GapMind for catabolism of small carbon sources

 

Protein WP_009134251.1 in Alistipes indistinctus YIT 12060

Annotation: NCBI__GCF_000231275.1:WP_009134251.1

Length: 217 amino acids

Source: GCF_000231275.1 in NCBI

Candidate for 87 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
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% 86% 155.2 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
L-glutamate catabolism gltL 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% 86% 155.2 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
L-arginine catabolism artP lo ABC transporter for L-Arginine, putative ATPase component (characterized) 39% 84% 154.8 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
L-citrulline catabolism AO353_03040 lo ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 35% 86% 147.1 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
L-lysine catabolism hisP lo ABC transporter for L-Lysine, ATPase component (characterized) 36% 86% 146 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 61% 144.8 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 61% 144.8 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 61% 144.8 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 61% 144.8 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 61% 144.8 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 61% 144.8 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 61% 144.8 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 61% 144.8 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
L-histidine catabolism BPHYT_RS24015 lo ABC transporter related (characterized, see rationale) 38% 86% 142.9 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
D-glucosamine (chitosamine) catabolism AO353_21725 lo ABC transporter for D-glucosamine, ATPase component (characterized) 36% 85% 141 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
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) 35% 85% 141 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
D-maltose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 39% 57% 140.6 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
D-maltose catabolism thuK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 39% 57% 140.6 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
putrescine catabolism potA lo spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) 37% 56% 140.6 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
sucrose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 39% 57% 140.6 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
trehalose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 39% 57% 140.6 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
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) 34% 79% 139.8 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
lactose catabolism lacK lo LacK, component of Lactose porter (characterized) 37% 58% 139.8 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
L-asparagine catabolism aatP lo Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 38% 89% 139.4 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
L-aspartate catabolism aatP lo Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 38% 89% 139.4 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 37% 61% 138.3 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
sucrose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 36% 62% 138.3 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
trehalose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 36% 62% 138.3 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
L-asparagine catabolism bgtA lo ATPase (characterized, see rationale) 38% 82% 137.1 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
L-aspartate catabolism bgtA lo ATPase (characterized, see rationale) 38% 82% 137.1 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 36% 58% 137.1 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 35% 58% 136.3 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 36% 60% 136 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 38% 55% 134.8 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 37% 60% 134.4 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 37% 60% 134.4 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
L-histidine catabolism aapP lo ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) 35% 83% 134.4 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
L-asparagine catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 36% 88% 134 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
L-aspartate catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 36% 88% 134 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
D-maltose catabolism malK lo Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 35% 56% 134 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
D-cellobiose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 34% 55% 133.3 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 34% 55% 133.3 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
D-glucose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 34% 55% 133.3 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
lactose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 34% 55% 133.3 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
D-maltose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 34% 55% 133.3 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
D-mannitol catabolism mtlK lo SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) 33% 63% 133.3 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
sucrose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 34% 55% 133.3 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
trehalose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 34% 55% 133.3 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 35% 55% 132.9 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
D-maltose catabolism malK1 lo MalK; aka Sugar ABC transporter, ATP-binding protein, component of The maltose, maltotriose, mannotetraose (MalE1)/maltose, maltotriose, trehalose (MalE2) porter (Nanavati et al., 2005). For MalG1 (823aas) and MalG2 (833aas), the C-terminal transmembrane domain with 6 putative TMSs is preceded by a single N-terminal TMS and a large (600 residue) hydrophilic region showing sequence similarity to MLP1 and 2 (9.A.14; e-12 & e-7) as well as other proteins (characterized) 35% 53% 132.5 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 37% 52% 132.5 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
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% 83% 131 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
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% 83% 131 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
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% 83% 131 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
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% 83% 131 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
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% 56% 131 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
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% 83% 131 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
L-tryptophan catabolism ecfA2 lo Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) 37% 74% 129 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
L-proline catabolism proV lo glycine betaine/l-proline transport atp-binding protein prov (characterized) 35% 50% 126.7 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
D-maltose catabolism musK lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 36% 56% 125.2 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 34% 58% 124.8 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
D-cellobiose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 33% 56% 122.9 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
D-glucose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 33% 56% 122.9 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
lactose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 33% 56% 122.9 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
D-maltose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 33% 56% 122.9 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
sucrose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 33% 56% 122.9 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
trehalose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 33% 56% 122.9 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 35% 62% 122.5 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
trehalose catabolism treV lo TreV, component of Trehalose porter (characterized) 32% 64% 120.9 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
trehalose catabolism malK lo MsmK aka SMU.882, component of The raffinose/stachyose transporter, MsmEFGK (MalK (3.A.1.1.27) can probably substitute for MsmK; Webb et al., 2008). This system may also transport melibiose, isomaltotriose and sucrose as well as isomaltosaccharides (characterized) 33% 50% 116.3 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
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) 34% 51% 115.5 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
L-histidine catabolism hutV lo HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) 30% 78% 111.7 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
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) 30% 78% 111.7 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
L-isoleucine catabolism livG lo High-affinity branched-chain amino acid ABC transporter ATP-binding protein LivG (characterized, see rationale) 31% 89% 110.2 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
L-phenylalanine catabolism livG lo High-affinity branched-chain amino acid ABC transporter ATP-binding protein LivG (characterized, see rationale) 31% 89% 110.2 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
L-arabinose catabolism xylGsa lo Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale) 31% 86% 106.3 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
D-lactate catabolism PGA1_c12640 lo D-lactate transporter, ATP-binding component (characterized) 30% 89% 104.8 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
glycerol catabolism glpT lo GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) 32% 55% 101.3 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
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) 32% 79% 100.9 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
glycerol catabolism glpS lo ABC transporter for Glycerol, ATPase component 1 (characterized) 32% 51% 99.4 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
L-isoleucine catabolism livF lo ABC transporter ATP-binding protein (characterized, see rationale) 32% 88% 98.6 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
L-leucine catabolism livF lo ABC transporter ATP-binding protein (characterized, see rationale) 32% 88% 98.6 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
L-phenylalanine catabolism livF lo ABC transporter ATP-binding protein (characterized, see rationale) 32% 88% 98.6 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
L-proline catabolism HSERO_RS00900 lo ABC transporter ATP-binding protein (characterized, see rationale) 32% 88% 98.6 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
L-serine catabolism Ac3H11_1692 lo ABC transporter ATP-binding protein (characterized, see rationale) 32% 88% 98.6 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
L-tyrosine catabolism Ac3H11_1692 lo ABC transporter ATP-binding protein (characterized, see rationale) 32% 88% 98.6 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6
D-cellobiose catabolism TM0028 lo TM0028, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized) 30% 66% 84.3 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 207.6

Sequence Analysis Tools

View WP_009134251.1 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

MIETKDVHKSFGTLEVLKGIDLRIDKGEVVSIVGPSGAGKTTLLQILGTLSRPTSGEVMI
DGTPVQMLSDKQISKFRNTKIGFVFQFHHLLPEFTAMENVCIPGYIARRDRTDVERQARE
LLEMLGMEHRTEHKPAELSGGEQQRVAIARALINSPAVLLADEPSGNLDTKNKEEIHKLF
FTLRDTLGQTVVIVTHDEQLARMSDREIMMVDGWIRP

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