GapMind for catabolism of small carbon sources

 

Protein WP_007703096.1 in Cronobacter universalis NCTC 9529

Annotation: NCBI__GCF_001277175.1:WP_007703096.1

Length: 312 amino acids

Source: GCF_001277175.1 in NCBI

Candidate for 19 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-cellobiose catabolism kguK hi 2-ketogluconokinase (EC 2.7.1.13) (characterized) 58% 96% 342.4 2-dehydro-3-deoxygluconokinase; 2-keto-3-deoxygluconokinase; 3-deoxy-2-oxo-D-gluconate kinase; KDG kinase; EC 2.7.1.45 51% 313.5
D-gluconate catabolism kguK hi 2-ketogluconokinase (EC 2.7.1.13) (characterized) 58% 96% 342.4 2-dehydro-3-deoxygluconokinase; 2-keto-3-deoxygluconokinase; 3-deoxy-2-oxo-D-gluconate kinase; KDG kinase; EC 2.7.1.45 51% 313.5
D-glucose catabolism kguK hi 2-ketogluconokinase (EC 2.7.1.13) (characterized) 58% 96% 342.4 2-dehydro-3-deoxygluconokinase; 2-keto-3-deoxygluconokinase; 3-deoxy-2-oxo-D-gluconate kinase; KDG kinase; EC 2.7.1.45 51% 313.5
lactose catabolism kguK hi 2-ketogluconokinase (EC 2.7.1.13) (characterized) 58% 96% 342.4 2-dehydro-3-deoxygluconokinase; 2-keto-3-deoxygluconokinase; 3-deoxy-2-oxo-D-gluconate kinase; KDG kinase; EC 2.7.1.45 51% 313.5
D-maltose catabolism kguK hi 2-ketogluconokinase (EC 2.7.1.13) (characterized) 58% 96% 342.4 2-dehydro-3-deoxygluconokinase; 2-keto-3-deoxygluconokinase; 3-deoxy-2-oxo-D-gluconate kinase; KDG kinase; EC 2.7.1.45 51% 313.5
sucrose catabolism kguK hi 2-ketogluconokinase (EC 2.7.1.13) (characterized) 58% 96% 342.4 2-dehydro-3-deoxygluconokinase; 2-keto-3-deoxygluconokinase; 3-deoxy-2-oxo-D-gluconate kinase; KDG kinase; EC 2.7.1.45 51% 313.5
trehalose catabolism kguK hi 2-ketogluconokinase (EC 2.7.1.13) (characterized) 58% 96% 342.4 2-dehydro-3-deoxygluconokinase; 2-keto-3-deoxygluconokinase; 3-deoxy-2-oxo-D-gluconate kinase; KDG kinase; EC 2.7.1.45 51% 313.5
D-galacturonate catabolism kdgK med 2-dehydro-3-deoxygluconokinase; 2-keto-3-deoxygluconokinase; 3-deoxy-2-oxo-D-gluconate kinase; KDG kinase; EC 2.7.1.45 (characterized) 51% 95% 313.5 2-ketogluconokinase (EC 2.7.1.13) 58% 342.4
D-glucosamine (chitosamine) catabolism kdgK med 2-dehydro-3-deoxygluconokinase; 2-keto-3-deoxygluconokinase; 3-deoxy-2-oxo-D-gluconate kinase; KDG kinase; EC 2.7.1.45 (characterized) 51% 95% 313.5 2-ketogluconokinase (EC 2.7.1.13) 58% 342.4
D-glucuronate catabolism kdgK med 2-dehydro-3-deoxygluconokinase; 2-keto-3-deoxygluconokinase; 3-deoxy-2-oxo-D-gluconate kinase; KDG kinase; EC 2.7.1.45 (characterized) 51% 95% 313.5 2-ketogluconokinase (EC 2.7.1.13) 58% 342.4
myo-inositol catabolism kdgK med 2-dehydro-3-deoxygluconokinase; 2-keto-3-deoxygluconokinase; 3-deoxy-2-oxo-D-gluconate kinase; KDG kinase; EC 2.7.1.45 (characterized) 51% 95% 313.5 2-ketogluconokinase (EC 2.7.1.13) 58% 342.4
D-galactose catabolism dgoK lo 2-dehydro-3-deoxyglucono/galactono-kinase (EC 2.7.1.178) (characterized) 33% 96% 141.4 2-ketogluconokinase (EC 2.7.1.13) 58% 342.4
lactose catabolism dgoK lo 2-dehydro-3-deoxyglucono/galactono-kinase (EC 2.7.1.178) (characterized) 33% 96% 141.4 2-ketogluconokinase (EC 2.7.1.13) 58% 342.4
D-fructose catabolism scrK lo Fructokinase-1; Fructokinase I; OsFKI; EC 2.7.1.4 (characterized) 32% 96% 122.9 2-ketogluconokinase (EC 2.7.1.13) 58% 342.4
D-mannitol catabolism scrK lo Fructokinase-1; Fructokinase I; OsFKI; EC 2.7.1.4 (characterized) 32% 96% 122.9 2-ketogluconokinase (EC 2.7.1.13) 58% 342.4
D-mannose catabolism scrK lo Fructokinase-1; Fructokinase I; OsFKI; EC 2.7.1.4 (characterized) 32% 96% 122.9 2-ketogluconokinase (EC 2.7.1.13) 58% 342.4
D-sorbitol (glucitol) catabolism scrK lo Fructokinase-1; Fructokinase I; OsFKI; EC 2.7.1.4 (characterized) 32% 96% 122.9 2-ketogluconokinase (EC 2.7.1.13) 58% 342.4
sucrose catabolism scrK lo Fructokinase-1; Fructokinase I; OsFKI; EC 2.7.1.4 (characterized) 32% 96% 122.9 2-ketogluconokinase (EC 2.7.1.13) 58% 342.4
myo-inositol catabolism iolC lo 5-dehydro-2-deoxygluconokinase; EC 2.7.1.92; 2-deoxy-5-keto-D-gluconate kinase; DKG kinase (uncharacterized) 31% 91% 119.8 2-ketogluconokinase (EC 2.7.1.13) 58% 342.4

Sequence Analysis Tools

View WP_007703096.1 at NCBI

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

Find the best match in UniProt

Compare to protein structures

Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

Find homologs in fast.genomics

Fitness BLAST: loading...

Sequence

MEQPLDVITIGEAMAMFVATEPGDLAQVEHFFKRVAGAELNVATGLARLGLQVSWVSRVG
NDSFGRFVLNQLEKEGIATRGVTIDDRYPTGFQLKSKVTDGTDPSVEYFRKGSAASHLSG
EDFNAPLFYSARHLHLSGVAAALSTTSYELLDHAARAMKSQGKTISFDPNLRPVLWKSEA
EMTEKLNQLACMADWVLPGLKEGQILTGQQSPEGIADFYLTRGVKAVVIKTGADGAWYQS
ASGEQGTVAAVKVENVVDTVGAGDGFAVGVISALLEGKTLREAATRGNKIGALAIQVQGD
SEGLPTRAQLGE

This GapMind analysis is from Sep 24 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:

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