GapMind for catabolism of small carbon sources

 

Protein WP_021235484.1 in Novosphingobium lindaniclasticum LE124

Annotation: NCBI__GCF_000445125.1:WP_021235484.1

Length: 321 amino acids

Source: GCF_000445125.1 in NCBI

Candidate for 82 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-histidine catabolism PA5503 hi Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) 58% 97% 354.8 Methionine import ATP-binding protein MetN; EC 7.4.2.11 47% 290.0
L-glutamate catabolism gltL med GluA aka CGL1950, component of Glutamate porter (characterized) 46% 98% 196.4 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8
L-citrulline catabolism PS417_17605 med ATP-binding cassette domain-containing protein; SubName: Full=Amino acid transporter; SubName: Full=Histidine ABC transporter ATP-binding protein; SubName: Full=Histidine transport system ATP-binding protein (characterized, see rationale) 42% 89% 181.4 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8
L-asparagine catabolism aatP med ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) 43% 96% 181 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8
L-aspartate catabolism aatP med ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) 43% 96% 181 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8
L-lysine catabolism hisP med Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) 41% 92% 181 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8
L-arginine catabolism artP med Arginine transport ATP-binding protein ArtM (characterized) 40% 99% 180.6 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8
L-histidine catabolism hisP med Histidine transport ATP-binding protein HisP (characterized) 42% 94% 179.5 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8
L-asparagine catabolism bgtA med ATPase (characterized, see rationale) 43% 92% 178.7 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8
L-aspartate catabolism bgtA med ATPase (characterized, see rationale) 43% 92% 178.7 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8
L-histidine catabolism BPHYT_RS24015 med ABC transporter related (characterized, see rationale) 41% 94% 174.9 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8
L-histidine catabolism hutV med ABC transporter for L-Histidine, ATPase component (characterized) 44% 77% 174.9 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8
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) 44% 84% 174.5 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8
L-histidine catabolism bgtA med BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 43% 96% 170.2 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8
L-asparagine catabolism glnQ med 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) 40% 97% 169.1 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8
L-citrulline catabolism AO353_03040 lo ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 40% 97% 176.4 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8
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) 39% 57% 174.5 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8
L-proline catabolism proV lo glycine betaine/l-proline transport atp-binding protein prov (characterized) 40% 59% 167.9 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8
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) 38% 92% 165.6 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8
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) 38% 92% 165.6 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8
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) 38% 92% 165.6 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8
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) 38% 92% 165.6 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8
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) 38% 92% 165.6 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8
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) 38% 92% 165.6 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8
D-glucosamine (chitosamine) catabolism AO353_21725 lo ABC transporter for D-glucosamine, ATPase component (characterized) 38% 94% 164.5 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8
L-asparagine catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 35% 91% 161.4 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8
L-aspartate catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 35% 91% 161.4 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8
D-alanine catabolism Pf6N2E2_5405 lo ABC transporter for D-Alanine, ATPase component (characterized) 37% 94% 161 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8
L-asparagine catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 37% 98% 159.8 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8
L-aspartate catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 37% 98% 159.8 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8
putrescine catabolism potA lo spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) 32% 84% 158.3 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8
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% 75% 157.1 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 38% 63% 152.5 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 38% 63% 152.5 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 35% 66% 151.8 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 35% 66% 151.8 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 35% 66% 151.8 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 35% 66% 151.8 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8
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) 33% 75% 142.1 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 72% 141.4 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 72% 141.4 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 72% 141.4 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 72% 141.4 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 72% 141.4 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 72% 141.4 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 72% 141.4 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 72% 141.4 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8
sucrose catabolism thuK lo ABC transporter (characterized, see rationale) 36% 59% 137.9 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 32% 69% 136.7 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8
D-mannitol catabolism mtlK lo ABC transporter for D-mannitol and D-mannose, ATPase component (characterized) 34% 60% 135.6 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8
L-tryptophan catabolism ecfA1 lo Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) 37% 74% 134.8 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8
L-tryptophan catabolism ecfA2 lo Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) 36% 78% 134.8 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 36% 55% 134.4 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8
D-maltose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 34% 66% 133.3 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8
trehalose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 34% 66% 133.3 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8
trehalose catabolism treV lo TreV, component of Trehalose porter (characterized) 30% 72% 133.3 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8
D-cellobiose catabolism cbtF lo CbtF, component of Cellobiose and cellooligosaccharide porter (characterized) 35% 73% 130.6 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8
D-cellobiose catabolism cbtD lo CbtD, component of Cellobiose and cellooligosaccharide porter (characterized) 34% 70% 127.5 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8
D-maltose catabolism musK lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 34% 57% 126.3 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8
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) 31% 75% 123.6 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8
L-alanine catabolism braF lo NatA, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 32% 91% 122.9 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8
L-isoleucine catabolism natA lo NatA, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 32% 91% 122.9 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8
L-leucine catabolism natA lo NatA, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 32% 91% 122.9 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8
L-proline catabolism natA lo NatA, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 32% 91% 122.9 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8
L-serine catabolism braF lo NatA, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 32% 91% 122.9 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8
L-threonine catabolism braF lo NatA, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 32% 91% 122.9 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8
L-valine catabolism natA lo NatA, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 32% 91% 122.9 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8
D-cellobiose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 31% 68% 119.8 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8
D-glucose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 31% 68% 119.8 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8
lactose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 31% 68% 119.8 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8
D-maltose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 31% 68% 119.8 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8
sucrose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 31% 68% 119.8 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8
trehalose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 31% 68% 119.8 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 31% 68% 119.8 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8
L-isoleucine catabolism livG lo High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter (characterized) 31% 98% 119 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8
L-leucine catabolism livG lo High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter (characterized) 31% 98% 119 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8
L-phenylalanine catabolism livG lo High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter (characterized) 31% 98% 119 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8
L-valine catabolism livG lo High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter (characterized) 31% 98% 119 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8
L-arabinose catabolism xylGsa lo Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale) 32% 86% 117.9 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8
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) 31% 86% 117.9 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8
L-histidine catabolism natA lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 32% 92% 116.7 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8
glycerol catabolism glpS lo GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized) 31% 62% 114 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 58% 354.8

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Sequence

MIRLEGVHKAFGGGHAALAGVDLEIGRGQVFGIIGRSGAGKSTLVRLLNGLERPTAGRVL
IDGTDVAVLSAEGLRGLRSRVGMIFQNFGLLWSRTVFDNVALPLRIGGASRAQIAAKVPA
LLDRVGLSDHGAKYPAQLSGGQKQRVGIARALATDPEILLCDEATSALDPETTRSILDLV
ADLNRELGLTIVLITHEMEVVRQVCDRVVVLHAGRVVEAGEVAEVFLHPRAPETRALIDE
TDGDVQPLGFDGPVVRLTLHGQAILDPVLTRIARDTGTDFIILDGRIGRLKNTSFGRLSL
GLVGGDTDRAIAALRLEGDVE

This GapMind analysis is from Sep 24 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 (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