GapMind for catabolism of small carbon sources

 

Protein WP_066922377.1 in Steroidobacter denitrificans DSM 18526

Annotation: NCBI__GCF_001579945.1:WP_066922377.1

Length: 596 amino acids

Source: GCF_001579945.1 in NCBI

Candidate for 95 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
putrescine catabolism potA med spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) 44% 81% 239.2 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
xylitol catabolism Dshi_0546 med ABC transporter for Xylitol, ATPase component (characterized) 42% 81% 224.6 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
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% 76% 218 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
D-maltose catabolism musK med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 41% 82% 217.6 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
D-mannitol catabolism mtlK med ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component (characterized) 41% 80% 215.3 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
trehalose catabolism thuK med Trehalose import ATP-binding protein SugC; EC 7.5.2.- (characterized) 42% 74% 214.5 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
D-cellobiose catabolism gtsD med Sugar ABC transporter ATP-binding protein (characterized, see rationale) 42% 83% 214.2 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
D-glucose catabolism gtsD med Sugar ABC transporter ATP-binding protein (characterized, see rationale) 42% 83% 214.2 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
lactose catabolism gtsD med Sugar ABC transporter ATP-binding protein (characterized, see rationale) 42% 83% 214.2 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
D-maltose catabolism gtsD med Sugar ABC transporter ATP-binding protein (characterized, see rationale) 42% 83% 214.2 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
sucrose catabolism gtsD med Sugar ABC transporter ATP-binding protein (characterized, see rationale) 42% 83% 214.2 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
trehalose catabolism gtsD med Sugar ABC transporter ATP-binding protein (characterized, see rationale) 42% 83% 214.2 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
L-fucose catabolism SM_b21106 med ABC transporter for L-Fucose, ATPase component (characterized) 40% 80% 207.2 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
D-maltose catabolism thuK med Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 42% 78% 206.8 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
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) 41% 80% 206.5 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
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) 41% 80% 206.5 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
D-glucosamine (chitosamine) catabolism SM_b21216 med ABC transporter for D-Glucosamine, ATPase component (characterized) 42% 79% 205.7 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
trehalose catabolism treV med TreV, component of Trehalose porter (characterized) 42% 79% 204.9 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
D-maltose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 40% 84% 201.8 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
sucrose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 40% 84% 201.8 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
trehalose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 40% 84% 201.8 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
L-arabinose catabolism xacJ med Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 42% 74% 201.1 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
lactose catabolism lacK med LacK, component of Lactose porter (characterized) 40% 85% 201.1 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
N-acetyl-D-glucosamine catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 40% 80% 200.7 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
D-glucosamine (chitosamine) catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 40% 80% 200.7 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
D-sorbitol (glucitol) catabolism mtlK med ABC transporter for D-Sorbitol, ATPase component (characterized) 43% 77% 198.7 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
L-histidine catabolism Ac3H11_2560 med ABC transporter for L-Histidine, ATPase component (characterized) 43% 78% 155.6 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
L-arginine catabolism artP med Arginine transport ATP-binding protein ArtP; EC 7.4.2.- (characterized) 41% 100% 151.4 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
L-asparagine catabolism bgtA med ATPase (characterized, see rationale) 41% 85% 150.2 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
L-aspartate catabolism bgtA med ATPase (characterized, see rationale) 41% 85% 150.2 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 38% 95% 220.7 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
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) 39% 95% 216.1 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 39% 80% 209.9 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 38% 89% 206.5 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 43% 68% 205.7 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 39% 77% 204.1 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
D-maltose catabolism malK lo Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 44% 64% 203 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
D-maltose catabolism malK_Aa lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 39% 76% 198.7 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 36% 91% 193.7 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
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) 37% 80% 192.6 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
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) 38% 79% 192.2 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 37% 84% 188.3 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 37% 84% 188.3 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 37% 84% 188.3 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 37% 84% 188.3 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
D-cellobiose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 39% 81% 187.2 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
D-glucose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 39% 81% 187.2 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
lactose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 39% 81% 187.2 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
D-maltose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 39% 81% 187.2 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
sucrose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 39% 81% 187.2 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
trehalose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 39% 81% 187.2 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
L-proline catabolism proV lo glycine betaine/l-proline transport atp-binding protein prov (characterized) 35% 77% 177.6 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
L-proline catabolism opuBA lo BusAA, component of Uptake system for glycine-betaine (high affinity) and proline (low affinity) (OpuAA-OpuABC) or BusAA-ABC of Lactococcus lactis). BusAA, the ATPase subunit, has a C-terminal tandem cystathionine β-synthase (CBS) domain which is the cytoplasmic K+ sensor for osmotic stress (osmotic strength)while the BusABC subunit has the membrane and receptor domains fused to each other (Biemans-Oldehinkel et al., 2006; Mahmood et al., 2006; Gul et al. 2012). An N-terminal amphipathic α-helix of OpuA is necessary for high activity but is not critical for biogenesis or the ionic regulation of transport (characterized) 38% 65% 174.9 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
glycerol catabolism glpT lo GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) 34% 81% 160.6 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
L-histidine catabolism hutV lo HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) 39% 81% 158.7 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
L-proline catabolism hutV lo HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) 39% 81% 158.7 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
glycerol catabolism glpS lo ABC transporter for Glycerol, ATPase component 1 (characterized) 36% 80% 156.8 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
L-glutamate catabolism gltL lo GluA aka CGL1950, component of Glutamate porter (characterized) 38% 98% 154.1 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
L-asparagine catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 37% 98% 150.6 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
L-aspartate catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 37% 98% 150.6 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
L-lysine catabolism hisP lo Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) 39% 91% 149.4 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
L-asparagine catabolism aatP lo Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 38% 98% 147.9 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
L-aspartate catabolism aatP lo Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 38% 98% 147.9 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
L-asparagine catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 37% 92% 145.6 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
L-aspartate catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 37% 92% 145.6 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
D-alanine catabolism Pf6N2E2_5405 lo ABC transporter for D-Alanine, ATPase component (characterized) 37% 93% 143.3 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
L-histidine catabolism aapP lo ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) 36% 92% 143.3 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
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) 34% 98% 143.3 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
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) 34% 98% 143.3 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
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) 34% 98% 143.3 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
L-histidine catabolism bgtA lo BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 36% 95% 142.9 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
L-asparagine catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 35% 93% 140.2 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
L-aspartate catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 35% 93% 140.2 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
L-glutamate catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 35% 93% 140.2 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
L-leucine catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 35% 93% 140.2 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
L-proline catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 35% 93% 140.2 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
L-tryptophan catabolism ecfA2 lo Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) 36% 91% 136 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
L-histidine catabolism hisP lo Histidine transport ATP-binding protein HisP (characterized) 35% 94% 132.1 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
D-mannose catabolism TM1750 lo TM1750, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized) 31% 93% 132.1 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
L-proline catabolism HSERO_RS00895 lo ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale) 33% 100% 121.7 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
L-phenylalanine catabolism livG lo ABC transporter ATP-binding protein (characterized, see rationale) 32% 94% 118.2 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
L-serine catabolism Ac3H11_1693 lo ABC transporter ATP-binding protein (characterized, see rationale) 32% 94% 118.2 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
L-tyrosine catabolism Ac3H11_1693 lo ABC transporter ATP-binding protein (characterized, see rationale) 32% 94% 118.2 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
L-isoleucine catabolism livF lo ABC transporter ATP-binding protein (characterized, see rationale) 33% 92% 110.5 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
L-leucine catabolism livF lo ABC transporter ATP-binding protein (characterized, see rationale) 33% 92% 110.5 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
L-phenylalanine catabolism livF lo ABC transporter ATP-binding protein (characterized, see rationale) 33% 92% 110.5 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
L-proline catabolism HSERO_RS00900 lo ABC transporter ATP-binding protein (characterized, see rationale) 33% 92% 110.5 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
L-serine catabolism Ac3H11_1692 lo ABC transporter ATP-binding protein (characterized, see rationale) 33% 92% 110.5 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
L-tyrosine catabolism Ac3H11_1692 lo ABC transporter ATP-binding protein (characterized, see rationale) 33% 92% 110.5 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
D-cellobiose catabolism cbtD lo CbtD, component of Cellobiose and cellooligosaccharide porter (characterized) 33% 65% 110.2 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
D-cellobiose catabolism cbtF lo CbtF, component of Cellobiose and cellooligosaccharide porter (characterized) 33% 69% 105.9 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
L-alanine catabolism braG lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 31% 100% 103.6 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
L-serine catabolism braG lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 31% 100% 103.6 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
L-threonine catabolism braG lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 31% 100% 103.6 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7
L-valine catabolism livF lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 31% 100% 103.6 CysA aka B2422, component of Sulfate/thiosulfate porter 50% 252.7

