GapMind for catabolism of small carbon sources

 

Protein WP_012676168.1 in Persephonella marina EX-H1

Annotation: NCBI__GCF_000021565.1:WP_012676168.1

Length: 287 amino acids

Source: GCF_000021565.1 in NCBI

Candidate for 82 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-sorbitol (glucitol) catabolism mtlK med ABC transporter for D-Sorbitol, ATPase component (characterized) 40% 71% 161.4 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7
L-asparagine catabolism glnQ med 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) 41% 88% 157.9 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7
L-glutamate catabolism gltL med 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) 41% 88% 157.9 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7
L-arginine catabolism artP med Arginine transport ATP-binding protein ArtP; EC 7.4.2.- (characterized) 40% 85% 141.4 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7
putrescine catabolism potA lo spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) 46% 59% 190.7 Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 44% 185.7
D-maltose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 44% 60% 185.7 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7
trehalose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 44% 60% 185.7 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 45% 53% 184.5 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 45% 59% 176.8 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7
D-cellobiose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 41% 61% 176 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7
D-glucose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 41% 61% 176 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7
lactose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 41% 61% 176 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7
D-maltose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 41% 61% 176 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7
sucrose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 41% 61% 176 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7
trehalose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 41% 61% 176 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7
sucrose catabolism thuK lo ABC transporter (characterized, see rationale) 42% 62% 175.3 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7
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) 45% 54% 172.9 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 36% 67% 170.2 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7
D-maltose catabolism malK lo Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 36% 73% 170.2 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 41% 64% 169.5 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7
lactose catabolism lacK lo ABC transporter for Lactose, ATPase component (characterized) 41% 70% 168.7 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7
D-mannitol catabolism mtlK lo SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) 42% 65% 167.5 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 42% 65% 166.8 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 42% 65% 166.8 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7
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% 66% 165.6 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 41% 66% 165.6 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 81% 164.1 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 81% 164.1 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 81% 164.1 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 81% 164.1 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 81% 164.1 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 81% 164.1 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 81% 164.1 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 81% 164.1 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7
trehalose catabolism treV lo TreV, component of Trehalose porter (characterized) 41% 65% 162.9 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7
D-maltose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 45% 56% 162.5 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7
sucrose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 45% 56% 162.5 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7
trehalose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 45% 56% 162.5 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7
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) 36% 76% 162.5 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 38% 72% 162.5 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7
D-maltose catabolism malK_Aa lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 39% 64% 161.8 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 35% 73% 160.2 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 35% 73% 160.2 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 35% 73% 160.2 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 35% 73% 160.2 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7
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) 37% 70% 158.7 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7
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) 40% 57% 158.3 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 38% 60% 157.9 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7
D-cellobiose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 39% 65% 156.4 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 35% 77% 156.4 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7
D-glucose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 39% 65% 156.4 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7
lactose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 39% 65% 156.4 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7
D-maltose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 39% 65% 156.4 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7
sucrose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 39% 65% 156.4 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7
trehalose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 39% 65% 156.4 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7
D-maltose catabolism musK lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 35% 69% 156 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 38% 57% 155.6 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7
L-proline catabolism proV lo Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized) 38% 57% 155.2 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7
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) 35% 64% 153.3 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7
L-asparagine catabolism aatP lo Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 37% 95% 150.2 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7
L-aspartate catabolism aatP lo Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 37% 95% 150.2 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 39% 60% 143.3 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7
L-asparagine catabolism bgtA lo ATPase (characterized, see rationale) 37% 85% 141.7 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7
L-aspartate catabolism bgtA lo ATPase (characterized, see rationale) 37% 85% 141.7 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7
L-tryptophan catabolism ecfA2 lo Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) 39% 76% 141.4 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7
D-glucosamine (chitosamine) catabolism AO353_21725 lo ABC transporter for D-glucosamine, ATPase component (characterized) 39% 81% 140.2 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7
L-histidine catabolism aapP lo ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) 36% 86% 139 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7
L-asparagine catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 35% 92% 138.7 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7
L-aspartate catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 35% 92% 138.7 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7
glycerol catabolism glpS lo ABC transporter for Glycerol, ATPase component 1 (characterized) 33% 56% 127.9 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7
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) 32% 88% 126.3 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7
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) 32% 88% 126.3 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7
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) 32% 88% 126.3 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7
L-phenylalanine catabolism livG lo ABC transporter ATP-binding protein (characterized, see rationale) 35% 92% 116.3 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7
L-proline catabolism HSERO_RS00895 lo ABC transporter ATP-binding protein (characterized, see rationale) 35% 92% 116.3 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7
L-serine catabolism Ac3H11_1693 lo ABC transporter ATP-binding protein (characterized, see rationale) 35% 92% 116.3 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7
L-tyrosine catabolism Ac3H11_1693 lo ABC transporter ATP-binding protein (characterized, see rationale) 35% 92% 116.3 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7
L-isoleucine catabolism livF lo high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized) 32% 82% 97.4 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7
L-leucine catabolism livF lo high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized) 32% 82% 97.4 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7
L-phenylalanine catabolism livF lo high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized) 32% 82% 97.4 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7
L-valine catabolism livF lo high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized) 32% 82% 97.4 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7
L-proline catabolism HSERO_RS00900 lo ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale) 30% 98% 92.8 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 190.7

Sequence Analysis Tools

View WP_012676168.1 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

MIRINIEKELLGDGGRFSLRLDLHIKKGEFVTLFGRSGSGKTTVLRMISGLEKPDRGKIE
IDGKVYFDSEKGIDLPPQKRNIGFVFQNYALFPNMTVLENILFAMDRPDREKAIELLKTV
HLEDLKDRYPDTLSGGQQQRVAVARALAREPSILLLDEPLSALDFSIREKLQEEIKRIHR
VFNLTTILVSHDKTEVFKLSDRVVWIEKGRIIKEGSPRKVFIEKNISGKFSFIGNVLQIK
KADTIYIATIEIGDNLVEVVLSDRDEISVGDKVIVSSKAFNPVVKKL

This GapMind analysis is from Sep 24 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 (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