 = gndL = gadh1; A4PIB1 = gndC = gadh2; BRENDA includes only A4PIB0. PMID:27392695 shows that overexpressing GOX1232 to GOX1230 (Q5FRK3 G5EBD9 Q5FRK5), paralogs of gndSLC, leads to increased production of 2-ketogluconate; BRENDA includes only Q5FRK5. Finally, C0LE03 is listed by BRENDA as a gluconate 2-dehydrogenase and is nearly identical to Q4KKM7 = link, so include that as well. Some papers also mention GOX0147 = 5FTU6 but that is the cytoplasmic 2-ketogluconate reductase.
Total: 5 characterized proteins

gadh2: gluconate 2-dehydrogenase cytochrome c subunit

Curated sequence O34215: Gluconate 2-dehydrogenase cytochrome c subunit; GA 2-DH cytochrome c subunit; GADH cytochrome c subunit; EC 1.1.99.3. gluconate 2-dehydrogenase cytochrome c subunit (EC 1.1.99.3)
Curated sequence MONOMER-12746: D-gluconate dehydrogenase cytochrome c subunit (EC 1.1.99.3)
UniProt sequence A4PIB1: SubName: Full=Gluconate 2-dehydrogenase cytochrome c {ECO:0000313|EMBL:BAF52628.1};
Curated sequence Q5FRK5: gluconate 2-dehydrogenase (EC 1.1.1.215)
Total: 4 characterized proteins

gadh3: gluconate 2-dehydrogenase subunit 3

Curated sequence O34213: Gluconate 2-dehydrogenase subunit 3; GA 2-DH subunit 3; GADH subunit 3; EC 1.1.99.3. gluconate 2-dehydrogenase subunit 3 (EC 1.1.99.3)
Curated sequence MONOMER-12747: D-gluconate dehydrogenase 21.7 kD subunit (EC 1.1.99.3)
UniProt sequence A4PIA9: SubName: Full=Gluconate 2-dehydrogenase small subunit {ECO:0000313|EMBL:BAF52626.1};
UniProt sequence Q5FRK3: SubName: Full=Gluconate 2-dehydrogenase gamma chain {ECO:0000313|EMBL:AAW60993.1}; EC=1.1.99.3 {ECO:0000313|EMBL:AAW60993.1};
Total: 4 characterized proteins

kguT: 2-ketogluconate transporter

UniProt sequence A0A167V864: SubName: Full=KguT {ECO:0000313|EMBL:ANB66397.1};
Comment: kguT = KU168042 = A0A167V864 was shown to be required for 2-ketogluconate utilization (PMID:30109560)
Total: 1 characterized proteins

kguK: 2-ketogluconokinase

Curated proteins or TIGRFams with EC 2.7.1.13
Total: 1 characterized proteins

kguD: 2-keto-6-phosphogluconate reductase

Curated proteins or TIGRFams with EC 1.1.1.43
Total: 1 characterized proteins

edd: phosphogluconate dehydratase

Curated proteins or TIGRFams with EC 4.2.1.12
Total: 1 HMMs and 3 characterized proteins

eda: 2-keto-3-deoxygluconate 6-phosphate aldolase

Curated proteins or TIGRFams with EC 4.1.2.14
Curated proteins or TIGRFams with EC 4.1.2.55
Total: 18 characterized proteins

