GapMind for catabolism of small carbon sources

 

Protein WP_010538045.1 in Bacteroides faecis MAJ27

Annotation: NCBI__GCF_000226135.1:WP_010538045.1

Length: 224 amino acids

Source: GCF_000226135.1 in NCBI

Candidate for 25 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) 42% 62% 151 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) 42% 62% 151 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) 42% 62% 151 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) 42% 62% 151 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) 42% 62% 151 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) 42% 62% 151 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) 42% 62% 151 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) 42% 62% 151 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
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 37% 63% 128.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 37% 63% 128.6 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
citrate catabolism fecE lo iron(III) dicitrate transport ATP-binding protein FecE (characterized) 32% 85% 110.9 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
L-arabinose catabolism xylGsa lo Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale) 35% 80% 104 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 48% 219.9

Sequence Analysis Tools

View WP_010538045.1 at NCBI

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

MIRTINLQKIFKTEEVETWALNNVSIEVKQGEFVAIMGPSGCGKSTLLNILGLLDNPTGG
EYYLNGTEVSKYTESQRTSLRKGVIGFVFQSFNLIDELNVYENIELPLLYMGISASERKK
RVETAMERMAITHRSKHFPQQLSGGQQQRVAIARAVVANPKLILADEPTGNLDSKNGKEV
MGLLSELNKEGTTIVMVTHSQHDAGYADRIINLFDGQVVTEVSM

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