GapMind for catabolism of small carbon sources

 

Protein N515DRAFT_1562 in Dyella japonica UNC79MFTsu3.2

Annotation: N515DRAFT_1562 sulfate transport system ATP-binding protein

Length: 384 amino acids

Source: Dyella79 in FitnessBrowser

Candidate for 99 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 PotG aka B0855, component of Putrescine porter (characterized) 41% 92% 242.3 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
D-maltose catabolism thuK med Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 45% 76% 229.6 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
trehalose catabolism thuK med Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 45% 76% 229.6 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
sucrose catabolism thuK med ABC transporter (characterized, see rationale) 44% 78% 229.2 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
D-cellobiose catabolism gtsD med Sugar ABC transporter ATP-binding protein (characterized, see rationale) 40% 85% 225.7 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
D-glucose catabolism gtsD med Sugar ABC transporter ATP-binding protein (characterized, see rationale) 40% 85% 225.7 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
lactose catabolism gtsD med Sugar ABC transporter ATP-binding protein (characterized, see rationale) 40% 85% 225.7 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
D-maltose catabolism gtsD med Sugar ABC transporter ATP-binding protein (characterized, see rationale) 40% 85% 225.7 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
sucrose catabolism gtsD med Sugar ABC transporter ATP-binding protein (characterized, see rationale) 40% 85% 225.7 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
trehalose catabolism gtsD med Sugar ABC transporter ATP-binding protein (characterized, see rationale) 40% 85% 225.7 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
N-acetyl-D-glucosamine catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 43% 80% 223.4 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
D-glucosamine (chitosamine) catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 43% 80% 223.4 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
D-glucosamine (chitosamine) catabolism SM_b21216 med ABC transporter for D-Glucosamine, ATPase component (characterized) 43% 85% 221.1 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
D-mannitol catabolism mtlK med SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) 41% 95% 221.1 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
xylitol catabolism HSERO_RS17020 med ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 43% 72% 215.7 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
D-sorbitol (glucitol) catabolism mtlK med MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized) 40% 80% 212.2 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
D-maltose catabolism malK med Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 41% 78% 210.7 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
trehalose catabolism treV med TreV, component of Trehalose porter (characterized) 42% 77% 207.2 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
D-cellobiose catabolism SMc04256 med ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 43% 80% 205.7 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
D-maltose catabolism malK_Sm med 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) 40% 79% 205.7 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
trehalose catabolism malK med 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) 40% 79% 205.7 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
D-maltose catabolism musK med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 41% 74% 205.3 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
D-maltose catabolism malK_Bb med ABC-type maltose transport, ATP binding protein (characterized, see rationale) 44% 70% 204.5 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
L-histidine catabolism hutV med ABC transporter for L-Histidine, ATPase component (characterized) 41% 85% 179.1 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
L-histidine catabolism PA5503 med Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) 42% 76% 178.7 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
L-arginine catabolism artP med Arginine transport ATP-binding protein ArtM (characterized) 41% 99% 173.7 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
L-asparagine catabolism bgtA med ATPase (characterized, see rationale) 42% 88% 157.9 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
L-aspartate catabolism bgtA med ATPase (characterized, see rationale) 42% 88% 157.9 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
L-histidine catabolism Ac3H11_2560 med ABC transporter for L-Histidine, ATPase component (characterized) 43% 83% 156 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
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% 89% 226.9 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 48% 69% 215.7 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
lactose catabolism lacK lo ABC transporter for Lactose, ATPase component (characterized) 38% 99% 213.8 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 38% 93% 213 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
D-maltose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 40% 88% 211.8 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
sucrose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 40% 88% 211.8 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
trehalose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 40% 88% 211.8 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 45% 64% 211.5 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 39% 98% 211.1 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
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) 38% 93% 210.7 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 38% 98% 206.8 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 40% 78% 203 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
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% 88% 198.7 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 94% 198.4 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 94% 198.4 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 94% 198.4 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 94% 198.4 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 94% 198.4 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 94% 198.4 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 94% 198.4 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 94% 198.4 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
D-maltose catabolism malK_Aa lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 40% 71% 197.2 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
D-cellobiose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 78% 192.6 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
D-glucose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 78% 192.6 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
