GapMind for catabolism of small carbon sources

 

Protein CCNA_01670 in Caulobacter crescentus NA1000

Annotation: CCNA_01670 sulfate transport ATP-binding protein cysA

Length: 339 amino acids

Source: Caulo in FitnessBrowser

Candidate for 97 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-mannitol catabolism mtlK med SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) 45% 80% 226.5 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
D-sorbitol (glucitol) catabolism mtlK med ABC transporter for D-Sorbitol, ATPase component (characterized) 44% 81% 221.1 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
L-arabinose catabolism xacK med Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 42% 80% 219.2 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
L-fucose catabolism SM_b21106 med ABC transporter for L-Fucose, ATPase component (characterized) 43% 77% 216.5 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
N-acetyl-D-glucosamine catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 42% 76% 215.3 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
D-glucosamine (chitosamine) catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 42% 76% 215.3 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
D-maltose catabolism thuK med ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 42% 78% 214.9 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
sucrose catabolism thuK med ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 42% 78% 214.9 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
trehalose catabolism thuK med ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 42% 78% 214.9 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
D-cellobiose catabolism SMc04256 med ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 42% 81% 212.2 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
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) 42% 73% 211.5 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
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) 44% 70% 210.7 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
xylitol catabolism Dshi_0546 med ABC transporter for Xylitol, ATPase component (characterized) 45% 72% 209.9 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
D-cellobiose catabolism gtsD med GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 42% 80% 209.5 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
D-glucose catabolism gtsD med GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 42% 80% 209.5 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
lactose catabolism gtsD med GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 42% 80% 209.5 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
D-maltose catabolism gtsD med GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 42% 80% 209.5 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
sucrose catabolism gtsD med GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 42% 80% 209.5 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
trehalose catabolism gtsD med GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 42% 80% 209.5 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
D-galactose catabolism PfGW456L13_1897 med ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 40% 80% 206.8 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
D-maltose catabolism musK med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 40% 77% 204.1 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
L-histidine catabolism hutV med HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) 41% 81% 169.5 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
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% 81% 169.5 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
L-histidine catabolism Ac3H11_2560 med ABC transporter for L-Histidine, ATPase component (characterized) 42% 86% 157.5 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
putrescine catabolism potA lo spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) 49% 64% 236.5 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 39% 96% 226.9 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 38% 95% 220.3 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
D-maltose catabolism malK lo Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 38% 95% 213.4 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 91% 213 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 91% 213 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 91% 213 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 91% 213 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 91% 213 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 91% 213 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 91% 213 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 91% 213 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
D-maltose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 38% 88% 207.2 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
sucrose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 38% 88% 207.2 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
trehalose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 38% 88% 207.2 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
lactose catabolism lacK lo LacK, component of Lactose porter (characterized) 36% 98% 206.5 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 40% 80% 206.5 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
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) 39% 85% 206.1 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
trehalose catabolism treV lo TreV, component of Trehalose porter (characterized) 40% 86% 206.1 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 39% 85% 204.1 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 36% 88% 201.4 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
D-maltose catabolism malK_Aa lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 39% 85% 195.7 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
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% 75% 195.3 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
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) 39% 74% 195.3 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
D-cellobiose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 39% 84% 193 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
D-glucose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 39% 84% 193 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
lactose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 39% 84% 193 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
D-maltose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 39% 84% 193 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
sucrose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 39% 84% 193 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
