GapMind for catabolism of small carbon sources

 

Protein WP_025329853.1 in Snodgrassella alvi wkB2

Annotation: NCBI__GCF_000600005.1:WP_025329853.1

Length: 360 amino acids

Source: GCF_000600005.1 in NCBI

Candidate for 90 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
putrescine catabolism potA med spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) 42% 77% 240.4 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
D-maltose catabolism malK_Bb med ABC-type maltose transport, ATP binding protein (characterized, see rationale) 41% 71% 201.1 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
N-acetyl-D-glucosamine catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 42% 70% 194.5 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
D-glucosamine (chitosamine) catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 42% 70% 194.5 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
L-histidine catabolism Ac3H11_2560 med ABC transporter for L-Histidine, ATPase component (characterized) 42% 76% 141 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
sucrose catabolism thuK lo ABC transporter (characterized, see rationale) 44% 62% 215.7 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
trehalose catabolism thuK lo Trehalose import ATP-binding protein SugC; EC 7.5.2.- (characterized) 38% 78% 211.1 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
D-maltose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 37% 88% 210.7 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 38% 89% 208.8 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 38% 80% 207.2 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
lactose catabolism lacK lo ABC transporter for Lactose, ATPase component (characterized) 35% 97% 206.1 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
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) 37% 88% 204.5 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
D-cellobiose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 36% 96% 204.1 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 36% 96% 204.1 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
D-glucose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 36% 96% 204.1 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
lactose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 36% 96% 204.1 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
D-maltose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 36% 96% 204.1 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
sucrose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 36% 96% 204.1 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
trehalose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 36% 96% 204.1 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
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) 35% 85% 202.6 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 34% 92% 201.8 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 34% 92% 201.8 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 34% 92% 201.8 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 34% 92% 201.8 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 34% 92% 201.8 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 34% 92% 201.8 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 34% 92% 201.8 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 34% 92% 201.8 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 32% 96% 200.7 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
D-maltose catabolism malK lo Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 37% 80% 199.9 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
D-maltose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 35% 89% 198.4 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
sucrose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 35% 89% 198.4 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
trehalose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 35% 89% 198.4 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 34% 92% 196.4 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
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) 37% 75% 196.1 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 36% 91% 195.3 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
D-maltose catabolism malK_Aa lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 35% 84% 194.9 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
D-maltose catabolism musK lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 37% 72% 194.1 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 35% 90% 193.7 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
D-mannitol catabolism mtlK lo ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component (characterized) 41% 63% 191.8 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 36% 76% 191 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 36% 78% 190.3 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
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) 33% 88% 190.3 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
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) 33% 88% 190.3 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 34% 84% 188 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 34% 84% 188 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 34% 84% 188 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 34% 84% 188 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 33% 93% 186.4 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
D-cellobiose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 67% 179.5 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
D-glucose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 67% 179.5 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
lactose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 67% 179.5 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
D-maltose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 67% 179.5 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
sucrose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 67% 179.5 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
trehalose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 67% 179.5 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
trehalose catabolism treV lo TreV, component of Trehalose porter (characterized) 35% 91% 176 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
L-proline catabolism opuBA lo BilEA aka OpuBA protein, component of A proline/glycine betaine uptake system. Also reported to be a bile exclusion system that exports oxgall and other bile compounds, BilEA/EB or OpuBA/BB (required for normal virulence) (characterized) 37% 76% 167.9 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
L-asparagine catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 37% 98% 166 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
L-aspartate catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 37% 98% 166 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
L-glutamate catabolism gltL lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 37% 98% 166 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
L-histidine catabolism aapP lo ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) 36% 93% 162.2 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
L-arginine catabolism artP lo Arginine transport ATP-binding protein ArtM (characterized) 35% 99% 161.4 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
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) 34% 93% 159.8 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
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) 34% 93% 159.8 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
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) 34% 93% 159.8 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
glycerol catabolism glpT lo GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) 34% 81% 159.8 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
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) 34% 93% 159.8 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
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) 34% 93% 159.8 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
L-asparagine catabolism aatP lo Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 34% 99% 157.9 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
L-aspartate catabolism aatP lo Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 34% 99% 157.9 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
L-histidine catabolism bgtA lo BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 36% 96% 151.8 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
L-lysine catabolism hisP lo BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 36% 96% 151.8 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
L-histidine catabolism hisP lo histidine transport ATP-binding protein hisP (characterized) 35% 96% 142.5 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
glycerol catabolism glpS lo GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized) 36% 65% 137.5 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
L-citrulline catabolism AO353_03040 lo ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 31% 98% 136 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
L-tryptophan catabolism ecfA2 lo Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) 32% 97% 132.5 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
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% 98% 126.7 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
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% 98% 126.7 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
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% 98% 126.7 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
L-arabinose catabolism xylGsa lo Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale) 31% 98% 114.4 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
L-isoleucine catabolism livF lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 31% 97% 108.2 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
L-leucine catabolism livF lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 31% 97% 108.2 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
L-valine catabolism livF lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 31% 97% 108.2 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
L-alanine catabolism braG lo NatE, 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) 30% 90% 99 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
L-isoleucine catabolism natE lo NatE, 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) 30% 90% 99 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
L-leucine catabolism natE lo NatE, 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) 30% 90% 99 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
L-proline catabolism natE lo NatE, 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) 30% 90% 99 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
L-serine catabolism braG lo NatE, 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) 30% 90% 99 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
L-threonine catabolism braG lo NatE, 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) 30% 90% 99 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8
L-valine catabolism natE lo NatE, 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) 30% 90% 99 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 312.8

Sequence Analysis Tools

View WP_025329853.1 at NCBI

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

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Compare to protein structures

Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MSIRIKQLNKYYGDYQALQNINLQVPTGSLTALLGPSGCGKTTLLRIIAGLERADSGELF
FADDEVSNLHVRERRVGFMFQHYALFRHMTVFDNVAFGLQVLPKRIRPNKAEIADRVHEL
LQLVQLDWLAKVYPQQLSGGQRQRIALARALATRPKLLLLDEPFGALDAKVRKELRQWLL
EIHHQLGITSVLVTHDQEEALEMAEQIVVMNQGKVEQSGAASSLYDNPENVFVTEFLGEV
NVFEDACIEHGQLCLGHYHEPITTGEKARQNVAVYIRPQEVQVLTHIQDNIIASACVEKI
HAIGAQIRLWLRREDNNQRIQVWLSPAEFRTLSLQPAQTVWFRPQRLTMFRLPEMVDYVI

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