GapMind for catabolism of small carbon sources

 

Protein WP_011938227.1 in Geotalea uraniireducens Rf4

Annotation: NCBI__GCF_000016745.1:WP_011938227.1

Length: 353 amino acids

Source: GCF_000016745.1 in NCBI

Candidate for 70 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 ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component (characterized) 42% 91% 229.9 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 45% 251.5
L-arabinose catabolism xacK med Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 46% 70% 228.4 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 45% 251.5
xylitol catabolism HSERO_RS17020 med ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 44% 75% 225.7 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 45% 251.5
D-sorbitol (glucitol) catabolism mtlK med MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized) 41% 91% 225.3 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 45% 251.5
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) 48% 71% 224.9 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 45% 251.5
trehalose catabolism thuK 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) 48% 71% 224.9 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 45% 251.5
lactose catabolism lacK med ABC transporter for Lactose, ATPase component (characterized) 41% 89% 224.2 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 45% 251.5
putrescine catabolism potA med spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) 42% 81% 224.2 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 45% 251.5
D-maltose catabolism malK_Bb med ABC-type maltose transport, ATP binding protein (characterized, see rationale) 46% 71% 214.5 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 45% 251.5
D-cellobiose catabolism gtsD 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) 40% 91% 214.2 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 45% 251.5
D-glucosamine (chitosamine) catabolism SM_b21216 med ABC transporter for D-Glucosamine, ATPase component (characterized) 41% 94% 214.2 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 45% 251.5
D-glucose catabolism gtsD 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) 40% 91% 214.2 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 45% 251.5
lactose catabolism gtsD 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) 40% 91% 214.2 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 45% 251.5
D-maltose catabolism gtsD 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) 40% 91% 214.2 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 45% 251.5
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) 40% 91% 214.2 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 45% 251.5
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) 40% 91% 214.2 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 45% 251.5
sucrose catabolism gtsD 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) 40% 91% 214.2 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 45% 251.5
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) 40% 91% 214.2 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 45% 251.5
trehalose catabolism gtsD 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) 40% 91% 214.2 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 45% 251.5
N-acetyl-D-glucosamine catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 48% 71% 212.2 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 45% 251.5
D-glucosamine (chitosamine) catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 48% 71% 212.2 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 45% 251.5
D-cellobiose catabolism SMc04256 med ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 42% 81% 209.9 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 45% 251.5
D-cellobiose catabolism glcV med monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 42% 76% 206.8 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 45% 251.5
D-galactose catabolism glcV med monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 42% 76% 206.8 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 45% 251.5
D-glucose catabolism glcV med monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 42% 76% 206.8 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 45% 251.5
lactose catabolism glcV med monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 42% 76% 206.8 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 45% 251.5
D-maltose catabolism glcV med monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 42% 76% 206.8 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 45% 251.5
D-mannose catabolism glcV med monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 42% 76% 206.8 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 45% 251.5
sucrose catabolism glcV med monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 42% 76% 206.8 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 45% 251.5
trehalose catabolism glcV med monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 42% 76% 206.8 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 45% 251.5
D-xylose catabolism gtsD med ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 42% 76% 206.8 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 45% 251.5
D-galactose catabolism PfGW456L13_1897 med ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 43% 76% 206.5 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 45% 251.5
xylitol catabolism Dshi_0546 med ABC transporter for Xylitol, ATPase component (characterized) 46% 75% 205.7 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 45% 251.5
L-arabinose catabolism xacJ med Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 41% 77% 202.2 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 45% 251.5
D-maltose catabolism malK med Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 43% 77% 201.8 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 45% 251.5
D-maltose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 41% 81% 201.4 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 45% 251.5
sucrose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 41% 81% 201.4 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 45% 251.5
trehalose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 41% 81% 201.4 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 45% 251.5
L-arabinose catabolism araV med AraV, component of Arabinose, fructose, xylose porter (characterized) 41% 72% 199.5 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 45% 251.5
D-fructose catabolism araV med AraV, component of Arabinose, fructose, xylose porter (characterized) 41% 72% 199.5 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 45% 251.5
sucrose catabolism araV med AraV, component of Arabinose, fructose, xylose porter (characterized) 41% 72% 199.5 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 45% 251.5
D-xylose catabolism araV med AraV, component of Arabinose, fructose, xylose porter (characterized) 41% 72% 199.5 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 45% 251.5
trehalose catabolism treV med TreV, component of Trehalose porter (characterized) 42% 72% 188.7 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 45% 251.5
D-maltose catabolism malK_Aa lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 50% 64% 227.6 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 45% 251.5
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 39% 94% 217.6 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 45% 251.5
D-maltose catabolism musK lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 39% 90% 214.2 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 45% 251.5
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) 39% 89% 204.1 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 45% 251.5
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) 37% 94% 199.1 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 45% 251.5
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) 37% 94% 199.1 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 45% 251.5
D-cellobiose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 43% 66% 189.9 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 45% 251.5
D-glucose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 43% 66% 189.9 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 45% 251.5
lactose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 43% 66% 189.9 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 45% 251.5
D-maltose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 43% 66% 189.9 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 45% 251.5
sucrose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 43% 66% 189.9 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 45% 251.5
trehalose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 43% 66% 189.9 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 45% 251.5
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) 34% 90% 177.9 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 45% 251.5
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% 97% 166.4 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 45% 251.5
L-glutamate catabolism gltL 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% 97% 166.4 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 45% 251.5
L-histidine catabolism BPHYT_RS24015 lo ABC transporter related (characterized, see rationale) 36% 96% 164.1 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 45% 251.5
L-histidine catabolism hisP lo histidine transport ATP-binding protein hisP (characterized) 37% 98% 163.7 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 45% 251.5
L-lysine catabolism hisP lo histidine transport ATP-binding protein hisP (characterized) 37% 98% 163.7 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 45% 251.5
glycerol catabolism glpT lo GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) 34% 79% 157.1 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 45% 251.5
D-glucosamine (chitosamine) catabolism AO353_21725 lo ABC transporter for D-glucosamine, ATPase component (characterized) 38% 94% 156.8 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 45% 251.5
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) 38% 81% 153.7 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 45% 251.5
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) 38% 81% 153.7 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 45% 251.5
L-asparagine catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 37% 98% 150.6 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 45% 251.5
L-aspartate catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 37% 98% 150.6 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 45% 251.5
L-citrulline catabolism AO353_03040 lo ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 33% 98% 147.1 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 45% 251.5
L-histidine catabolism bgtA lo BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 33% 96% 140.6 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 45% 251.5
glycerol catabolism glpS lo ABC transporter for Glycerol, ATPase component 1 (characterized) 33% 80% 139 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 45% 251.5

Sequence Analysis Tools

View WP_011938227.1 at NCBI

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MTSIELSVHDLHVTLGKNHILKGVSLDVNKGEIVALLGPSGSGKTTLLRSIAGLELPSHG
SIRIGEQMVFESAKKIEVSVEKRCLGFVFQSYALWPHRTVYENVAYGLKLRKVPDGEIRQ
RVQEVLANLGLGDLSERHPHQLSGGQQQRVALARSLVYNPQVILLDEPLSNLDAKLREEA
RIWLRQLIIDLNLSAVCVTHDQAEAMAMADKVVLLKDGVIEQAGTPQEMYGAPKSLFVAE
FMGANNTISGLVTDVDGDSARIEGNGWALRGRLRTPLKAGDRATAVVRLEKIKLAQTPKE
NSLRLPLTASVYLGNTWEYVFDLAGATIRGYGNEFMQPGEQLVDIPAEHLWLF

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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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