GapMind for catabolism of small carbon sources

 

Protein 350994 in Bacteroides thetaiotaomicron VPI-5482

Annotation: BT1466 ABC transporter ATP-binding protein (NCBI ptt file)

Length: 238 amino acids

Source: Btheta in FitnessBrowser

Candidate for 16 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-asparagine catabolism bgtA med ATPase (characterized, see rationale) 41% 79% 146 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 46% 211.1
L-aspartate catabolism bgtA med ATPase (characterized, see rationale) 41% 79% 146 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 46% 211.1
D-maltose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 42% 60% 144.8 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 46% 211.1
sucrose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 42% 60% 144.8 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 46% 211.1
trehalose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 42% 60% 144.8 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 46% 211.1
D-maltose catabolism malK lo ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized) 40% 57% 140.2 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 46% 211.1
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 38% 64% 139 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 46% 211.1
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) 36% 54% 136.3 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 46% 211.1
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 39% 62% 136 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 46% 211.1
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 39% 62% 136 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 46% 211.1
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 37% 54% 132.9 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 46% 211.1
glycerol catabolism glpT lo GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) 34% 57% 119.4 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 46% 211.1
L-histidine catabolism hutV lo ABC transporter for L-Histidine, ATPase component (characterized) 32% 86% 119 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 46% 211.1
citrate catabolism fecE lo iron(III) dicitrate transport ATP-binding protein FecE (characterized) 31% 85% 115.9 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 46% 211.1
D-mannose catabolism TM1749 lo TM1749, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized) 33% 73% 114.8 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 46% 211.1
glycerol catabolism glpS lo GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized) 34% 53% 104 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 46% 211.1

Sequence Analysis Tools

View 350994 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

MIKTEKLSMLFTTEEVQTKALNEVTLHVEQGEFVAIMGPSGCGKSTLLNILGTLDSPTSG
SYFFEGKQVDKMNENQLTALRKNNLGFIFQSFNLIDELTVYENVELPLVYMGIKTAQRKE
KVNKVLEKVNLLHRANHYPQQLSGGQQQRVAIARAVVTDCKLLLADEPTGNLDSVNGVEV
MELLSELNRQGTTIIIVTHSQRDATYAHRIIRLLDGQIVSENINRPLEKSTSSKNEAV

This GapMind analysis is from Sep 17 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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