GapMind for catabolism of small carbon sources

 

Protein WP_091367688.1 in Mucilaginibacter mallensis MP1X4

Annotation: NCBI__GCF_900105165.1:WP_091367688.1

Length: 343 amino acids

Source: GCF_900105165.1 in NCBI

Candidate for 85 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 med Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) 41% 100% 270 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
L-asparagine catabolism peb1C med PEB1C, component of Uptake system for glutamate and aspartate (characterized) 41% 99% 183.7 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
L-aspartate catabolism peb1C med PEB1C, component of Uptake system for glutamate and aspartate (characterized) 41% 99% 183.7 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
L-glutamate catabolism gltL med PEB1C, component of Uptake system for glutamate and aspartate (characterized) 41% 99% 183.7 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
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% 98% 176.4 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
L-arginine catabolism artP med BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 40% 86% 157.5 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
L-histidine catabolism bgtA med BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 40% 86% 157.5 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
L-lysine catabolism hisP med BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 40% 86% 157.5 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
L-histidine catabolism hisP lo Probable ATP-binding component of ABC transporter, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized) 38% 96% 173.7 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
L-asparagine catabolism bgtA lo ATPase (characterized, see rationale) 38% 92% 169.1 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
L-aspartate catabolism bgtA lo ATPase (characterized, see rationale) 38% 92% 169.1 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
putrescine catabolism potA lo PotG aka B0855, component of Putrescine porter (characterized) 35% 72% 168.7 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 31% 87% 168.3 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 31% 87% 168.3 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 31% 87% 168.3 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 31% 87% 168.3 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
L-asparagine catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 36% 91% 166 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
L-aspartate catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 36% 91% 166 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
L-histidine catabolism aapP lo ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) 36% 93% 166 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
L-histidine catabolism BPHYT_RS24015 lo ABC transporter related (characterized, see rationale) 37% 96% 165.6 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
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) 36% 59% 164.5 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
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) 35% 93% 162.2 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
L-asparagine catabolism aatP lo Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 37% 100% 162.2 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
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) 35% 93% 162.2 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
L-aspartate catabolism aatP lo Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 37% 100% 162.2 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
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) 35% 93% 162.2 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
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) 35% 93% 162.2 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
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) 35% 93% 162.2 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
L-citrulline catabolism PS417_17605 lo 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) 36% 88% 158.7 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
D-alanine catabolism Pf6N2E2_5405 lo ABC transporter for D-Alanine, ATPase component (characterized) 34% 95% 158.3 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
L-proline catabolism proV lo Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized) 34% 63% 158.3 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
L-citrulline catabolism AO353_03040 lo ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 33% 98% 157.9 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
D-glucosamine (chitosamine) catabolism AO353_21725 lo ABC transporter for D-Glucosamine, putative ATPase component (characterized) 34% 95% 157.1 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
L-histidine catabolism hutV lo ABC transporter for L-Histidine, ATPase component (characterized) 34% 95% 151 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 65% 149.8 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 65% 149.8 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 65% 149.8 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 65% 149.8 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 65% 149.8 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 65% 149.8 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 65% 149.8 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 65% 149.8 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
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) 33% 64% 149.1 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
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) 33% 64% 149.1 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 32% 75% 147.9 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 32% 75% 147.9 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
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) 34% 72% 147.9 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
D-maltose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 35% 64% 146.7 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
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) 34% 95% 146 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
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% 77% 144.1 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 34% 63% 142.9 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
D-maltose catabolism malK lo Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 33% 66% 142.5 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
D-cellobiose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 33% 60% 141.7 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
D-glucose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 33% 60% 141.7 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
lactose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 33% 60% 141.7 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
D-maltose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 33% 60% 141.7 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
sucrose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 33% 60% 141.7 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
trehalose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 33% 60% 141.7 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 33% 60% 141.7 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 32% 70% 139.8 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
D-cellobiose catabolism cbtF lo CbtF, component of Cellobiose and cellooligosaccharide porter (characterized) 35% 77% 138.7 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 31% 67% 138.7 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 32% 69% 134.4 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 32% 62% 132.9 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 32% 62% 132.5 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
D-maltose catabolism musK lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 33% 58% 132.5 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
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) 32% 80% 132.1 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
D-cellobiose catabolism cbtD lo CbtD, component of Cellobiose and cellooligosaccharide porter (characterized) 33% 70% 130.2 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 33% 54% 128.3 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
L-isoleucine catabolism livG lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 31% 93% 124.8 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
L-leucine catabolism livG lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 31% 93% 124.8 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
L-valine catabolism livG lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 31% 93% 124.8 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
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) 30% 65% 119.8 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
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) 30% 65% 119.8 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
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% 88% 114.4 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
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% 88% 114.4 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
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% 88% 114.4 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
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% 88% 114.4 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
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% 88% 114.4 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
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% 88% 114.4 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
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% 88% 114.4 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
glycerol catabolism glpS lo ABC transporter for Glycerol, ATPase component 1 (characterized) 32% 61% 109.8 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
D-lactate catabolism PGA1_c12640 lo D-lactate transporter, ATP-binding component (characterized) 30% 91% 109.4 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
citrate catabolism fecE lo iron(III) dicitrate transport ATP-binding protein FecE (characterized) 31% 89% 104.4 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0
D-galactose catabolism BPHYT_RS16930 lo Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale) 30% 53% 96.3 Methionine import ATP-binding protein MetN; EC 7.4.2.11 66% 448.0

Sequence Analysis Tools

View WP_091367688.1 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

MIELRNITKTFYKKNSQVSALSNVSLIVPKGKILGVIGASGAGKSTLIRCVNLLERPTSG
EVIIGGLNLTQLAPSALAKARREIGMIFQHFNLLSSRTVAGNVAFPLELSNRPGDEIKKR
VAELLELVGLGDKANEYPANLSGGQKQRVAIARTLANNPRVLLCDEATSALDPATTLSIL
NLLKDINKRFQITILLITHEMNVVKAICDEVAIISEGKLIERGSISEVFAYPETTIAKQF
IASSLHATLPAEYEQRLSATPAGKNHPVIKLEFNGHSAEASILSEASRMFQVDNNIISAQ
MDYTGGVKYGVMLIEVTGSKKDTQNSLEYYRSKHIEVEVLGYV

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