GapMind for catabolism of small carbon sources

 

Protein WP_020176902.1 in Methyloferula stellata AR4T

Annotation: NCBI__GCF_000385335.1:WP_020176902.1

Length: 370 amino acids

Source: GCF_000385335.1 in NCBI

Candidate for 84 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
putrescine catabolism potA hi PotG aka B0855, component of Putrescine porter (characterized) 48% 99% 346.3 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 41% 265.4
D-mannitol catabolism mtlK med SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) 41% 89% 216.5 PotG aka B0855, component of Putrescine porter 48% 346.3
trehalose catabolism thuK med Trehalose import ATP-binding protein SugC; EC 7.5.2.- (characterized) 42% 77% 215.7 PotG aka B0855, component of Putrescine porter 48% 346.3
L-arabinose catabolism xacJ med Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 43% 75% 215.3 PotG aka B0855, component of Putrescine porter 48% 346.3
xylitol catabolism HSERO_RS17020 med ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 42% 73% 214.9 PotG aka B0855, component of Putrescine porter 48% 346.3
N-acetyl-D-glucosamine catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 45% 71% 212.6 PotG aka B0855, component of Putrescine porter 48% 346.3
D-glucosamine (chitosamine) catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 45% 71% 212.6 PotG aka B0855, component of Putrescine porter 48% 346.3
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) 40% 76% 211.1 PotG aka B0855, component of Putrescine porter 48% 346.3
L-fucose catabolism SM_b21106 med ABC transporter for L-Fucose, ATPase component (characterized) 40% 78% 207.6 PotG aka B0855, component of Putrescine porter 48% 346.3
D-maltose catabolism malK_Bb med ABC-type maltose transport, ATP binding protein (characterized, see rationale) 44% 70% 201.8 PotG aka B0855, component of Putrescine porter 48% 346.3
trehalose catabolism treV med TreV, component of Trehalose porter (characterized) 44% 72% 201.8 PotG aka B0855, component of Putrescine porter 48% 346.3
L-glutamate catabolism gltL med GluA aka CGL1950, component of Glutamate porter (characterized) 40% 98% 161.4 PotG aka B0855, component of Putrescine porter 48% 346.3
D-cellobiose catabolism gtsD 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% 91% 240.4 PotG aka B0855, component of Putrescine porter 48% 346.3
D-glucose catabolism gtsD 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% 91% 240.4 PotG aka B0855, component of Putrescine porter 48% 346.3
lactose catabolism gtsD 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% 91% 240.4 PotG aka B0855, component of Putrescine porter 48% 346.3
D-maltose catabolism gtsD 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% 91% 240.4 PotG aka B0855, component of Putrescine porter 48% 346.3
D-maltose catabolism thuK 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% 91% 240.4 PotG aka B0855, component of Putrescine porter 48% 346.3
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% 91% 240.4 PotG aka B0855, component of Putrescine porter 48% 346.3
sucrose catabolism gtsD 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% 91% 240.4 PotG aka B0855, component of Putrescine porter 48% 346.3
sucrose catabolism thuK 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% 91% 240.4 PotG aka B0855, component of Putrescine porter 48% 346.3
trehalose catabolism gtsD 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% 91% 240.4 PotG aka B0855, component of Putrescine porter 48% 346.3
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-sorbitol, ATPase component (characterized) 36% 93% 225.7 PotG aka B0855, component of Putrescine porter 48% 346.3
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 39% 93% 224.6 PotG aka B0855, component of Putrescine porter 48% 346.3
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 37% 100% 222.6 PotG aka B0855, component of Putrescine porter 48% 346.3
D-maltose catabolism malK lo Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 39% 94% 222.6 PotG aka B0855, component of Putrescine porter 48% 346.3
D-cellobiose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 97% 220.7 PotG aka B0855, component of Putrescine porter 48% 346.3
D-glucose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 97% 220.7 PotG aka B0855, component of Putrescine porter 48% 346.3
