GapMind for catabolism of small carbon sources

 

Protein H281DRAFT_03746 in Paraburkholderia bryophila 376MFSha3.1

Annotation: H281DRAFT_03746 carbohydrate ABC transporter membrane protein 1, CUT1 family

Length: 296 amino acids

Source: Burk376 in FitnessBrowser

Candidate for 8 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-maltose catabolism thuF lo Maltose transport system permease protein malF aka TT_C1628, 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) 33% 96% 191.4 ABC-type maltose transporter (EC 7.5.2.1) 36% 201.1
sucrose catabolism thuF lo Maltose transport system permease protein malF aka TT_C1628, 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) 33% 96% 191.4 ABC-type maltose transporter (EC 7.5.2.1) 36% 201.1
trehalose catabolism thuF lo Maltose transport system permease protein malF aka TT_C1628, 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) 33% 96% 191.4 ABC-type maltose transporter (EC 7.5.2.1) 36% 201.1
D-glucosamine (chitosamine) catabolism SM_b21220 lo ABC transporter for D-Glucosamine, permease component 2 (characterized) 34% 94% 169.9 ABC-type maltose transporter (EC 7.5.2.1) 36% 201.1
lactose catabolism lacF lo ABC transporter for Lactose, permease component 1 (characterized) 35% 94% 154.1 ABC-type maltose transporter (EC 7.5.2.1) 36% 201.1
xylitol catabolism Dshi_0548 lo ABC transporter for Xylitol, permease component 1 (characterized) 31% 95% 138.3 ABC-type maltose transporter (EC 7.5.2.1) 36% 201.1
D-mannitol catabolism mtlF lo SmoF, component of Hexitol (glucitol; mannitol) porter (characterized) 34% 95% 127.5 ABC-type maltose transporter (EC 7.5.2.1) 36% 201.1
D-sorbitol (glucitol) catabolism mtlF lo SmoF, component of Hexitol (glucitol; mannitol) porter (characterized) 34% 95% 127.5 ABC-type maltose transporter (EC 7.5.2.1) 36% 201.1

Sequence Analysis Tools

View H281DRAFT_03746 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

MSRSASSRLQAPWLLIAPSLVLALFIISYPIFNIVWQSLHEVSRFGAIRDFTGLQNFYTI
FGDPAFLAAARRTIVWTVFVVGGTVLISVPVALVLNQDFYGRGVARTIVMLPWSVSLTMT
AVVWRWAFNDDYGMVNVTLQRLGLIGGPIHWLATPEFAFPVEIAVGILVSIPFTVTILLG
GLSSVPGDIYEAARIDGASAWQQFRKLTLPLLRPFINMTILLNVIYVFNSFPIIWVMTQG
GPDNSTHILVTYLYELGFRLGRPGEAAAVSLIMLVMLFVFSMAYLRLQPAKEGEPS

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