GapMind for catabolism of small carbon sources

 

Protein 350222 in Bacteroides thetaiotaomicron VPI-5482

Annotation: FitnessBrowser__Btheta:350222

Length: 224 amino acids

Source: Btheta in FitnessBrowser

Candidate for 30 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 39% 61% 152.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 220.7
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 39% 61% 152.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 220.7
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 39% 61% 152.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 220.7
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 39% 61% 152.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 220.7
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 39% 61% 152.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 220.7
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 39% 61% 152.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 220.7
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 39% 61% 152.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 220.7
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 39% 61% 152.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 220.7
L-arginine catabolism artP 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) 38% 87% 147.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 220.7
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) 38% 87% 147.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 220.7
L-lysine 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) 38% 87% 147.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 220.7
L-histidine catabolism BPHYT_RS24015 lo ABC transporter related (characterized, see rationale) 37% 87% 143.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 220.7
putrescine catabolism potA lo Spermidine/putrescine import ATP-binding protein PotA, component of The spermidine/putrescine uptake porter, PotABCD (characterized) 39% 56% 141 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 220.7
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) 37% 57% 137.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 220.7
trehalose catabolism thuK 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) 37% 57% 137.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 220.7
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) 36% 56% 135.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 220.7
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) 36% 56% 135.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 220.7
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) 36% 56% 135.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 220.7
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) 36% 56% 135.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 220.7
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) 36% 56% 135.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 220.7
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) 36% 56% 135.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 220.7
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) 36% 56% 135.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 220.7
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) 36% 56% 135.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 220.7
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 36% 55% 134 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 220.7
D-mannitol catabolism mtlK lo SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) 37% 63% 130.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 220.7
L-isoleucine catabolism livG lo High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter (characterized) 32% 77% 95.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 220.7
L-leucine catabolism livG lo High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter (characterized) 32% 77% 95.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 220.7
L-phenylalanine catabolism livG lo High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter (characterized) 32% 77% 95.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 220.7
L-valine catabolism livG lo High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter (characterized) 32% 77% 95.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 220.7
D-cellobiose catabolism TM0028 lo TM0028, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized) 30% 71% 89.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 220.7

Sequence Analysis Tools

View 350222 at FitnessBrowser

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

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Sequence

MIQIENISKVFRTTEVETVALNHVNLEVKEGEFVAIMGPSGCGKSTLLNILGLLDNPTEG
SYRLLGEEVAGLKEKERTGVRKGKLGFVFQSFNLIDELNVFENVELPLTYLGIKSSERRR
MVEDILKRMNISHRAKHFPQQLSGGQQQRVAIARAVVTNPKLILADEPTGNLDSKNGAEV
MNLLTELNKEGTTIIMVTHSQHDASFAHRTVHLFDGSVVASVTA

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

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About GapMind

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

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

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

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

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

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

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

For more information, see:

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

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory