Definition of D-galactose catabolism

GapMind for catabolism of small carbon sources

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:

mglA, mglB and mglC
or ytfQ, ytfR, ytfT and yjtF
or gguA, gguB and chvE
or glcS, glcT, glcU and glcV
or PfGW456L13_1894, PfGW456L13_1895, PfGW456L13_1896 and PfGW456L13_1897
or BPHYT_RS16935, BPHYT_RS16930 and BPHYT_RS16925
or galP
or HP1174
or gal2
or SGLT1
or CeSWEET1
or sglS
or MST1
or lacP
Comment: Transporters and PTS systems were identified using: query: transporter:galactose:D-galactose:D-galactofuranose:D-galactopyranose:CPD0-2486:CPD0-2485:alpha-d-galactose:CPD-15590

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)

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

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

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

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

Curated sequence A2RJV0: PTS system galactose-specific EIIC component
Total: 1 characterized proteins

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

Curated sequence CH_091029: galactose transporter. Galactose, glucose uniporter, Gal2. Also transports xylose
Total: 1 characterized proteins

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

Curated sequence A0ZXK6: The monosaccharide (MST) (glucose > mannose > galactose > fructose):H+ symporter, MST1
Total: 1 characterized proteins

lacP: galactose:H+ symporter

Curated sequence P07921: Lactose, galactose:H+ symporter
Total: 1 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

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)

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

Downloads

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

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 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