GapMind for catabolism of small carbon sources

 

Protein BWI76_RS03135 in Klebsiella michiganensis M5al

Annotation: BWI76_RS03135 sugar ABC transporter permease

Length: 290 amino acids

Source: Koxy in FitnessBrowser

Candidate for 18 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
N-acetyl-D-glucosamine catabolism ngcF lo NgcF, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) (characterized) 32% 93% 141.7 ABC-type glycerol 3-phosphate transporter (EC 7.6.2.10) 32% 164.5
D-glucosamine (chitosamine) catabolism ngcF lo NgcF, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) (characterized) 32% 93% 141.7 ABC-type glycerol 3-phosphate transporter (EC 7.6.2.10) 32% 164.5
D-cellobiose catabolism aglF' lo Inner membrane ABC transporter permease protein (characterized, see rationale) 31% 79% 133.7 ABC-type glycerol 3-phosphate transporter (EC 7.6.2.10) 32% 164.5
D-glucose catabolism aglF' lo Inner membrane ABC transporter permease protein (characterized, see rationale) 31% 79% 133.7 ABC-type glycerol 3-phosphate transporter (EC 7.6.2.10) 32% 164.5
lactose catabolism aglF' lo Inner membrane ABC transporter permease protein (characterized, see rationale) 31% 79% 133.7 ABC-type glycerol 3-phosphate transporter (EC 7.6.2.10) 32% 164.5
D-maltose catabolism aglF lo Inner membrane ABC transporter permease protein (characterized, see rationale) 31% 79% 133.7 ABC-type glycerol 3-phosphate transporter (EC 7.6.2.10) 32% 164.5
D-maltose catabolism aglF' lo Inner membrane ABC transporter permease protein (characterized, see rationale) 31% 79% 133.7 ABC-type glycerol 3-phosphate transporter (EC 7.6.2.10) 32% 164.5
sucrose catabolism aglF lo Inner membrane ABC transporter permease protein (characterized, see rationale) 31% 79% 133.7 ABC-type glycerol 3-phosphate transporter (EC 7.6.2.10) 32% 164.5
sucrose catabolism aglF' lo Inner membrane ABC transporter permease protein (characterized, see rationale) 31% 79% 133.7 ABC-type glycerol 3-phosphate transporter (EC 7.6.2.10) 32% 164.5
trehalose catabolism aglF lo Inner membrane ABC transporter permease protein (characterized, see rationale) 31% 79% 133.7 ABC-type glycerol 3-phosphate transporter (EC 7.6.2.10) 32% 164.5
trehalose catabolism aglF' lo Inner membrane ABC transporter permease protein (characterized, see rationale) 31% 79% 133.7 ABC-type glycerol 3-phosphate transporter (EC 7.6.2.10) 32% 164.5
D-glucosamine (chitosamine) catabolism SM_b21220 lo ABC transporter for D-Glucosamine, permease component 2 (characterized) 31% 93% 123.6 ABC-type glycerol 3-phosphate transporter (EC 7.6.2.10) 32% 164.5
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) 30% 94% 122.5 ABC-type glycerol 3-phosphate transporter (EC 7.6.2.10) 32% 164.5
N-acetyl-D-glucosamine catabolism SMc02872 lo ABC transporter for N-Acetyl-D-glucosamine, permease protein 1 (characterized) 30% 92% 121.3 ABC-type glycerol 3-phosphate transporter (EC 7.6.2.10) 32% 164.5
D-glucosamine (chitosamine) catabolism SMc02872 lo ABC transporter for N-Acetyl-D-glucosamine, permease protein 1 (characterized) 30% 92% 121.3 ABC-type glycerol 3-phosphate transporter (EC 7.6.2.10) 32% 164.5
lactose catabolism lacF lo LacF, component of Lactose porter (characterized) 31% 83% 119 ABC-type glycerol 3-phosphate transporter (EC 7.6.2.10) 32% 164.5
D-cellobiose catabolism msdC1 lo Binding-protein-dependent transport systems inner membrane component (characterized, see rationale) 30% 95% 113.6 ABC-type glycerol 3-phosphate transporter (EC 7.6.2.10) 32% 164.5
D-sorbitol (glucitol) catabolism mtlF lo ABC transporter for D-Sorbitol, permease component 2 (characterized) 31% 91% 105.1 ABC-type glycerol 3-phosphate transporter (EC 7.6.2.10) 32% 164.5

Sequence Analysis Tools

View BWI76_RS03135 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

MRKTWLPWLILSPSLLFLLLFTWFPLGRSVYDSLFDTRMVSDGGQYVGLENFSRLFADSV
FWQSLVNNLLYILLTVVPGVTLALLLAVALTENHRVNRWLRTAFFFPMIIPMVSAAALWL
FIFMPGLGLLDHYLAKLFGPMNNNWLGRSNSALLALALIGVWKFAGYYMLFFLAGLQSIP
ASTREAAIMEGATRTQVFFKVTLPLLRPTLSFVITTALIYSITQIDHVAVMTRGGPDNAT
TVLLYYIQNLAWDTHDLGKASAATFLTLAGLFAFSLINLKLLEKGAHYER

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