glk: glucokinase

Curated proteins or TIGRFams with EC 2.7.1.1
Curated proteins or TIGRFams with EC 2.7.1.2
UniProt sequence A8LLL9: SubName: Full=Glucokinase {ECO:0000313|EMBL:ABV93397.1}; EC=2.7.1.2 {ECO:0000313|EMBL:ABV93397.1};
UniProt sequence Q5GAN8: SubName: Full=General specificity hexokinase {ECO:0000313|EMBL:AAT74901.1};
Curated sequence MONOMER-19002: N-acetylglucosamine kinase (EC 2.7.1.59)
Ignore hits to CH_123431 when looking for 'other' hits (N-acetylglucosamine kinase)
Ignore hits to Q9ADE8 when looking for 'other' hits (polyphosphate-glucose phosphotransferase (EC 2.7.1.63))
UniProt sequence I7DXX1: SubName: Full=Glucokinase Glk {ECO:0000313|EMBL:AFO90274.1}; EC=2.7.1.2 {ECO:0000313|EMBL:AFO90274.1};
Comment: Dshi_1655 (A8LLL9) was identified using fitness data, is very important for growth on glucose and several glucose-containing disaccharides; and functional residues seem to be conserved. The related protein PGA1_c05420 (I7DXX1) also seems to be glk. Q5GAN8 = hexA from B. fragilis is a broad-specificity hexokinase (PMID:15659667). Q5GBH5 = rokA = MONOMER-19002 from B. fragilis is a glucose/mannose/NAG kinase (PMID:15659667). (MetaCyc lists it as NAG kinase only but it is just as active on glucose.) CH_123431 is nearly identical to a characterized broad-specificity hexose kinase, so ignore. SCO5059 (Q9ADE8) is reported to have ATP-glucokinase activity (PMID:24200789), so ignore.
Total: 1 HMMs and 98 characterized proteins

lacL: heteromeric lactase, large subunit

Curated sequence A0SWS3: beta-galactosidase (EC 3.2.1.23)
Curated sequence AAA25267.1: β-galactosidase L+M (LacL+LacM) (EC 3.2.1.23)
Curated sequence AAL09167.1: β-galactosidase (LacL+LacM) (EC 3.2.1.23)
Curated sequence ABF72116.1: β-galactosidase (Lreu?gal) (LacL + LacM) (EC 3.2.1.23). beta-galactosidase (EC 3.2.1.23)
Curated sequence ABJ65308.1: LVIS_2259 + LVIS_2258 (EC 3.2.1.23)
Curated sequence ACC38286.1: β-galactosidase large subunit (LacL) (EC 3.2.1.23)
Curated sequence AEG39988.1: β-galactosidase large subunit (LacL;WANG_0293) (EC 3.2.1.23)
Curated sequence AEJ32720.1: β-galactosidase (LacLM;LacL+LacM) (EC 3.2.1.23)
Curated sequence BAA20536.1: β-galactosidase (LacL) (EC 3.2.1.23)
Curated sequence CAA57730.1: β-galactosidase L+S (LacL+LacS) (heterodimer) (EC 3.2.1.23)
Curated sequence CAD65569.1: β-galactosidase (LacL+LacM,lp_3483+lp_3484) (EC 3.2.1.23)
Curated sequence CAZ66936.1: β-galactosidase (LacL+LacM) (EC 3.2.1.23)
Curated sequence Q7WTB4: Beta-galactosidase large subunit; Beta-gal large subunit; Lactase large subunit; EC 3.2.1.23
Total: 13 characterized proteins

lacM: heteromeric lactase, small subunit

Curated sequence A0SWS4: beta-galactosidase (EC 3.2.1.23)
Curated sequence Q19R71: beta-galactosidase (EC 3.2.1.23)
Curated sequence Q7WTB3: Beta-galactosidase small subunit; Beta-gal small subunit; Lactase small subunit; EC 3.2.1.23
Total: 3 characterized proteins

lacZ: lactase (homomeric)

