GapMind for catabolism of small carbon sources

 

Protein WP_083509566.1 in Hyphomicrobium sulfonivorans WDL6

Annotation: NCBI__GCF_001541235.1:WP_083509566.1

Length: 392 amino acids

Source: GCF_001541235.1 in NCBI

Candidate for 94 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
N-acetyl-D-glucosamine catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 40% 79% 199.9 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
D-glucosamine (chitosamine) catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 40% 79% 199.9 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
D-glucosamine (chitosamine) catabolism AO353_21725 med ABC transporter for D-glucosamine, ATPase component (characterized) 42% 91% 164.9 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
L-histidine catabolism Ac3H11_2560 med ABC transporter for L-Histidine, ATPase component (characterized) 42% 87% 163.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
L-asparagine catabolism aatP med ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) 40% 91% 156.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
L-aspartate catabolism aatP med ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) 40% 91% 156.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
L-glutamate catabolism gltL med ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) 40% 91% 156.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
putrescine catabolism potA lo spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) 38% 89% 212.6 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
D-maltose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 38% 96% 205.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
trehalose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 38% 96% 205.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
sucrose catabolism thuK lo ABC transporter (characterized, see rationale) 36% 92% 205.3 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
D-maltose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 37% 97% 204.9 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
sucrose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 37% 97% 204.9 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
trehalose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 37% 97% 204.9 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 35% 95% 202.6 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
lactose catabolism lacK lo LacK, component of Lactose porter (characterized) 37% 97% 200.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 95% 199.9 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 95% 199.9 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 95% 199.9 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 95% 199.9 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 95% 199.9 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 95% 199.9 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 95% 199.9 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 95% 199.9 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
D-maltose catabolism malK lo Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 35% 95% 197.2 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
D-mannitol catabolism mtlK lo SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) 37% 95% 197.2 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 40% 74% 196.1 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
D-cellobiose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 34% 93% 196.1 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 34% 93% 196.1 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
D-glucose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 34% 93% 196.1 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
lactose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 34% 93% 196.1 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
D-maltose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 34% 93% 196.1 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
sucrose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 34% 93% 196.1 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
trehalose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 34% 93% 196.1 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 38% 89% 193.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 34% 93% 191 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 38% 80% 189.1 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
D-maltose catabolism malK_Aa lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 35% 95% 189.1 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 37% 81% 186.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 35% 97% 186.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 38% 81% 186 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
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) 36% 96% 186 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
D-cellobiose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 34% 95% 185.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
D-glucose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 34% 95% 185.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
lactose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 34% 95% 185.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
D-maltose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 34% 95% 185.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
sucrose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 34% 95% 185.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
trehalose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 34% 95% 185.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
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) 36% 86% 184.9 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
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) 35% 98% 184.1 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 36% 78% 183.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 36% 78% 183.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 36% 78% 183.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 36% 78% 183.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
D-maltose catabolism musK lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 37% 84% 182.6 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
L-proline catabolism proV lo Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized) 34% 83% 181 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 32% 99% 172.9 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
L-proline catabolism opuBA lo 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) 32% 87% 169.9 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 41% 54% 169.9 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
glycerol catabolism glpS lo ABC transporter for Glycerol, ATPase component 1 (characterized) 32% 95% 167.9 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
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% 98% 166 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
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% 98% 166 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
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) 37% 90% 163.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
L-asparagine catabolism bgtA lo ATPase (characterized, see rationale) 38% 95% 162.9 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
L-aspartate catabolism bgtA lo ATPase (characterized, see rationale) 38% 95% 162.9 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
trehalose catabolism treV lo TreV, component of Trehalose porter (characterized) 36% 73% 162.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
L-histidine catabolism hutV lo ABC transporter for L-Histidine, ATPase component (characterized) 39% 88% 160.2 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
L-arginine catabolism artP lo Arginine transport ATP-binding protein ArtM (characterized) 37% 94% 159.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
L-histidine catabolism bgtA lo BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 37% 97% 159.1 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
L-lysine catabolism hisP lo BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 37% 97% 159.1 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
L-proline catabolism hutV lo HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) 37% 87% 157.1 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
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) 33% 98% 154.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
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) 33% 98% 154.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
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) 33% 98% 154.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
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) 33% 98% 154.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
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) 33% 98% 154.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
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) 33% 98% 154.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
L-asparagine catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 33% 91% 152.9 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
L-aspartate catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 33% 91% 152.9 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
D-alanine catabolism Pf6N2E2_5405 lo ABC transporter for D-Alanine, ATPase component (characterized) 34% 94% 149.1 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
L-histidine catabolism BPHYT_RS24015 lo ABC transporter related (characterized, see rationale) 37% 92% 142.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
L-asparagine catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 31% 100% 136.3 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
L-aspartate catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 31% 100% 136.3 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
L-citrulline catabolism AO353_03040 lo ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 34% 93% 136 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
L-histidine catabolism hisP lo Histidine transport ATP-binding protein HisP (characterized) 34% 91% 133.3 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
L-tryptophan catabolism ecfA1 lo Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) 32% 91% 124.8 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
L-arabinose catabolism xylGsa lo Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale) 34% 90% 119.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
myo-inositol catabolism PGA1_c07320 lo Inositol transport system ATP-binding protein (characterized) 31% 88% 117.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
D-cellobiose catabolism mglA lo glucose transporter, ATPase component (characterized) 30% 87% 95.1 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
D-glucose catabolism mglA lo glucose transporter, ATPase component (characterized) 30% 87% 95.1 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
lactose catabolism mglA lo glucose transporter, ATPase component (characterized) 30% 87% 95.1 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
D-maltose catabolism mglA lo glucose transporter, ATPase component (characterized) 30% 87% 95.1 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
sucrose catabolism mglA lo glucose transporter, ATPase component (characterized) 30% 87% 95.1 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8
trehalose catabolism mglA lo glucose transporter, ATPase component (characterized) 30% 87% 95.1 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 228.8

Sequence Analysis Tools

View WP_083509566.1 at NCBI

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MSSSQTASHSDAPSVDVPDVARRSAAGAAAGDAGKGRAAAAFSACLTFEDVRRNFGTTQA
LAGVSLEIDRGEVVCLLGPSGCGKTTLLRIAAGIERPTGGRVLINGHEVAGPSSFVVPEK
RSVGLMFQDFALFPHLTIAGNVAFGLKSLPRAEAKREALAALKRVGLEHMADEYPHVLSG
GQQQRVALARALVPRPAVMLMDEPFSGLDVQLRDAMQEETLSLLRETGATAMVVTHNPEE
AMRIGDRIVVMRAGGLIQQGQAEALYHQPADLFVARLFSEINEVAYRVGADGKIDTPIGK
LSPPAGLQAHDAVTIGVRERDIRLSDNGEGLSGRVLDAKFLGDVVRLEVGIEGFDQPLKV
RVRESAGFRQGHDVRAQIDPERALVFAAELQK

This GapMind analysis is from Apr 09 2024. 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 (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:

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. 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:

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