GapMind for catabolism of small carbon sources

 

Protein WP_057508907.1 in Stenotrophomonas chelatiphaga DSM 21508

Annotation: NCBI__GCF_001431535.1:WP_057508907.1

Length: 335 amino acids

Source: GCF_001431535.1 in NCBI

Candidate for 79 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) 73% 100% 477.6 Methionine import ATP-binding protein MetN; EC 7.4.2.11 52% 315.5
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) 42% 96% 186 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 73% 477.6
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) 42% 96% 186 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 73% 477.6
L-arginine catabolism artP med BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 43% 96% 181.4 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 73% 477.6
L-histidine catabolism bgtA med BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 43% 96% 181.4 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 73% 477.6
L-lysine catabolism hisP med BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 43% 96% 181.4 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 73% 477.6
L-histidine catabolism hutV med ABC transporter for L-Histidine, ATPase component (characterized) 42% 83% 179.1 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 73% 477.6
L-asparagine catabolism bgtA med ATPase (characterized, see rationale) 41% 92% 174.5 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 73% 477.6
L-aspartate catabolism bgtA med ATPase (characterized, see rationale) 41% 92% 174.5 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 73% 477.6
L-histidine catabolism hisP med Histidine transport ATP-binding protein HisP (characterized) 42% 95% 171.4 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 73% 477.6
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) 41% 85% 166.8 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 73% 477.6
L-asparagine catabolism aatP med ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component (characterized) 40% 89% 161.4 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 73% 477.6
L-aspartate catabolism aatP med ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component (characterized) 40% 89% 161.4 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 73% 477.6
L-proline catabolism proV lo glycine betaine/l-proline transport atp-binding protein prov (characterized) 42% 60% 180.6 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 73% 477.6
D-alanine catabolism Pf6N2E2_5405 lo ABC transporter for D-Alanine, ATPase component (characterized) 39% 95% 172.6 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 73% 477.6
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) 39% 93% 171.8 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 73% 477.6
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) 39% 93% 171.8 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 73% 477.6
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) 39% 93% 171.8 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 73% 477.6
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) 39% 93% 171.8 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 73% 477.6
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) 39% 93% 171.8 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 73% 477.6
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) 39% 93% 171.8 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 73% 477.6
D-glucosamine (chitosamine) catabolism AO353_21725 lo ABC transporter for D-glucosamine, ATPase component (characterized) 39% 94% 169.1 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 73% 477.6
L-asparagine catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 37% 90% 167.9 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 73% 477.6
L-aspartate catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 37% 90% 167.9 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 73% 477.6
L-citrulline catabolism AO353_03040 lo ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 38% 98% 166.8 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 73% 477.6
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% 77% 163.3 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 73% 477.6
putrescine catabolism potA lo PotG aka B0855, component of Putrescine porter (characterized) 37% 64% 161.4 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 73% 477.6
L-histidine catabolism BPHYT_RS24015 lo ABC transporter related (characterized, see rationale) 38% 97% 157.1 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 73% 477.6
L-asparagine catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 37% 98% 156.4 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 73% 477.6
L-aspartate catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 37% 98% 156.4 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 73% 477.6
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) 38% 89% 156.4 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 73% 477.6
D-maltose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 32% 88% 154.8 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 73% 477.6
trehalose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 32% 88% 154.8 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 73% 477.6
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 33% 77% 149.1 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 73% 477.6
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) 33% 84% 147.9 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 73% 477.6
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) 32% 84% 147.5 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 73% 477.6
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 30% 85% 146.4 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 73% 477.6
lactose catabolism lacK lo ABC transporter for Lactose, ATPase component (characterized) 33% 80% 144.8 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 73% 477.6
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 31% 85% 143.7 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 73% 477.6
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 31% 85% 143.7 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 73% 477.6
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 34% 68% 143.3 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 73% 477.6
