GapMind for catabolism of small carbon sources

 

Protein H281DRAFT_01451 in Paraburkholderia bryophila 376MFSha3.1

Annotation: H281DRAFT_01451 carbohydrate ABC transporter ATP-binding protein, CUT1 family

Length: 415 amino acids

Source: Burk376 in FitnessBrowser

Candidate for 11 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-cellobiose catabolism SMc04256 hi ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 52% 100% 359 AlgS, component of Alginate (MW 27,000 Da) (and Alginate oligosaccharides) uptake porter. Sphingomonas species A1 is a 'pit-forming' bacterium that directly incorporates alginate into its cytoplasm through a pit-dependent transport system, termed a 'superchannel' (Murata et al., 2008). The pit is a novel organ acquired through the fluidity and reconstitution of cell surface molecules, and through cooperation with the transport machinery in the cells. It confers upon bacterial cells a more efficient way to secure and assimilate macromolecules 47% 320.9
D-cellobiose catabolism gtsD med ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 45% 94% 319.3 ABC transporter for D-Cellobiose and D-Salicin, ATPase component 52% 359.0
D-glucose catabolism gtsD med ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 45% 94% 319.3 ABC transporter for D-Cellobiose and D-Salicin, ATPase component 52% 359.0
lactose catabolism gtsD med ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 45% 94% 319.3 ABC transporter for D-Cellobiose and D-Salicin, ATPase component 52% 359.0
D-maltose catabolism gtsD med ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 45% 94% 319.3 ABC transporter for D-Cellobiose and D-Salicin, ATPase component 52% 359.0
sucrose catabolism gtsD med ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 45% 94% 319.3 ABC transporter for D-Cellobiose and D-Salicin, ATPase component 52% 359.0
trehalose catabolism gtsD med ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 45% 94% 319.3 ABC transporter for D-Cellobiose and D-Salicin, ATPase component 52% 359.0
D-xylose catabolism gtsD med ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 45% 94% 319.3 ABC transporter for D-Cellobiose and D-Salicin, ATPase component 52% 359.0
D-galactose catabolism PfGW456L13_1897 med ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 44% 94% 309.3 ABC transporter for D-Cellobiose and D-Salicin, ATPase component 52% 359.0
L-arabinose catabolism xacK med Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 46% 91% 286.6 ABC transporter for D-Cellobiose and D-Salicin, ATPase component 52% 359.0
glycerol catabolism glpS lo GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized) 34% 98% 198.4 ABC transporter for D-Cellobiose and D-Salicin, ATPase component 52% 359.0

Sequence Analysis Tools

View H281DRAFT_01451 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MTYVVKQANTLASPLTGAADMTESADTARTDNMPGVADTADTAHAANVAVRNLTIRLGGN
TVIENLDLDVQPGEFVVLLGPSGCGKSTLLHSIAGLIDVTDGSIEIAGEDMTWADPKDRR
IALVFQSYALYPTMSVERNLSFALRINGTPKAEIARRVARAAEMLQLGPLLKRKPAQLSG
GQRQRVAIGRAIVREADVFLFDEPLSNLDAKLRTELRRELKQLHQRLGATMIYVTHDQVE
AMMLATRMAVMRGGAIQQFGTPAEVYARPANLFVATFLGTPAMNLVNGTLEQRDGALHFC
TEQWRLDVSNYAFVDRSGESQPQSQPQSPPRPCVLGVRAEDVRIGPTQGEGAGEHAKISL
VEPMGNHRVVWLDYHGVQIASIDQSKTPVMPGDTLAFSLDSTHVSLFDAASGARL

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 (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 paper from 2022 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