Curated proteins or TIGRFams with EC 3.2.1.108
Curated proteins or TIGRFams with EC 3.2.1.23
Ignore hits to A0SWS3 when looking for 'other' hits (beta-galactosidase (EC 3.2.1.23))
Ignore hits to AAA25267.1 when looking for 'other' hits (β-galactosidase L+M (LacL+LacM) (EC 3.2.1.23))
Ignore hits to AAL09167.1 when looking for 'other' hits (β-galactosidase (LacL+LacM) (EC 3.2.1.23))
Ignore hits to ABF72116.1 when looking for 'other' hits (β-galactosidase (Lreu?gal) (LacL + LacM) (EC 3.2.1.23). beta-galactosidase (EC 3.2.1.23))
Ignore hits to ABJ65308.1 when looking for 'other' hits (LVIS_2259 + LVIS_2258 (EC 3.2.1.23))
Ignore hits to ACC38286.1 when looking for 'other' hits (β-galactosidase large subunit (LacL) (EC 3.2.1.23))
Ignore hits to AEG39988.1 when looking for 'other' hits (β-galactosidase large subunit (LacL;WANG_0293) (EC 3.2.1.23))
Ignore hits to AEJ32720.1 when looking for 'other' hits (β-galactosidase (LacLM;LacL+LacM) (EC 3.2.1.23))
Ignore hits to BAA20536.1 when looking for 'other' hits (β-galactosidase (LacL) (EC 3.2.1.23))
Ignore hits to CAA57730.1 when looking for 'other' hits (β-galactosidase L+S (LacL+LacS) (heterodimer) (EC 3.2.1.23))
Ignore hits to CAD65569.1 when looking for 'other' hits (β-galactosidase (LacL+LacM,lp_3483+lp_3484) (EC 3.2.1.23))
Ignore hits to CAZ66936.1 when looking for 'other' hits (β-galactosidase (LacL+LacM) (EC 3.2.1.23))
Ignore hits to Q7WTB4 when looking for 'other' hits (Beta-galactosidase large subunit; Beta-gal large subunit; Lactase large subunit; EC 3.2.1.23)
Ignore hits to A0SWS4 when looking for 'other' hits (beta-galactosidase (EC 3.2.1.23))
Ignore hits to Q19R71 when looking for 'other' hits (beta-galactosidase (EC 3.2.1.23))
Ignore hits to Q7WTB3 when looking for 'other' hits (Beta-galactosidase small subunit; Beta-gal small subunit; Lactase small subunit; EC 3.2.1.23)
Ignore hits to P83252 when looking for 'other' hits (Beta-galactosidase; Acid beta-galactosidase; Lactase; Exo-(1-->4)-beta-D-galactanase; EC 3.2.1.23. beta-galactosidase (EC 3.2.1.23))
Ignore hits to AAA79030.1 when looking for 'other' hits (β-glycosidase (Bgly;SSG) (EC 3.2.1.-))
Ignore hits to AAN05439.1 when looking for 'other' hits (β-glycosidase / β-glucosidase (TTHB087) (EC 3.2.1.21))
Ignore hits to AAF36392.1 when looking for 'other' hits (β-glycosidase (Gly) (EC 3.2.1.21))
Ignore hits to AAN05441.1 when looking for 'other' hits (β-glycosidase (BglA) (EC 3.2.1.-))
Ignore hits to ABW87307.1 when looking for 'other' hits (β-glycosidase (β-gly) (EC 3.2.1.-))
Ignore hits to AAO15361.1 when looking for 'other' hits (β-glycosidase / β-glucosidase (BglT;BglA) (EC 3.2.1.21|3.2.1.-))
Ignore hits to AAN05440.1 when looking for 'other' hits (β-glycosidase (tfi β-gly) (EC 3.2.1.-))
Ignore hits to ABW01253.1 when looking for 'other' hits (Cmaq_0408 (EC 3.2.1.21))
Ignore hits to AAY81155.1 when looking for 'other' hits (β-glycosidase (BgaS;Saci_1849) (EC 3.2.1.-))
Ignore hits to CAA34074.1 when looking for 'other' hits (β-glycosidase / β-galactosidase (EC 3.2.1.-))
Ignore hits to ADL19795.1 when looking for 'other' hits (β-glycosidase (β-Gly;As?-Gly;ASAC_1390) (EC 3.2.1.-))
Ignore hits to AEE47485.1 when looking for 'other' hits (β-glycosidase (CfBgl3C;Celf_3372) (Bgl3C) (EC 3.2.1.-))
Ignore hits to ACK41548.1 when looking for 'other' hits (β-glucosidase / β-glycosidase (Dtur_0219) (EC 3.2.1.21))
Ignore hits to ABX04075.1 when looking for 'other' hits (β-glycosidase (HaGH03;Haur_1431) (EC 3.2.1.-))
Ignore hits to BAA78713.1 when looking for 'other' hits (β-glycosidase (Tk?gly;TK1761) (EC 3.2.1.-))
Ignore hits to Q8DR24 when looking for 'other' hits (beta-galactosidase (EC 3.2.1.23))
Comment: Mark the sequences for lacL or lacM as ignore, and also BGAL_HORVU. Also mark some similar enzymes annotated as beta-glycosidases as ignore.
Total: 236 characterized proteins

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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

GapMind for catabolism of small carbon sources