GapMind for catabolism of small carbon sources

 

Protein 202699 in Shewanella oneidensis MR-1

Annotation: FitnessBrowser__MR1:202699

Length: 376 amino acids

Source: MR1 in FitnessBrowser

Candidate for 79 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

Sequence Analysis Tools

View 202699 at FitnessBrowser

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Predict transmenbrane helices: Phobius

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Sequence

MSIRLTNISKKFGQFQALSPLNLDIQEGEMIGLLGPSGSGKTTLLRIIAGLEGADSGHIH
FGNRDVTQVHVRDRRVGFVFQNYALFRHMTVADNVAFGLEVIPKKQRPSAAEIQKRVSHL
LEMVQLGHLAQRYPEQLSGGQKQRIALARALATQPEVLLLDEPFGALDAKVRKELRRWLR
SLHDELKFTSVFVTHDQDEALELSDRVVVMSNGNIEQVNTPIELYAQPNSRFVFDFLGNV
NRFEANWQQNRWTNGDAFIVPPEQTPLQQNGALYVRSHELALADKPNSQAHIPFTIVAIT
PIGAEVRVELAPIGWQSEELWEAKFTHHHLQELGLQKGSVVYATPRTGYFFGKQGDGSPI
RQSWPFLPPGSLAFDI

This GapMind analysis is from Apr 09 2024. 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