Definition of D-galactose catabolism
As rules and steps, or see full text
Rules
Overview: Galactose utilization in GapMind is based on MetaCyc pathways lactose and galactose degradation I via tagatose 6-phosphate (link), the Leloir pathway via UDP-galactose (link), and the oxidative pathway via D-galactonate (link). Pathway IV via galactitol (link) is not reported in prokaryotes and is not included. (There is no pathway III.)
- all: galactose-utilization
- galactose-utilization:
- galactose-PTS and galactose-6-phosphate-degradation
- or galactose-transport and galactose-degradation
- 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)
- galactose-PTS: ptcA, ptcB and ptcEIIC
- galactose-transport:
Steps
mglA: galactose ABC transporter, ATPase component MglA
- 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 P23924: Galactose/methyl galactoside import ATP-binding protein MglA; EC 7.5.2.11
- Comment: Salmonella typhimurium also has mglABC; but only mglA is listed
- Total: 2 characterized proteins
mglB: galactose ABC transporter, substrate-binding component MglB
- 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
- Total: 1 characterized proteins
mglC: galactose ABC transporter, permease component MglC
- 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
- Total: 1 characterized proteins
ytfQ: galactose ABC transporter, substrate-binding component
- Curated sequence P39325: Galactofuranose-binding protein YtfQ. galactofuranose ABC transporter periplasmic binding protein (EC 7.5.2.9). galactofuranose ABC transporter periplasmic binding protein (EC 7.5.2.9)
- Total: 1 characterized proteins
ytfR: galactose ABC transporter, ATPase component
- Curated sequence YTFR-MONOMER: galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9). galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9)
- Total: 1 characterized proteins
ytfT: galactose ABC transporter, permease component 1
- Curated sequence P39328: Galactofuranose transporter permease protein YtfT. galactofuranose ABC transporter putative membrane subunit YtfT (EC 7.5.2.9). galactofuranose ABC transporter putative membrane subunit YtfT (EC 7.5.2.9)
- Total: 1 characterized proteins
yjtF: galactose ABC transporter, permease component 2
- Curated sequence P37772: Inner membrane ABC transporter permease protein YjfF. galactofuranose ABC transporter putative membrane subunit YjtF (EC 7.5.2.9). galactofuranose ABC transporter putative membrane subunit YjtF (EC 7.5.2.9)
- Total: 1 characterized proteins
gguA: galactose ABC transporter, ATPase component GguA
- Curated sequence O05176: GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter
- Comment: Agrobacterium tumefaciens / radiobacter has a 3-part transporter (GguAB-ChvE, also known as CVE1)
- Total: 1 characterized proteins
gguB: galactose ABC transporter, permease component GguB
- Curated sequence O05177: GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter
- Total: 1 characterized proteins
chvE: galactose ABC transporter, substrate-binding component ChvE
- Curated sequence P25548: CVE1 aka ChvE aka ATU2348 aka AGR_C_4267, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter
- Ignore hits to P54083 when looking for 'other' hits (Multiple sugar-binding periplasmic protein SbpA; Sugar-binding protein A)
- Comment: SbpA from Azospirillum brasilense (P543083) is involved in chemotaxis towards galactose, and could well be part of a galactose transport system
- Total: 1 characterized proteins
glcS: galactose ABC transporter, substrate-binding component GlcS
- Curated sequence Q97UZ1: Glucose-binding protein GlcS; GBP. GlcS, component of Glucose, mannose, galactose porter
- Comment: Sulfolobus (Saccharolobus) solfataricus has a 4-part transporter glcSTUV
- Total: 1 characterized proteins
glcT: galactose ABC transporter, permease component 1 (GlcT)
glcU: galactose ABC transporter, permease component 2 (GlcU)
glcV: galactose ABC transporter, ATPase component (GlcV)
- 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
PfGW456L13_1894: ABC transporter for D-Galactose and D-Glucose, periplasmic substrate-binding component
- Curated sequence PfGW456L13_1894: ABC transporter for D-Galactose and D-Glucose, periplasmic substrate-binding component
- Ignore hits to GFF4324 when looking for 'other' hits (ABC transporter for D-Glucose-6-Phosphate, periplasmic substrate-binding component)
- Ignore hits to Q88P38 when looking for 'other' hits (GtsA (GLcE), component of Glucose porter, GtsABCD)
- Comment: Pseudomonas fluorescens has a 4-part transporter. A related system in P. simiae WCS417 is slightly deleterious during growth on galactose, so it could be a galactose transporter; it is marked ignore. A related system is also found in P. putida (gtsABCD), which does not utilize galactose, but similar systems in other Pseudomonas do seem to be involved in galactose transport (i.e., AO356_05195:AO356_05180 from FW300-N2C3), so gtsABCD is also marked ignore..