Sequence Analysis Tools

View WP_066922377.1 at NCBI

Find papers: PaperBLAST

Find functional residues: SitesBLAST

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MSITLDQITKRYQGSPVVNDVSLEVTEGEFYVLLGPSGSGKSTLLRSIAGLTGIDHGRIA
LHGNDVTRVSARQRGVGLVFQNYALFRHMTVGENIEFALRVRHVKAAERRARRRELLRLV
ALEGMDDRLPTQLSGGQQQRVAVARALAHKPPVLLLDEPFGALDAKIREELRRTIRQVQR
ELNITTVLVTHDQEEAFALADRIGVMNLGRLLESGKPDELYARPATRFVATFLGAANLLL
ARQTSQGIRFNAAPAGIRDADKPEGGREHEVVAVLRPEEVELAPTRDNLHTSCIASGVIE
EQVFTGAYERLRIRMTCNTTDLQIANATTQDVQSQAAFLDVTRTQHEQRLFPAVLGQSVA
IGVRRIHLLPTPLSSYTVCAADEATAGRLAAHPFLVELAGRMKTRIAKRVMPMLQSCSQV
LAEPIAGVAVIGSHPQQAAQIEWLLGNGAAEVLVMPSQAIPPQRVLIHWADDAARRSTLA
VAASLLRHVAAEAVYVGILPEGAGEAQRPLGVRTLLDARSEAQSVHGLDMRTELRFGEAA
EELQHRLGELPEQMLILGVSARAQLRDRFAPLLAKIGALPVMIVYRTAHDADGAVE

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