GapMind for catabolism of small carbon sources

 

Protein 202699 in Shewanella oneidensis MR-1

Annotation: SO3602 sulfate ABC transporter, ATP-binding protein (NCBI ptt file)

Length: 376 amino acids

Source: MR1 in FitnessBrowser

Candidate for 80 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-maltose catabolism malK_Bb med ABC-type maltose transport, ATP binding protein (characterized, see rationale) 43% 82% 227.3 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 368.2
xylitol catabolism Dshi_0546 med ABC transporter for Xylitol, ATPase component (characterized) 47% 72% 226.1 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 368.2
D-cellobiose catabolism SMc04256 med ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 42% 86% 210.3 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 368.2
N-acetyl-D-glucosamine catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 44% 70% 209.5 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 368.2
D-glucosamine (chitosamine) catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 44% 70% 209.5 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 368.2
D-mannitol catabolism mtlK med SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) 44% 70% 208 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 368.2
xylitol catabolism HSERO_RS17020 med ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 41% 73% 207.6 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 368.2
trehalose catabolism treV med TreV, component of Trehalose porter (characterized) 42% 73% 190.3 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 368.2
L-histidine catabolism Ac3H11_2560 med ABC transporter for L-Histidine, ATPase component (characterized) 41% 80% 154.5 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 368.2
putrescine catabolism potA lo spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) 53% 63% 242.3 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 368.2
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 39% 86% 224.2 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 368.2
D-maltose catabolism malK_Aa lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 39% 85% 219.5 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 368.2
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) 46% 62% 219.2 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 368.2
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) 46% 62% 219.2 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 368.2
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) 46% 62% 219.2 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 368.2
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) 46% 62% 219.2 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 368.2
D-maltose catabolism thuK 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) 46% 62% 219.2 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 368.2
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) 46% 62% 219.2 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 368.2
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) 46% 62% 219.2 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 368.2
sucrose catabolism thuK 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) 46% 62% 219.2 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 368.2
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) 46% 62% 219.2 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 368.2
trehalose catabolism thuK 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) 46% 62% 219.2 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 368.2
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 36% 89% 218.8 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 368.2
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 35% 98% 218.4 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 368.2
D-maltose catabolism malK lo ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized) 45% 63% 214.5 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 368.2
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-sorbitol, ATPase component (characterized) 36% 84% 214.5 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 368.2
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 39% 88% 209.5 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 368.2
D-maltose catabolism musK lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 40% 78% 207.6 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 368.2
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 44% 61% 207.6 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 368.2
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) 38% 86% 206.1 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 368.2
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 44% 61% 204.5 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 368.2
lactose catabolism lacK lo LacK, component of Lactose porter (characterized) 43% 64% 204.1 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 368.2
D-cellobiose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 44% 63% 201.8 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 368.2
D-glucose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 44% 63% 201.8 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 368.2
lactose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 44% 63% 201.8 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 368.2
D-maltose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 44% 63% 201.8 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 368.2
D-maltose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 44% 63% 201.8 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 368.2
sucrose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 44% 63% 201.8 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 368.2
sucrose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 44% 63% 201.8 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 368.2
trehalose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 44% 63% 201.8 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 368.2
trehalose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 44% 63% 201.8 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 368.2
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) 45% 58% 201.4 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 368.2
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) 36% 88% 200.3 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 368.2
