GapMind for catabolism of small carbon sources

 

Protein 351279 in Bacteroides thetaiotaomicron VPI-5482

Annotation: BT1751 Glycine betaine transport ATP-binding protein (NCBI ptt file)

Length: 408 amino acids

Source: Btheta in FitnessBrowser

Candidate for 80 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-proline catabolism opuBA med BusAA, component of Uptake system for glycine-betaine (high affinity) and proline (low affinity) (OpuAA-OpuABC) or BusAA-ABC of Lactococcus lactis). BusAA, the ATPase subunit, has a C-terminal tandem cystathionine β-synthase (CBS) domain which is the cytoplasmic K+ sensor for osmotic stress (osmotic strength)while the BusABC subunit has the membrane and receptor domains fused to each other (Biemans-Oldehinkel et al., 2006; Mahmood et al., 2006; Gul et al. 2012). An N-terminal amphipathic α-helix of OpuA is necessary for high activity but is not critical for biogenesis or the ionic regulation of transport (characterized) 50% 97% 395.2 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5
L-proline catabolism proV med glycine betaine/l-proline transport atp-binding protein prov (characterized) 47% 99% 367.1 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5
L-histidine catabolism hutV med ABC transporter for L-Histidine, ATPase component (characterized) 56% 98% 317 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5
L-proline catabolism hutV med HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) 55% 97% 297.4 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5
putrescine catabolism potA lo Spermidine/putrescine import ATP-binding protein PotA, component of The spermidine/putrescine uptake porter, PotABCD (characterized) 41% 61% 192.2 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5
D-maltose catabolism malK1 lo MalK; aka Sugar ABC transporter, ATP-binding protein, component of The maltose, maltotriose, mannotetraose (MalE1)/maltose, maltotriose, trehalose (MalE2) porter (Nanavati et al., 2005). For MalG1 (823aas) and MalG2 (833aas), the C-terminal transmembrane domain with 6 putative TMSs is preceded by a single N-terminal TMS and a large (600 residue) hydrophilic region showing sequence similarity to MLP1 and 2 (9.A.14; e-12 & e-7) as well as other proteins (characterized) 43% 59% 188 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5
trehalose catabolism thuK lo MalK; aka Sugar ABC transporter, ATP-binding protein, component of The maltose, maltotriose, mannotetraose (MalE1)/maltose, maltotriose, trehalose (MalE2) porter (Nanavati et al., 2005). For MalG1 (823aas) and MalG2 (833aas), the C-terminal transmembrane domain with 6 putative TMSs is preceded by a single N-terminal TMS and a large (600 residue) hydrophilic region showing sequence similarity to MLP1 and 2 (9.A.14; e-12 & e-7) as well as other proteins (characterized) 43% 59% 188 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5
D-maltose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 40% 63% 179.5 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 41% 60% 179.1 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5
D-cellobiose catabolism gtsD lo GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 35% 72% 177.2 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5
D-glucose catabolism gtsD lo GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 35% 72% 177.2 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5
lactose catabolism gtsD lo GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 35% 72% 177.2 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5
D-maltose catabolism gtsD lo GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 35% 72% 177.2 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5
sucrose catabolism gtsD lo GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 35% 72% 177.2 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5
trehalose catabolism gtsD lo GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 35% 72% 177.2 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 40% 58% 177.2 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 39% 57% 174.5 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5
D-maltose catabolism musK lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 40% 58% 174.5 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5
D-mannose catabolism TT_C0211 lo 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 (characterized) 35% 85% 174.5 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5
sucrose catabolism thuK lo 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 (characterized) 35% 85% 174.5 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5
D-mannitol catabolism mtlK lo ABC transporter for D-mannitol and D-mannose, ATPase component (characterized) 35% 74% 173.7 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 36% 70% 172.9 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 39% 62% 170.6 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 41% 66% 170.6 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5
D-maltose catabolism malK_Aa lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 33% 83% 169.9 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5
trehalose catabolism treV lo TreV, component of Trehalose porter (characterized) 38% 70% 167.5 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 37% 67% 166.4 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 36% 69% 165.6 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 36% 69% 165.6 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component (characterized) 39% 59% 165.2 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5
D-maltose catabolism malK_Sm lo MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized) 32% 90% 164.9 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5
trehalose catabolism malK lo MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized) 32% 90% 164.9 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5
D-cellobiose catabolism msiK lo MsiK protein, component of The cellobiose/cellotriose (and possibly higher cellooligosaccharides), CebEFGMsiK [MsiK functions to energize several ABC transporters including those for maltose/maltotriose and trehalose] (characterized) 38% 58% 164.5 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5
L-histidine catabolism PA5503 lo Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) 39% 70% 162.9 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5
D-maltose catabolism malK lo ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized) 34% 80% 162.5 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5
L-arginine catabolism artP lo ABC transporter for L-Arginine, putative ATPase component (characterized) 38% 94% 161.8 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 35% 74% 160.6 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5
lactose catabolism lacK lo LacK, component of Lactose porter (characterized) 33% 88% 159.5 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5
D-maltose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 37% 64% 159.5 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5
sucrose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 37% 64% 159.5 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5
