GapMind for catabolism of small carbon sources

 

Protein HSERO_RS16725 in Herbaspirillum seropedicae SmR1

Annotation: HSERO_RS16725 ABC transporter permease

Length: 299 amino acids

Source: HerbieS in FitnessBrowser

Candidate for 13 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-glucosamine (chitosamine) catabolism SM_b21220 med ABC transporter for D-Glucosamine, permease component 2 (characterized) 33% 95% 174.9 ABC-type transporter, integral membrane subunit, component of Trehalose porter. Also binds sucrose (Boucher and Noll, 2011). Induced by glucose and trehalose. Directly regulated by trehalose-responsive regulator TreR 35% 171.4
trehalose catabolism thuF lo ABC-type transporter, integral membrane subunit, component of Trehalose porter. Also binds sucrose (Boucher and Noll, 2011). Induced by glucose and trehalose. Directly regulated by trehalose-responsive regulator TreR (characterized) 35% 92% 171.4 ABC transporter for D-Glucosamine, permease component 2 33% 174.9
sucrose catabolism thuF lo ABC transporter permease (characterized, see rationale) 33% 89% 165.6 ABC transporter for D-Glucosamine, permease component 2 33% 174.9
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% 164.5 ABC transporter for D-Glucosamine, permease component 2 33% 174.9
D-maltose catabolism malF_Aa lo Binding-protein-dependent transport systems inner membrane component (characterized, see rationale) 32% 87% 139 ABC transporter for D-Glucosamine, permease component 2 33% 174.9
D-cellobiose catabolism msdB1 lo Binding-protein-dependent transport systems inner membrane component (characterized, see rationale) 30% 89% 134.8 ABC transporter for D-Glucosamine, permease component 2 33% 174.9
L-fucose catabolism SM_b21104 lo ABC transporter for L-Fucose, permease component 1 (characterized) 32% 92% 132.5 ABC transporter for D-Glucosamine, permease component 2 33% 174.9
lactose catabolism lacF lo ABC transporter for Lactose, permease component 1 (characterized) 33% 95% 131.7 ABC transporter for D-Glucosamine, permease component 2 33% 174.9
D-cellobiose catabolism cebF lo CBP protein aka CebF, component of The cellobiose/cellotriose (and possibly higher cellooligosaccharides), CebEFGMsiK [MsiK functions to energize several ABC transporters including those for maltose/maltotriose and trehalose] (characterized) 31% 89% 117.1 ABC transporter for D-Glucosamine, permease component 2 33% 174.9
D-mannitol catabolism mtlF lo SmoF, component of Hexitol (glucitol; mannitol) porter (characterized) 31% 94% 110.2 ABC transporter for D-Glucosamine, permease component 2 33% 174.9
D-sorbitol (glucitol) catabolism mtlF lo SmoF, component of Hexitol (glucitol; mannitol) porter (characterized) 31% 94% 110.2 ABC transporter for D-Glucosamine, permease component 2 33% 174.9
D-maltose catabolism malF lo Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 32% 51% 102.4 ABC transporter for D-Glucosamine, permease component 2 33% 174.9
D-maltose catabolism malG lo ABC-type maltose transporter (subunit 2/3) (EC 7.5.2.1) (characterized) 36% 55% 70.5 ABC transporter for D-Glucosamine, permease component 2 33% 174.9

Sequence Analysis Tools

View HSERO_RS16725 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

MLSRFLNNRNVLGMLFMAPAVILLVVFLTYPLGLGIWLGFTDTKIGGEGSFIGLDNFTYL
AGDSLAQLSLFNTVFYTVSASILKFMLGLWLAILLNKNVPLKTFFRAIVLLPWIVPTALS
ALAFWWLYDAQFSVISWALHKMGLIDRYIDFLGDPWNARWSTVFANVWRGIPFVAISLLA
GLQTISPSLYEAAAIDGATPWQQFRHVTLPLLTPIIAVVMTFSVLFTFTDFQLIYVLTRG
GPLNATHLMATLSFQRAIPGGALGEGAALATYMIPFLLAAIMFSYFGLQRRGWQQGGDK

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