GapMind for catabolism of small carbon sources

 

Protein WP_068863546.1 in Porphyrobacter dokdonensis DSW-74

Annotation: NCBI__GCF_001677335.1:WP_068863546.1

Length: 260 amino acids

Source: GCF_001677335.1 in NCBI

Candidate for 75 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-proline catabolism opuBA med 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) 43% 73% 183.3 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 46% 218.8
L-histidine catabolism Ac3H11_2560 med ABC transporter for L-Histidine, ATPase component (characterized) 41% 73% 123.2 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 46% 218.8
putrescine catabolism potA lo PotG aka B0855, component of Putrescine porter (characterized) 43% 58% 170.2 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 46% 218.8
sucrose catabolism thuK lo ABC transporter (characterized, see rationale) 39% 65% 167.5 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 46% 218.8
D-maltose catabolism malK lo Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 38% 64% 163.7 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 46% 218.8
L-histidine catabolism hutV lo ABC transporter for L-Histidine, ATPase component (characterized) 39% 83% 160.2 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 46% 218.8
L-proline catabolism proV lo glycine betaine/l-proline transport atp-binding protein prov (characterized) 40% 56% 158.7 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 46% 218.8
D-maltose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 37% 70% 156.8 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 46% 218.8
trehalose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 37% 70% 156.8 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 46% 218.8
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 36% 71% 156 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 46% 218.8
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 36% 71% 156 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 46% 218.8
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 37% 65% 154.5 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 46% 218.8
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) 39% 65% 153.7 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 46% 218.8
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 35% 76% 153.3 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 46% 218.8
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 39% 64% 153.3 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 46% 218.8
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 39% 56% 152.9 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 46% 218.8
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 34% 66% 152.9 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 46% 218.8
L-histidine catabolism PA5503 lo Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) 42% 66% 152.9 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 46% 218.8
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) 38% 83% 152.9 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 46% 218.8
D-cellobiose catabolism gtsD 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) 37% 66% 152.5 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 46% 218.8
D-glucose catabolism gtsD 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) 37% 66% 152.5 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 46% 218.8
lactose catabolism gtsD 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) 37% 66% 152.5 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 46% 218.8
D-maltose catabolism gtsD 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) 37% 66% 152.5 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 46% 218.8
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) 37% 66% 152.5 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 46% 218.8
sucrose catabolism gtsD 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) 37% 66% 152.5 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 46% 218.8
trehalose catabolism gtsD 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) 37% 66% 152.5 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 46% 218.8
lactose catabolism lacK lo ABC transporter for Lactose, ATPase component (characterized) 36% 68% 150.2 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 46% 218.8
D-mannitol catabolism mtlK lo SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) 33% 71% 148.7 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 46% 218.8
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 35% 68% 148.3 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 46% 218.8
L-arginine catabolism artP lo Arginine transport ATP-binding protein ArtM (characterized) 36% 99% 146 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 46% 218.8
D-maltose catabolism musK lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 36% 66% 146 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 46% 218.8
L-tryptophan catabolism ecfA2 lo Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) 40% 83% 145.6 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 46% 218.8
D-alanine catabolism Pf6N2E2_5405 lo ABC transporter for D-Alanine, ATPase component (characterized) 35% 89% 143.7 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 46% 218.8
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) 34% 67% 143.7 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 46% 218.8
L-asparagine catabolism aatP lo ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) 39% 89% 142.5 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 46% 218.8
L-aspartate catabolism aatP lo ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) 39% 89% 142.5 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 46% 218.8
L-glutamate catabolism gltL lo ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) 39% 89% 142.5 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 46% 218.8
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 33% 71% 142.5 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 46% 218.8
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 35% 62% 142.1 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 46% 218.8
L-histidine catabolism aapP lo ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) 35% 88% 141 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 46% 218.8
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 34% 68% 140.6 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 46% 218.8
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) 36% 83% 140.2 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 46% 218.8
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) 36% 83% 140.2 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 46% 218.8
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) 36% 83% 140.2 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 46% 218.8
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) 36% 83% 140.2 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 46% 218.8
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) 36% 83% 140.2 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 46% 218.8
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) 35% 61% 136 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 46% 218.8
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) 35% 61% 136 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 46% 218.8
D-glucosamine (chitosamine) catabolism AO353_21725 lo ABC transporter for D-Glucosamine, putative ATPase component (characterized) 36% 91% 135.6 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 46% 218.8
L-asparagine catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 35% 80% 135.2 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 46% 218.8
L-aspartate catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 35% 80% 135.2 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 46% 218.8
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) 37% 89% 135.2 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 46% 218.8
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 60% 133.7 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 46% 218.8
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 60% 133.7 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 46% 218.8
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 60% 133.7 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 46% 218.8
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 60% 133.7 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 46% 218.8
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 60% 133.7 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 46% 218.8
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 60% 133.7 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 46% 218.8
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 60% 133.7 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 46% 218.8
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 60% 133.7 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 46% 218.8
glycerol catabolism glpT lo GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) 35% 55% 119.8 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 46% 218.8
D-cellobiose catabolism cbtD lo CbtD, component of Cellobiose and cellooligosaccharide porter (characterized) 33% 69% 116.3 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 46% 218.8
myo-inositol catabolism PGA1_c07320 lo Inositol transport system ATP-binding protein (characterized) 32% 100% 115.2 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 46% 218.8
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% 74% 112.8 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 46% 218.8
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) 31% 92% 111.7 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 46% 218.8
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) 31% 92% 111.7 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 46% 218.8
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) 31% 92% 111.7 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 46% 218.8
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) 31% 92% 111.7 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 46% 218.8
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) 31% 92% 111.7 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 46% 218.8
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) 31% 92% 111.7 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 46% 218.8
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) 31% 92% 111.7 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 46% 218.8
L-arabinose catabolism xylGsa lo Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale) 34% 86% 110.5 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 46% 218.8
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) 34% 69% 108.2 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 46% 218.8
D-cellobiose catabolism cbtF lo CbtF, component of Cellobiose and cellooligosaccharide porter (characterized) 33% 65% 101.7 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 46% 218.8
L-histidine catabolism natA lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 30% 88% 100.9 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 46% 218.8

Sequence Analysis Tools

View WP_068863546.1 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

MTSRDPLLRFEGAARAYGDVLAVAGVTCSIAAGSFVALVGASGSGKSTLLKMVNTLVEPT
AGRVLFGGEDVASLHPAHLRRRVGYVFQGIGLFPHMSVAENIAIGPRLTGEKLPDKRIAE
LLELVELEPAMGSRMPDELSGGQRQRVGVARALAGEPELLLMDEPFGALDPLTRDALGTK
VRELHDTLGLTTVMVTHDMAEALLLADRVLVMDAGALVADESPRALLAGAGGEIAQGLVS
VPRQQAERLAALEGVGETRR

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