trehalose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 37% 64% 159.5 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 32% 80% 157.1 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 32% 80% 157.1 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 32% 80% 157.1 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 32% 80% 157.1 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5
L-asparagine catabolism glnQ lo Glutamine ABC transporter ATP-binding protein, component of Glutamine transporter, GlnQP. Takes up glutamine, asparagine and glutamate which compete for each other for binding both substrate and the transmembrane protein constituent of the system (Fulyani et al. 2015). Tandem substrate binding domains (SBDs) differ in substrate specificity and affinity, allowing cells to efficiently accumulate different amino acids via a single ABC transporter. Analysis revealed the roles of individual residues in determining the substrate affinity (characterized) 35% 98% 156.8 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5
L-glutamate catabolism gltL lo Glutamine ABC transporter ATP-binding protein, component of Glutamine transporter, GlnQP. Takes up glutamine, asparagine and glutamate which compete for each other for binding both substrate and the transmembrane protein constituent of the system (Fulyani et al. 2015). Tandem substrate binding domains (SBDs) differ in substrate specificity and affinity, allowing cells to efficiently accumulate different amino acids via a single ABC transporter. Analysis revealed the roles of individual residues in determining the substrate affinity (characterized) 35% 98% 156.8 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5
L-asparagine catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 38% 98% 156 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5
L-aspartate catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 38% 98% 156 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 39% 52% 153.3 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5
L-histidine catabolism hisP lo histidine transport ATP-binding protein hisP (characterized) 36% 95% 152.9 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5
L-lysine catabolism hisP lo histidine transport ATP-binding protein hisP (characterized) 36% 95% 152.9 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5
L-histidine catabolism Ac3H11_2560 lo ABC transporter for L-Histidine, ATPase component (characterized) 40% 76% 151.8 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 35% 61% 151 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5
L-asparagine catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 35% 89% 150.6 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5
L-aspartate catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 35% 89% 150.6 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5
L-asparagine catabolism aatP lo ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) 36% 94% 147.5 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5
L-aspartate catabolism aatP lo ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) 36% 94% 147.5 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5
D-cellobiose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 35% 70% 145.6 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5
D-glucose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 35% 70% 145.6 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5
lactose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 35% 70% 145.6 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5
D-maltose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 35% 70% 145.6 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5
sucrose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 35% 70% 145.6 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5
trehalose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 35% 70% 145.6 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5
L-asparagine catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 34% 87% 144.8 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5
L-aspartate catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 34% 87% 144.8 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5
L-glutamate catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 34% 87% 144.8 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5
L-histidine catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 34% 87% 144.8 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5
L-leucine catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 34% 87% 144.8 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5
L-proline catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 34% 87% 144.8 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5
L-citrulline catabolism AO353_03040 lo ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 32% 99% 142.5 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5
D-mannose catabolism TM1750 lo TM1750, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized) 36% 78% 142.5 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5
D-mannose catabolism TM1749 lo TM1749, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized) 35% 79% 141 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5
D-cellobiose catabolism cbtD lo CbtD, component of Cellobiose and cellooligosaccharide porter (characterized) 32% 82% 135.2 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5
L-tryptophan catabolism ecfA2 lo Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) 38% 78% 134 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5
L-tryptophan catabolism ecfA1 lo Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) 37% 74% 132.9 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5
glycerol catabolism glpS lo ABC transporter for Glycerol, ATPase component 1 (characterized) 32% 62% 125.9 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5
D-cellobiose catabolism cbtF lo CbtF, component of Cellobiose and cellooligosaccharide porter (characterized) 32% 72% 125.6 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5
D-cellobiose catabolism TM0027 lo TM0027, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized) 35% 88% 119.4 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5
D-cellobiose catabolism TM0028 lo TM0028, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized) 31% 72% 95.9 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5

Sequence Analysis Tools

View 351279 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

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Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices: TMHMM

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Sequence

MSKIEIKDLYLVFGNEKQKALKMLKEGKTKSEILKATGCTVAVKDANLSINEGEIFVIMG
LSGSGKSTLLRCINRLIRPTSGEVIINGTDIAKVSDKELLQIRRKELAMVFQNFGLLPHR
SVLHNIAFGLELQGVKKGEREQKAMESMQLVGLKGYENQMVSELSGGMQQRVGLARALAN
NPEVLLMDEAFSALDPLIRVQMQDELLTLQSKMKKTIVFITHDLSEAIKLGDRIAIMKDG
EIVQIGTSEEILTEPANAYVERFVENVDRSKIITASSVMVDKPIVARLKKEGPEVLIRKM
RERNLTVLPVVDSNNLLVGEVRLNDLLKLRKEQIRSIESVVRHEVHSVLGDTVLEDILPL
MTKTNSPIWVVNENREFEGVVPLSSLIIEVTGKDKEEINEIIQNAIEL

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

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:

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. Gaps may be due to:

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, 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