lactose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 97% 220.7 PotG aka B0855, component of Putrescine porter 48% 346.3
D-maltose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 97% 220.7 PotG aka B0855, component of Putrescine porter 48% 346.3
D-maltose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 97% 220.7 PotG aka B0855, component of Putrescine porter 48% 346.3
sucrose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 97% 220.7 PotG aka B0855, component of Putrescine porter 48% 346.3
sucrose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 97% 220.7 PotG aka B0855, component of Putrescine porter 48% 346.3
trehalose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 97% 220.7 PotG aka B0855, component of Putrescine porter 48% 346.3
trehalose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 97% 220.7 PotG aka B0855, component of Putrescine porter 48% 346.3
D-maltose catabolism malK_Aa lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 40% 90% 218.4 PotG aka B0855, component of Putrescine porter 48% 346.3
lactose catabolism lacK lo LacK, component of Lactose porter (characterized) 38% 89% 218 PotG aka B0855, component of Putrescine porter 48% 346.3
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% 90% 218 PotG aka B0855, component of Putrescine porter 48% 346.3
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 38% 92% 214.9 PotG aka B0855, component of Putrescine porter 48% 346.3
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 36% 91% 205.3 PotG aka B0855, component of Putrescine porter 48% 346.3
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) 35% 93% 205.3 PotG aka B0855, component of Putrescine porter 48% 346.3
D-maltose catabolism musK lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 37% 91% 204.1 PotG aka B0855, component of Putrescine porter 48% 346.3
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 36% 87% 203.8 PotG aka B0855, component of Putrescine porter 48% 346.3
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 87% 202.6 PotG aka B0855, component of Putrescine porter 48% 346.3
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 87% 202.6 PotG aka B0855, component of Putrescine porter 48% 346.3
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 87% 202.6 PotG aka B0855, component of Putrescine porter 48% 346.3
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 87% 202.6 PotG aka B0855, component of Putrescine porter 48% 346.3
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 87% 202.6 PotG aka B0855, component of Putrescine porter 48% 346.3
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 87% 202.6 PotG aka B0855, component of Putrescine porter 48% 346.3
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 87% 202.6 PotG aka B0855, component of Putrescine porter 48% 346.3
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 87% 202.6 PotG aka B0855, component of Putrescine porter 48% 346.3
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) 36% 96% 200.7 PotG aka B0855, component of Putrescine porter 48% 346.3
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 36% 91% 197.6 PotG aka B0855, component of Putrescine porter 48% 346.3
L-proline catabolism opuBA lo BilEA aka OpuBA protein, component of A proline/glycine betaine uptake system. Also reported to be a bile exclusion system that exports oxgall and other bile compounds, BilEA/EB or OpuBA/BB (required for normal virulence) (characterized) 35% 93% 175.6 PotG aka B0855, component of Putrescine porter 48% 346.3
L-proline catabolism proV lo glycine betaine/l-proline transport atp-binding protein prov (characterized) 39% 61% 175.6 PotG aka B0855, component of Putrescine porter 48% 346.3
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 36% 78% 172.2 PotG aka B0855, component of Putrescine porter 48% 346.3
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 36% 78% 172.2 PotG aka B0855, component of Putrescine porter 48% 346.3
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 36% 78% 172.2 PotG aka B0855, component of Putrescine porter 48% 346.3
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 36% 78% 172.2 PotG aka B0855, component of Putrescine porter 48% 346.3
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% 89% 169.9 PotG aka B0855, component of Putrescine porter 48% 346.3
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% 89% 169.9 PotG aka B0855, component of Putrescine porter 48% 346.3