lactose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 78% 192.6 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
D-maltose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 78% 192.6 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
sucrose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 78% 192.6 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
trehalose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 78% 192.6 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
L-proline catabolism proV lo Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized) 44% 59% 189.1 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 35% 79% 182.6 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 35% 79% 182.6 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 35% 79% 182.6 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 35% 79% 182.6 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
glycerol catabolism glpT lo GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) 33% 97% 176.8 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
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% 90% 172.2 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
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% 59% 170.2 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
L-lysine catabolism hisP lo Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) 40% 91% 169.1 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
L-asparagine catabolism aatP lo ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) 36% 100% 161.4 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
L-aspartate catabolism aatP lo ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) 36% 100% 161.4 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
L-glutamate catabolism gltL lo Amino acid ABC transporter ATP binding protein, component of Amino acid transporter, AatJMQP. Probably transports L-glutamic acid, D-glutamine acid, L-glutamine and N-acetyl L-glutamic acid (Johnson et al. 2008). Very similar to 3.A.1.3.19 of P. putida (characterized) 39% 92% 161.4 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
D-alanine catabolism Pf6N2E2_5405 lo ABC transporter for D-Alanine, ATPase component (characterized) 38% 89% 160.2 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
D-glucosamine (chitosamine) catabolism AO353_21725 lo ABC transporter for D-glucosamine, ATPase component (characterized) 38% 92% 159.8 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
L-histidine catabolism aapP lo ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) 36% 88% 157.9 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
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) 36% 89% 156.8 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
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) 36% 89% 156.8 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
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) 36% 89% 156.8 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
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) 36% 89% 156.8 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
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) 36% 89% 156.8 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
L-asparagine catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 34% 92% 155.6 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
L-aspartate catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 34% 92% 155.6 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
glycerol catabolism glpS lo ABC transporter for Glycerol, ATPase component 1 (characterized) 40% 61% 154.8 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
L-histidine catabolism BPHYT_RS24015 lo ABC transporter related (characterized, see rationale) 38% 95% 154.5 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
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) 37% 93% 154.1 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
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) 35% 97% 152.1 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
L-histidine catabolism bgtA lo BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 36% 95% 147.9 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
L-asparagine catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 34% 98% 142.9 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
L-aspartate catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 34% 98% 142.9 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
L-citrulline catabolism AO353_03040 lo ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 33% 98% 140.6 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
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) 34% 91% 140.2 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
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) 35% 93% 136 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
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) 35% 93% 136 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
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) 35% 93% 136 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
L-tryptophan catabolism ecfA2 lo Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) 38% 77% 132.9 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
L-tryptophan catabolism ecfA1 lo Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) 38% 80% 131.7 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
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% 77% 127.9 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
L-proline catabolism HSERO_RS00895 lo ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale) 30% 98% 123.2 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
D-cellobiose catabolism cbtF lo CbtF, component of Cellobiose and cellooligosaccharide porter (characterized) 34% 73% 121.3 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
D-mannose catabolism TM1749 lo TM1749, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized) 32% 78% 120.6 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
D-cellobiose catabolism cbtD lo CbtD, component of Cellobiose and cellooligosaccharide porter (characterized) 31% 67% 114.8 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
citrate catabolism fecE lo iron(III) dicitrate transport ATP-binding protein FecE (characterized) 35% 88% 111.3 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4

Sequence Analysis Tools

View N515DRAFT_1562 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

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

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

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices: TMHMM

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MSLSIRQLTRRYGAFAALDDFSLDIAEGEFVALLGPSGSGKSSLLRILAGLDDPDRGDVL
RDGTDLLALPAQRRDIGLVFQHYALFPHMTVADNIAFGLRVRPRARRPSRRDIAARVEDL
LRRVQLEELGRRYPTQLSGGQRQRVALARALAVEPSLLLLDEPFGALDAQVRGTLRVWLR
DLQRSLGLTTVLVTHDQDEALELADRVVVMNRGRIEQVGAPSEIYREPATPFVHGFVGRA
NRIRGHVERDRLHLGGHSFQGELPGDLAGREIEAWLRPEHLALASRGLGGWTGRLQHLDL
AGPVARARLAMHGDGLVLDAEWNAAEVAAHGLAIGEVVTLQPREFTLFADVPGGVRRLRF
VPAPAGPHADSHPIDFAAWLHRKA

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory