GapMind for catabolism of small carbon sources

 

Protein 350388 in Bacteroides thetaiotaomicron VPI-5482

Annotation: BT0860 putative ABC transporter ATP-binding protein (NCBI ptt file)

Length: 224 amino acids

Source: Btheta in FitnessBrowser

Candidate for 22 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) 41% 62% 149.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 41% 62% 149.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 41% 62% 149.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 41% 62% 149.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 41% 62% 149.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 41% 62% 149.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 41% 62% 149.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 41% 62% 149.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
L-asparagine catabolism bgtA lo ATPase (characterized, see rationale) 38% 85% 145.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
L-aspartate catabolism bgtA lo ATPase (characterized, see rationale) 38% 85% 145.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
D-maltose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 41% 60% 143.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
sucrose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 41% 60% 143.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
trehalose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 41% 60% 143.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
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% 135.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
D-maltose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 38% 54% 134.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
sucrose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 38% 54% 134.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
trehalose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 38% 54% 134.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
D-maltose catabolism musK lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 38% 52% 129.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 36% 56% 129.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 38% 54% 119 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
D-cellobiose catabolism TM0027 lo TM0027, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized) 33% 85% 108.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
D-cellobiose catabolism cbtD lo CbtD, component of Cellobiose and cellooligosaccharide porter (characterized) 37% 59% 105.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9

Sequence Analysis Tools

View 350388 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 and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MIKTINLQKIFKTEEVETWALNNVSIEVKQGEFVAIMGPSGCGKSTLLNILGLLDNPTGG
EYYLNGTEVSKYTESQRTSLRKGVIGFVFQSFNLIDELNVYENIELPLLYMGISASERKK
RVETAMERMAITHRSKHFPQQLSGGQQQRVAIARAVVANPKLILADEPTGNLDSKNGKEV
MGLLSELNKEGTTIVMVTHSQHDAGYADRIINLFDGQVVTEVSM

This GapMind analysis is from Sep 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, 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