GapMind for catabolism of small carbon sources

 

Protein 5208927 in Shewanella loihica PV-4

Annotation: Shew_1428 fructokinase (RefSeq)

Length: 296 amino acids

Source: PV4 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
D-cellobiose catabolism glk hi glucokinase (EC 2.7.1.2) (characterized) 77% 99% 485.3 Fructokinase; D-fructose kinase; Manno(fructo)kinase; EC 2.7.1.4 61% 389.8
D-glucose catabolism glk hi glucokinase (EC 2.7.1.2) (characterized) 77% 99% 485.3 Fructokinase; D-fructose kinase; Manno(fructo)kinase; EC 2.7.1.4 61% 389.8
lactose catabolism glk hi glucokinase (EC 2.7.1.2) (characterized) 77% 99% 485.3 Fructokinase; D-fructose kinase; Manno(fructo)kinase; EC 2.7.1.4 61% 389.8
D-maltose catabolism glk hi glucokinase (EC 2.7.1.2) (characterized) 77% 99% 485.3 Fructokinase; D-fructose kinase; Manno(fructo)kinase; EC 2.7.1.4 61% 389.8
sucrose catabolism glk hi glucokinase (EC 2.7.1.2) (characterized) 77% 99% 485.3 Fructokinase; D-fructose kinase; Manno(fructo)kinase; EC 2.7.1.4 61% 389.8
trehalose catabolism glk hi glucokinase (EC 2.7.1.2) (characterized) 77% 99% 485.3 Fructokinase; D-fructose kinase; Manno(fructo)kinase; EC 2.7.1.4 61% 389.8
D-fructose catabolism scrK med Fructokinase; D-fructose kinase; Manno(fructo)kinase; EC 2.7.1.4 (characterized) 61% 99% 389.8 glucokinase (EC 2.7.1.2) 77% 485.3
D-mannitol catabolism mak med Fructokinase; D-fructose kinase; Manno(fructo)kinase; EC 2.7.1.4 (characterized) 61% 99% 389.8 glucokinase (EC 2.7.1.2) 77% 485.3
D-mannitol catabolism scrK med Fructokinase; D-fructose kinase; Manno(fructo)kinase; EC 2.7.1.4 (characterized) 61% 99% 389.8 glucokinase (EC 2.7.1.2) 77% 485.3
D-mannose catabolism mannokinase med Fructokinase; D-fructose kinase; Manno(fructo)kinase; EC 2.7.1.4 (characterized) 61% 99% 389.8 glucokinase (EC 2.7.1.2) 77% 485.3
D-mannose catabolism scrK med Fructokinase; D-fructose kinase; Manno(fructo)kinase; EC 2.7.1.4 (characterized) 61% 99% 389.8 glucokinase (EC 2.7.1.2) 77% 485.3
D-sorbitol (glucitol) catabolism scrK med Fructokinase; D-fructose kinase; Manno(fructo)kinase; EC 2.7.1.4 (characterized) 61% 99% 389.8 glucokinase (EC 2.7.1.2) 77% 485.3
sucrose catabolism scrK med Fructokinase; D-fructose kinase; Manno(fructo)kinase; EC 2.7.1.4 (characterized) 61% 99% 389.8 glucokinase (EC 2.7.1.2) 77% 485.3
N-acetyl-D-glucosamine catabolism nagK med N-acetyl-D-glucosamine kinase; EC 2.7.1.59; GlcNAc kinase (uncharacterized) 41% 99% 221.5 glucokinase (EC 2.7.1.2) 77% 485.3
D-glucosamine (chitosamine) catabolism nagK med N-acetyl-D-glucosamine kinase; EC 2.7.1.59; GlcNAc kinase (uncharacterized) 41% 99% 221.5 glucokinase (EC 2.7.1.2) 77% 485.3
D-glucosamine (chitosamine) catabolism glc-kinase lo ADP-specific glucokinase (EC 2.7.1.147) (characterized) 31% 100% 134.4 glucokinase (EC 2.7.1.2) 77% 485.3

Sequence Analysis Tools

View 5208927 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

MMRMGVDLGGTKIELVALSEAGKELFRKRIPTPREYKATLDAIEALVNEAESTLGQKGTV
GVGIPGVISPFSGLVKNANSTWINGHPLDLDLGARLEREVRVANDANCFAVSEAVDGAAA
GKGLVFGVIIGTGCGGGIAINGKVHGGGNGIGGEWGHNPLPWMTPDEFNSTECFCGNKDC
IETFISGTGFVRDYKAAGGDAPSGIEIARRMEQGEALATAAFERYIDRLARSLAHMINML
DPDIIVLGGGVSNIEAIYPRLPEALSKYVLGGECRTPVVQNMYGGSSGVRGAAWLW

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