- Total: 1 characterized proteins
PfGW456L13_1895: ABC transporter for D-Galactose and D-Glucose, permease component 1
- Curated sequence PfGW456L13_1895: ABC transporter for D-Galactose and D-Glucose, permease component 1
- Ignore hits to GFF4323 when looking for 'other' hits (ABC transporter for D-Glucose-6-Phosphate, permease component 2)
- Ignore hits to Q88P37 when looking for 'other' hits (GtsB (GLcF), component of Glucose porter, GtsABCD)
- Total: 1 characterized proteins
PfGW456L13_1896: ABC transporter for D-Galactose and D-Glucose, permease component 2
- Curated sequence PfGW456L13_1896: ABC transporter for D-Galactose and D-Glucose, permease component 2
- Ignore hits to GFF4322 when looking for 'other' hits (ABC transporter for D-Glucose-6-Phosphate, permease component 1)
- Ignore hits to Q88P36 when looking for 'other' hits (GtsC (GLcG), component of Glucose porter, GtsABCD)
- Total: 1 characterized proteins
PfGW456L13_1897: ABC transporter for D-Galactose and D-Glucose, ATPase component
- Curated sequence PfGW456L13_1897: ABC transporter for D-Galactose and D-Glucose, ATPase component
- Ignore hits to GFF4321 when looking for 'other' hits (ABC transporter for D-Glucose-6-Phosphate, ATPase component)
- Ignore hits to Q88P35 when looking for 'other' hits (GtsD (GLcK), component of Glucose porter, GtsABCD)
- Total: 1 characterized proteins
BPHYT_RS16935: galactose ABC transporter, substrate-binding component
- UniProt sequence B2SYR6: RecName: Full=L-arabinose-binding periplasmic protein {ECO:0000256|PIRNR:PIRNR002816}; Short=ABP {ECO:0000256|PIRNR:PIRNR002816}; Flags: Precursor;
- UniProt sequence A0A161H4E4: RecName: Full=L-arabinose-binding periplasmic protein {ECO:0000256|PIRNR:PIRNR002816}; Short=ABP {ECO:0000256|PIRNR:PIRNR002816};
- Comment: Burkholderia phytofirmans and some other Pseudomonas fluorescens (such as FW300-N2E2) have a 3-part galactose transporter. It is related to araFGH and also transports L-arabinose. BPHYT_RS16935 = B2SYR6; Pf6N2E2_5968 = A0A161H4E4
- Total: 2 characterized proteins
BPHYT_RS16930: galactose ABC transporter, ATPase component
- UniProt sequence B2SYR5: RecName: Full=Arabinose import ATP-binding protein AraG {ECO:0000256|HAMAP-Rule:MF_01721}; EC=7.5.2.12 {ECO:0000256|HAMAP-Rule:MF_01721};
- UniProt sequence A0A165ZSX8: RecName: Full=Arabinose import ATP-binding protein AraG {ECO:0000256|HAMAP-Rule:MF_01721}; EC=7.5.2.12 {ECO:0000256|HAMAP-Rule:MF_01721};
- Comment: BPHYT_RS16930 = B2SYR5; Pf6N2E2_5969 = A0A165ZSX8
- Total: 2 characterized proteins
BPHYT_RS16925: galactose ABC transporter, permease component
- UniProt sequence B2SYR4: SubName: Full=Monosaccharide-transporting ATPase {ECO:0000313|EMBL:ACD17799.1}; EC=3.6.3.17 {ECO:0000313|EMBL:ACD17799.1};
- UniProt sequence A0A161GM94: SubName: Full=Arabinose ABC transporter permease {ECO:0000313|EMBL:AMZ75092.1};
- Comment: BPHYT_RS16925 = B2SYR4; Pf6N2E2_5970 = A0A161GM94
- Total: 2 characterized proteins
ptcA: galactose PTS system, EIIA component
- Curated sequence A2RIE7: PTS system galactose-specific EIIA component
- Ignore hits to Q9CIE9 when looking for 'other' hits (PTS system cellobiose-specific EIIA component. PtcA, component of The cellobiose-specific (PtcA-PtcB-CelB) porter (Kowalczyk et al., 2008 ))
- Comment: A close homolog of ptcAB from another strain of Lactococcus lactis is annotated as being cellobiose-specific
- Total: 1 characterized proteins
ptcB: galactose PTS system, EIIB component
- Curated sequence A2RIE6: PTS system galactose-specific EIIB component; Galactose-specific phosphotransferase enzyme IIB component; EC 2.7.1.204
- Ignore hits to Q9CIF0 when looking for 'other' hits (PTS system cellobiose-specific EIIB component; Cellobiose-specific phosphotransferase enzyme IIB component; EC 2.7.1.205. PtcB, component of The cellobiose-specific (PtcA-PtcB-CelB) porter (Kowalczyk et al., 2008 ))
- Total: 1 characterized proteins
ptcEIIC: galactose PTS system, EIIC component
galP: galactose:H+ symporter GalP
- 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 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 P0AE24: Arabinose-proton symporter; Arabinose transporter. Arabinose (xylose; galactose):H+ symporter, AraE (low affinity high capacity). arabinose:H+ symporter. arabinose:H+ symporter
- Curated sequence P96710: Arabinose-proton symporter; Arabinose transporter. L-arabinose:proton symporter, AraE (Sa-Nogueira and Ramos, 1997). Also transports xylose, galactose and α-1,5 arabinobiose
- 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
- Total: 5 characterized proteins
HP1174: Na+-dependent galactose transporter
- 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
- Total: 2 characterized proteins
gal2: galactose transporter
SGLT1: sodium/galactose cotransporter
- 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
- Total: 1 characterized proteins
CeSWEET1: galactose transporter
- Curated sequence O45102: Sugar transporter SWEET1; CeSWEET1. Golgi/E.R. Sweet1 glucose/galactose facilitator (Km ≥ 50mM)
- Total: 1 characterized proteins
sglS: sodium/galactose cotransporter
- 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
- UniProt sequence L0FZF3: SubName: Full=SSS sodium solute transporter {ECO:0000313|EMBL:AGA78126.1};
- UniProt sequence A0A1X9Z2P8: SubName: Full=Sodium transporter {ECO:0000313|EMBL:ARS39271.1};
- Comment: Echvi_1871 (L0FZF3) seems to be a glucose/galactose transporter. CA265_RS06130 (A0A1X9Z2P8) seems to be a galactose transporter.
- Total: 3 characterized proteins
MST1: galactose:H+ symporter
lacP: galactose:H+ symporter
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
lacC: D-tagatose-6-phosphate kinase
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
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
galK: galactokinase (-1-phosphate forming)
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
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
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
Links
Downloads
Related tools
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