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 33% 67% 142.9 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 73% 477.6
D-mannitol catabolism mtlK lo ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component (characterized) 33% 61% 142.1 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 73% 477.6
L-tryptophan catabolism ecfA1 lo Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) 38% 74% 138.3 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 73% 477.6
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 33% 62% 137.1 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 73% 477.6
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) 35% 77% 137.1 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 73% 477.6
D-cellobiose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 33% 61% 136 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 73% 477.6
D-glucose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 33% 61% 136 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 73% 477.6
lactose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 33% 61% 136 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 73% 477.6
D-maltose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 33% 61% 136 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 73% 477.6
sucrose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 33% 61% 136 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 73% 477.6
trehalose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 33% 61% 136 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 73% 477.6
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 33% 61% 136 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 73% 477.6
D-maltose catabolism malK lo ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized) 33% 61% 135.2 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 73% 477.6
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) 32% 60% 134.8 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 73% 477.6
trehalose catabolism treV lo TreV, component of Trehalose porter (characterized) 32% 65% 132.1 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 73% 477.6
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 33% 61% 131.7 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 73% 477.6
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 31% 68% 130.6 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 73% 477.6
sucrose catabolism thuK lo ABC transporter (characterized, see rationale) 34% 61% 130.2 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 73% 477.6
L-tryptophan catabolism ecfA2 lo Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) 33% 78% 127.5 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 73% 477.6
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 31% 83% 126.7 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 73% 477.6
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) 31% 66% 126.7 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 73% 477.6
D-cellobiose catabolism cbtD lo CbtD, component of Cellobiose and cellooligosaccharide porter (characterized) 34% 70% 126.3 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 73% 477.6
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) 31% 88% 122.1 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 73% 477.6
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) 31% 60% 120.6 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 73% 477.6
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% 119.8 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 73% 477.6
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% 119.8 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 73% 477.6
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% 119.8 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 73% 477.6
D-cellobiose catabolism cbtF lo CbtF, component of Cellobiose and cellooligosaccharide porter (characterized) 31% 76% 119.4 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 73% 477.6
D-cellobiose catabolism mglA lo glucose transporter, ATPase component (characterized) 32% 85% 111.7 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 73% 477.6
D-glucose catabolism mglA lo glucose transporter, ATPase component (characterized) 32% 85% 111.7 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 73% 477.6
lactose catabolism mglA lo glucose transporter, ATPase component (characterized) 32% 85% 111.7 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 73% 477.6
D-maltose catabolism mglA lo glucose transporter, ATPase component (characterized) 32% 85% 111.7 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 73% 477.6
sucrose catabolism mglA lo glucose transporter, ATPase component (characterized) 32% 85% 111.7 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 73% 477.6
trehalose catabolism mglA lo glucose transporter, ATPase component (characterized) 32% 85% 111.7 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 73% 477.6
L-phenylalanine catabolism livG lo ABC transporter ATP-binding protein (characterized, see rationale) 32% 86% 110.5 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 73% 477.6
L-proline catabolism HSERO_RS00895 lo ABC transporter ATP-binding protein (characterized, see rationale) 32% 86% 110.5 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 73% 477.6
L-serine catabolism Ac3H11_1693 lo ABC transporter ATP-binding protein (characterized, see rationale) 32% 86% 110.5 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 73% 477.6
L-tyrosine catabolism Ac3H11_1693 lo ABC transporter ATP-binding protein (characterized, see rationale) 32% 86% 110.5 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 73% 477.6

Sequence Analysis Tools

View WP_057508907.1 at NCBI

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

Find the best match in UniProt

Compare to protein structures

Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

Find homologs in fast.genomics

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Sequence

MIEFQRLHKSYAVAGRAISALQPLDLTIQEGEVFGIIGHSGAGKSTLIRMINRLEDPSGG
RLLIAGEDVTALETAGLRTLRRRIGMIFQHFNLLSSRTVASNVAFPLELAGTPRAQIDAR
VAELLQTVGLQAHADKYPAQLSGGQKQRVGIARALATGPQILLCDEATSALDPQTTASVL
ALLSKINRELGLTIVLITHEMDVIRRVCDRVAVLDAGEMVEMGPVTDVFLHPQHPTTRRF
VSESEHIDEGTLHGDFDTVGGTIVRLTFLGADTYQPLLGSVARQTGVDYNILSGRIDRIK
DTPYGQLVVSLVGGDQAAAQQAFAAAGVHVEELRR

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