glycerol catabolism glpS lo ABC transporter for Glycerol, ATPase component 1 (characterized) 33% 93% 164.1 PotG aka B0855, component of Putrescine porter 48% 346.3
glycerol catabolism glpT lo GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) 32% 81% 164.1 PotG aka B0855, component of Putrescine porter 48% 346.3
D-alanine catabolism Pf6N2E2_5405 lo ABC transporter for D-Alanine, ATPase component (characterized) 37% 90% 153.7 PotG aka B0855, component of Putrescine porter 48% 346.3
L-asparagine catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 35% 90% 152.1 PotG aka B0855, component of Putrescine porter 48% 346.3
L-aspartate catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 35% 90% 152.1 PotG aka B0855, component of Putrescine porter 48% 346.3
L-lysine catabolism hisP lo Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) 36% 95% 149.1 PotG aka B0855, component of Putrescine porter 48% 346.3
L-asparagine catabolism aatP lo Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 39% 98% 148.3 PotG aka B0855, component of Putrescine porter 48% 346.3
L-aspartate catabolism aatP lo Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 39% 98% 148.3 PotG aka B0855, component of Putrescine porter 48% 346.3
L-histidine catabolism aapP lo ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) 36% 88% 148.3 PotG aka B0855, component of Putrescine porter 48% 346.3
D-glucosamine (chitosamine) catabolism AO353_21725 lo ABC transporter for D-Glucosamine, putative ATPase component (characterized) 35% 98% 144.4 PotG aka B0855, component of Putrescine porter 48% 346.3
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% 92% 144.1 PotG aka B0855, component of Putrescine porter 48% 346.3
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% 92% 144.1 PotG aka B0855, component of Putrescine porter 48% 346.3
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% 92% 144.1 PotG aka B0855, component of Putrescine porter 48% 346.3
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% 92% 144.1 PotG aka B0855, component of Putrescine porter 48% 346.3
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% 92% 144.1 PotG aka B0855, component of Putrescine porter 48% 346.3
D-xylose catabolism xylK_Tm lo Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale) 31% 51% 120.6 PotG aka B0855, component of Putrescine porter 48% 346.3
L-arabinose catabolism xylGsa lo Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale) 32% 86% 110.9 PotG aka B0855, component of Putrescine porter 48% 346.3
myo-inositol catabolism PGA1_c07320 lo Inositol transport system ATP-binding protein (characterized) 30% 89% 110.5 PotG aka B0855, component of Putrescine porter 48% 346.3
D-cellobiose catabolism mglA lo glucose transporter, ATPase component (characterized) 32% 85% 108.2 PotG aka B0855, component of Putrescine porter 48% 346.3
D-glucose catabolism mglA lo glucose transporter, ATPase component (characterized) 32% 85% 108.2 PotG aka B0855, component of Putrescine porter 48% 346.3
lactose catabolism mglA lo glucose transporter, ATPase component (characterized) 32% 85% 108.2 PotG aka B0855, component of Putrescine porter 48% 346.3
D-maltose catabolism mglA lo glucose transporter, ATPase component (characterized) 32% 85% 108.2 PotG aka B0855, component of Putrescine porter 48% 346.3
sucrose catabolism mglA lo glucose transporter, ATPase component (characterized) 32% 85% 108.2 PotG aka B0855, component of Putrescine porter 48% 346.3
trehalose catabolism mglA lo glucose transporter, ATPase component (characterized) 32% 85% 108.2 PotG aka B0855, component of Putrescine porter 48% 346.3

Sequence Analysis Tools

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

Find the best match in UniProt

Compare to protein structures

Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

Find homologs in fast.genomics

Fitness BLAST: loading...

Sequence

MTVPSPDERSLPIISLDRVSKRFAETHAVDDVSLDITRGEFFCLVGGSGSGKTTLLRLIA
GFEQPDVGRILIDGEDMAGEPAYRRPVNMMFQSYALFPHLSVERNIAFGLEEEHRSKAEI
RERVRAALDLFEMDGLAKRRPHQLSGGQRQRVALARALVKRPKILLLDEPLAALDKKLRE
RAQSELVALRARIGITFVMVTHDQEEAMSMASRIALMRDGKIVQIGRPGDLYDTPKSRFA
ADFFGAANLFEGHVTGIAAGEATLESAEASSALRARCDADITIGAAAAVMVRPEQLRVSR
ETPQADNVLRGQIRSLVFLGSTVLCHVGIDSGKTIIARLSPMEYIAAGSPAEGDGVHLSW
PAAAARVLTE

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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