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) 36% 88% 200.3 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 368.2
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 36% 86% 189.1 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 368.2
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 36% 86% 189.1 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 368.2
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 36% 86% 189.1 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 368.2
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 36% 86% 189.1 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 368.2
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) 38% 93% 186 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 368.2
L-proline catabolism proV lo Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized) 38% 59% 166.4 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 368.2
glycerol catabolism glpT lo ABC transporter for Glycerol, ATPase component 2 (characterized) 36% 85% 165.6 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 368.2
L-glutamate catabolism gltL lo GluA aka CGL1950, component of Glutamate porter (characterized) 40% 98% 164.1 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 368.2
L-arginine catabolism artP lo Arginine transport ATP-binding protein ArtM (characterized) 39% 99% 163.3 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 368.2
L-histidine catabolism PA5503 lo Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) 41% 68% 159.8 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 368.2
L-asparagine catabolism bgtA lo ATPase (characterized, see rationale) 39% 92% 156.4 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 368.2
L-aspartate catabolism bgtA lo ATPase (characterized, see rationale) 39% 92% 156.4 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 368.2
L-asparagine catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 36% 98% 152.9 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 368.2
L-aspartate catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 36% 98% 152.9 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 368.2
L-histidine catabolism BPHYT_RS24015 lo ABC transporter related (characterized, see rationale) 36% 98% 151.8 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 368.2
L-histidine catabolism hutV lo ABC transporter for L-Histidine, ATPase component (characterized) 37% 82% 151.8 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 368.2
L-histidine catabolism bgtA lo BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 38% 96% 151 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 368.2
L-lysine catabolism hisP lo BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 38% 96% 151 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 368.2
L-asparagine catabolism aatP lo Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 36% 99% 147.1 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 368.2
L-aspartate catabolism aatP lo Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 36% 99% 147.1 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 368.2
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) 34% 97% 146.4 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 368.2
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) 35% 90% 146 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 368.2
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) 32% 98% 135.6 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 368.2
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) 32% 98% 135.6 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 368.2
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) 32% 98% 135.6 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 368.2
L-phenylalanine catabolism livG lo ABC transporter ATP-binding protein (characterized, see rationale) 33% 95% 133.3 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 368.2
L-proline catabolism HSERO_RS00895 lo ABC transporter ATP-binding protein (characterized, see rationale) 33% 95% 133.3 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 368.2
L-serine catabolism Ac3H11_1693 lo ABC transporter ATP-binding protein (characterized, see rationale) 33% 95% 133.3 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 368.2
L-tyrosine catabolism Ac3H11_1693 lo ABC transporter ATP-binding protein (characterized, see rationale) 33% 95% 133.3 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 368.2
D-cellobiose catabolism mglA lo glucose transporter, ATPase component (characterized) 31% 83% 104.8 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 368.2
D-glucose catabolism mglA lo glucose transporter, ATPase component (characterized) 31% 83% 104.8 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 368.2
lactose catabolism mglA lo glucose transporter, ATPase component (characterized) 31% 83% 104.8 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 368.2
D-maltose catabolism mglA lo glucose transporter, ATPase component (characterized) 31% 83% 104.8 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 368.2
sucrose catabolism mglA lo glucose transporter, ATPase component (characterized) 31% 83% 104.8 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 368.2
trehalose catabolism mglA lo glucose transporter, ATPase component (characterized) 31% 83% 104.8 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 368.2
myo-inositol catabolism PGA1_c07320 lo Inositol transport system ATP-binding protein (characterized) 31% 84% 92 CysA aka B2422, component of Sulfate/thiosulfate porter 57% 368.2

Sequence Analysis Tools

View 202699 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Search PFam (including for weak hits, up to E = 1)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices: TMHMM

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MSIRLTNISKKFGQFQALSPLNLDIQEGEMIGLLGPSGSGKTTLLRIIAGLEGADSGHIH
FGNRDVTQVHVRDRRVGFVFQNYALFRHMTVADNVAFGLEVIPKKQRPSAAEIQKRVSHL
LEMVQLGHLAQRYPEQLSGGQKQRIALARALATQPEVLLLDEPFGALDAKVRKELRRWLR
SLHDELKFTSVFVTHDQDEALELSDRVVVMSNGNIEQVNTPIELYAQPNSRFVFDFLGNV
NRFEANWQQNRWTNGDAFIVPPEQTPLQQNGALYVRSHELALADKPNSQAHIPFTIVAIT
PIGAEVRVELAPIGWQSEELWEAKFTHHHLQELGLQKGSVVYATPRTGYFFGKQGDGSPI
RQSWPFLPPGSLAFDI

This GapMind analysis is from Sep 17 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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