GapMind for catabolism of small carbon sources

 

Protein Synpcc7942_0947 in Synechococcus elongatus PCC 7942

Annotation: Synpcc7942_0947 ATPase

Length: 355 amino acids

Source: SynE in FitnessBrowser

Candidate for 58 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-cellobiose catabolism gtsD med Sugar ABC transporter ATP-binding protein (characterized, see rationale) 46% 99% 295.8 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] 44% 290.0
D-glucose catabolism gtsD med Sugar ABC transporter ATP-binding protein (characterized, see rationale) 46% 99% 295.8 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] 44% 290.0
lactose catabolism gtsD med Sugar ABC transporter ATP-binding protein (characterized, see rationale) 46% 99% 295.8 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] 44% 290.0
D-maltose catabolism gtsD med Sugar ABC transporter ATP-binding protein (characterized, see rationale) 46% 99% 295.8 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] 44% 290.0
sucrose catabolism gtsD med Sugar ABC transporter ATP-binding protein (characterized, see rationale) 46% 99% 295.8 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] 44% 290.0
trehalose catabolism gtsD med Sugar ABC transporter ATP-binding protein (characterized, see rationale) 46% 99% 295.8 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] 44% 290.0
D-cellobiose catabolism msiK med 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) 44% 97% 290 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 46% 287.0
D-maltose catabolism thuK med 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% 86% 287 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] 44% 290.0
D-mannose catabolism TT_C0211 med 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% 86% 287 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] 44% 290.0
sucrose catabolism thuK med 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% 86% 287 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] 44% 290.0
trehalose catabolism thuK med 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% 86% 287 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] 44% 290.0
D-glucosamine (chitosamine) catabolism SM_b21216 med ABC transporter for D-Glucosamine, ATPase component (characterized) 43% 99% 286.6 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] 44% 290.0
D-xylose catabolism gtsD med ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 44% 94% 286.2 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] 44% 290.0
D-maltose catabolism musK med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 45% 94% 284.6 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] 44% 290.0
D-maltose catabolism malK_Aa med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 46% 87% 282.7 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] 44% 290.0
D-galactose catabolism PfGW456L13_1897 med ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 43% 94% 280.8 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] 44% 290.0
D-maltose catabolism malK1 med 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) 42% 98% 280.4 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] 44% 290.0
D-sorbitol (glucitol) catabolism mtlK med ABC transporter for D-sorbitol, ATPase component (characterized) 42% 96% 280 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] 44% 290.0
L-fucose catabolism SM_b21106 med ABC transporter for L-Fucose, ATPase component (characterized) 44% 99% 279.6 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] 44% 290.0
D-mannitol catabolism mtlK med ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component (characterized) 44% 89% 276.6 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] 44% 290.0
D-maltose catabolism malK med ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized) 42% 96% 274.6 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] 44% 290.0
lactose catabolism lacK med ABC transporter for Lactose, ATPase component (characterized) 47% 84% 274.2 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] 44% 290.0
D-maltose catabolism malK_Bb med ABC-type maltose transport, ATP binding protein (characterized, see rationale) 43% 98% 272.7 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] 44% 290.0
xylitol catabolism Dshi_0546 med ABC transporter for Xylitol, ATPase component (characterized) 40% 97% 265 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] 44% 290.0
L-arabinose catabolism xacJ med Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 43% 94% 259.6 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] 44% 290.0
N-acetyl-D-glucosamine catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 42% 96% 257.3 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] 44% 290.0
D-glucosamine (chitosamine) catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 42% 96% 257.3 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] 44% 290.0
D-cellobiose catabolism SMc04256 med ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 42% 99% 255.8 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] 44% 290.0
D-cellobiose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 44% 94% 255.8 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] 44% 290.0
D-glucose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 44% 94% 255.8 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] 44% 290.0
lactose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 44% 94% 255.8 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] 44% 290.0
D-maltose catabolism aglK med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 44% 94% 255.8 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] 44% 290.0
D-maltose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 44% 94% 255.8 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] 44% 290.0
sucrose catabolism aglK med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 44% 94% 255.8 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] 44% 290.0
sucrose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 44% 94% 255.8 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] 44% 290.0
trehalose catabolism aglK med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 44% 94% 255.8 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] 44% 290.0
trehalose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 44% 94% 255.8 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] 44% 290.0
xylitol catabolism HSERO_RS17020 med ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 40% 89% 255.8 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] 44% 290.0
L-arabinose catabolism xacK med Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 42% 95% 253.1 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] 44% 290.0
trehalose catabolism treV med TreV, component of Trehalose porter (characterized) 45% 75% 214.2 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] 44% 290.0
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) 39% 99% 246.9 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] 44% 290.0
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) 39% 99% 246.9 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] 44% 290.0
putrescine catabolism potA lo spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) 48% 62% 216.9 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] 44% 290.0
glycerol catabolism glpT lo GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) 32% 96% 199.9 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] 44% 290.0
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 37% 80% 197.2 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] 44% 290.0
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 37% 80% 197.2 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] 44% 290.0
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 37% 80% 197.2 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] 44% 290.0
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 37% 80% 197.2 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] 44% 290.0
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 37% 80% 197.2 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] 44% 290.0
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 37% 80% 197.2 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] 44% 290.0
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 37% 80% 197.2 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] 44% 290.0
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 37% 80% 197.2 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] 44% 290.0
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 31% 92% 191.8 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] 44% 290.0
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 31% 92% 191.8 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] 44% 290.0
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 31% 92% 191.8 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] 44% 290.0
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 31% 92% 191.8 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] 44% 290.0
glycerol catabolism glpS lo GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized) 35% 95% 186.8 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] 44% 290.0
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) 35% 73% 164.5 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] 44% 290.0

Sequence Analysis Tools

View Synpcc7942_0947 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 and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MASFALELRQLRKAYSPSVVPVANLSLQLQPGEFLTLLGPSGCGKSTTLRLIAGLDQPTS
GSIWLGDREITTLPPGDRDMAMVFQSYALYPHLNVRQNLTLGLQIRRTSAAEIEQRLQQV
AHNLELDHLLDRRPAQLSGGQRQRVALGRALVRQPSVFLLDEPLSNLDALLREQVRAQMK
ALFSQQASPVVYVTHDQTEALSLSHRIAILNGGHLQQLDSPDRIYQAPANAFVAGFIGSP
RMNLLPLPIHSGQAWLGSRALPIPSHLAARSQVLWGLRPEHLKLATPEVERAIPVQLHLT
ENLGMQRLLTVAIAANPEVRLRLLMPSDQPIPTDLQVTFEPESQHWFCPSTGDRL

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, the preprint on GapMind for carbon sources, 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