trehalose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 39% 84% 193 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 36% 84% 186.4 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 36% 84% 186.4 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 36% 84% 186.4 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 36% 84% 186.4 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
glycerol catabolism glpT lo GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) 35% 88% 178.3 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
L-proline catabolism proV lo Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized) 36% 70% 169.9 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
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) 37% 78% 166 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
glycerol catabolism glpS lo ABC transporter for Glycerol, ATPase component 1 (characterized) 36% 86% 162.9 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
L-arginine catabolism artP lo Arginine transport ATP-binding protein ArtM (characterized) 37% 95% 157.5 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
L-histidine catabolism PA5503 lo Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) 39% 74% 157.1 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
D-glucosamine (chitosamine) catabolism AO353_21725 lo ABC transporter for D-glucosamine, ATPase component (characterized) 36% 94% 156 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
L-asparagine catabolism bgtA lo ATPase (characterized, see rationale) 39% 88% 151.4 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
L-aspartate catabolism bgtA lo ATPase (characterized, see rationale) 39% 88% 151.4 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
L-histidine catabolism BPHYT_RS24015 lo ABC transporter related (characterized, see rationale) 37% 89% 148.3 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
L-lysine catabolism hisP lo ABC transporter for L-Lysine, ATPase component (characterized) 36% 98% 146.7 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
L-asparagine catabolism glnQ lo 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) 36% 92% 144.8 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
L-asparagine catabolism aatP lo ABC transporter for L-Asparagine and possibly other L-amino acids, putative ATPase component (characterized) 38% 87% 141.7 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
L-aspartate catabolism aatP lo ABC transporter for L-Asparagine and possibly other L-amino acids, putative ATPase component (characterized) 38% 87% 141.7 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
D-alanine catabolism Pf6N2E2_5405 lo ABC transporter for D-Alanine, ATPase component (characterized) 36% 90% 141.4 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
L-asparagine catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 32% 98% 134.8 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
L-aspartate catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 32% 98% 134.8 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
L-histidine catabolism hisP lo Histidine transport ATP-binding protein HisP (characterized) 33% 93% 132.9 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
L-tryptophan catabolism ecfA2 lo Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) 35% 93% 125.6 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
myo-inositol catabolism PGA1_c07320 lo Inositol transport system ATP-binding protein (characterized) 35% 86% 123.2 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
D-fructose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 31% 93% 120.2 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
D-mannose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 31% 93% 120.2 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
D-ribose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 31% 93% 120.2 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
sucrose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 31% 93% 120.2 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
L-alanine catabolism braG lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 33% 92% 118.2 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
L-histidine catabolism natE lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 33% 92% 118.2 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
L-leucine catabolism natE lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 33% 92% 118.2 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
L-proline catabolism natE lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 33% 92% 118.2 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
L-serine catabolism braG lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 33% 92% 118.2 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
L-threonine catabolism braG lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 33% 92% 118.2 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
L-arginine catabolism braG lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 31% 91% 113.2 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
L-glutamate catabolism braG lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 31% 91% 113.2 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
L-histidine catabolism braG lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 31% 91% 113.2 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
L-isoleucine catabolism livF lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 31% 91% 113.2 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
L-leucine catabolism livF lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 31% 91% 113.2 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
L-valine catabolism livF lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 31% 91% 113.2 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
citrate catabolism fecE lo iron(III) dicitrate transport ATP-binding protein FecE (characterized) 32% 88% 108.6 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
D-alanine catabolism AZOBR_RS08250 lo Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) 32% 92% 105.1 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6
L-proline catabolism AZOBR_RS08250 lo Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) 32% 92% 105.1 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 296.6

Sequence Analysis Tools

View CCNA_01670 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

MTIAIRSVEKQFGRYPALNKVDLEIADGELLALLGPSGSGKTTLLRTIAGLEFPDAGQVL
FDGQDVTYASAAARRVGFVFQQYALFKHMTVAKNIAFGLDVRKGKDKPSKAEIARRVEEL
LKLVELEGLGGRYPSQLSGGQRQRVALSRALAVQPSVLLLDEPFGALDATVRKSLRRELR
RVHDATGVTTIFVTHDQEEALELADRVAILNNGRIEQIGTPDQVHDAPETAFVCGFVGEA
NRFDGQVSGGRFKAGALTVPASALKDGAATAYVRPHDFALDEAGFEVLIERAQVQGALTA
VTALTSDGRRLEISASRADADRFTGAVKIVARKAHVYAA

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