GapMind for catabolism of small carbon sources

 

Protein Synpcc7942_2111 in Synechococcus elongatus PCC 7942

Annotation: Synpcc7942_2111 xylose repressor

Length: 302 amino acids

Source: SynE 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 med Glucokinase; ATP-dependent glucokinase; ATP-GLK; Glucose kinase; EC 2.7.1.2 (characterized) 35% 98% 183.3 ADP-specific glucokinase (EC 2.7.1.147) 33% 163.7
D-glucose catabolism glk med Glucokinase; ATP-dependent glucokinase; ATP-GLK; Glucose kinase; EC 2.7.1.2 (characterized) 35% 98% 183.3 ADP-specific glucokinase (EC 2.7.1.147) 33% 163.7
lactose catabolism glk med Glucokinase; ATP-dependent glucokinase; ATP-GLK; Glucose kinase; EC 2.7.1.2 (characterized) 35% 98% 183.3 ADP-specific glucokinase (EC 2.7.1.147) 33% 163.7
D-maltose catabolism glk med Glucokinase; ATP-dependent glucokinase; ATP-GLK; Glucose kinase; EC 2.7.1.2 (characterized) 35% 98% 183.3 ADP-specific glucokinase (EC 2.7.1.147) 33% 163.7
sucrose catabolism glk med Glucokinase; ATP-dependent glucokinase; ATP-GLK; Glucose kinase; EC 2.7.1.2 (characterized) 35% 98% 183.3 ADP-specific glucokinase (EC 2.7.1.147) 33% 163.7
trehalose catabolism glk med Glucokinase; ATP-dependent glucokinase; ATP-GLK; Glucose kinase; EC 2.7.1.2 (characterized) 35% 98% 183.3 ADP-specific glucokinase (EC 2.7.1.147) 33% 163.7
D-glucosamine (chitosamine) catabolism glc-kinase lo ADP-specific glucokinase (EC 2.7.1.147) (characterized) 33% 99% 163.7 Glucokinase; ATP-dependent glucokinase; ATP-GLK; Glucose kinase; EC 2.7.1.2 35% 183.3
N-acetyl-D-glucosamine catabolism nagK lo N-acetylglucosamine kinase (EC 2.7.1.59) (characterized) 30% 98% 151 Glucokinase; ATP-dependent glucokinase; ATP-GLK; Glucose kinase; EC 2.7.1.2 35% 183.3
D-glucosamine (chitosamine) catabolism nagK lo N-acetylglucosamine kinase (EC 2.7.1.59) (characterized) 30% 98% 151 Glucokinase; ATP-dependent glucokinase; ATP-GLK; Glucose kinase; EC 2.7.1.2 35% 183.3
D-fructose catabolism scrK lo Fructokinase; D-fructose kinase; Manno(fructo)kinase; EC 2.7.1.4 (characterized) 30% 99% 102.8 Glucokinase; ATP-dependent glucokinase; ATP-GLK; Glucose kinase; EC 2.7.1.2 35% 183.3
D-mannitol catabolism mak lo Fructokinase; D-fructose kinase; Manno(fructo)kinase; EC 2.7.1.4 (characterized) 30% 99% 102.8 Glucokinase; ATP-dependent glucokinase; ATP-GLK; Glucose kinase; EC 2.7.1.2 35% 183.3
D-mannitol catabolism scrK lo Fructokinase; D-fructose kinase; Manno(fructo)kinase; EC 2.7.1.4 (characterized) 30% 99% 102.8 Glucokinase; ATP-dependent glucokinase; ATP-GLK; Glucose kinase; EC 2.7.1.2 35% 183.3
D-mannose catabolism mannokinase lo Fructokinase; D-fructose kinase; Manno(fructo)kinase; EC 2.7.1.4 (characterized) 30% 99% 102.8 Glucokinase; ATP-dependent glucokinase; ATP-GLK; Glucose kinase; EC 2.7.1.2 35% 183.3
D-mannose catabolism scrK lo Fructokinase; D-fructose kinase; Manno(fructo)kinase; EC 2.7.1.4 (characterized) 30% 99% 102.8 Glucokinase; ATP-dependent glucokinase; ATP-GLK; Glucose kinase; EC 2.7.1.2 35% 183.3
D-sorbitol (glucitol) catabolism scrK lo Fructokinase; D-fructose kinase; Manno(fructo)kinase; EC 2.7.1.4 (characterized) 30% 99% 102.8 Glucokinase; ATP-dependent glucokinase; ATP-GLK; Glucose kinase; EC 2.7.1.2 35% 183.3
sucrose catabolism scrK lo Fructokinase; D-fructose kinase; Manno(fructo)kinase; EC 2.7.1.4 (characterized) 30% 99% 102.8 Glucokinase; ATP-dependent glucokinase; ATP-GLK; Glucose kinase; EC 2.7.1.2 35% 183.3

Sequence Analysis Tools

View Synpcc7942_2111 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

MAYPATVIGVDLGGTAMKLGRYTIEGQCQQELTVPTPTPSTPSNVRAALVEAIRQLDPQA
EALAIGIGTPGPADAAGRVARVAINLDGWTEVPLADWLEADLQRPVILANDANCAGLGEV
WLGGGRGYRDAILLTLGTGVGGAIVLNGELFVGRTGTAAELGLITLDPAGPHCNSGNQGS
LEQYASIGAVQRRFGCDPKDLGDRASQGDPEAIAAWQDYGRTLAAGLASLVYVLTPEVII
LGGGISGSAAFFLPALTEELHRRVLPTSREDLQIAIAALGNEAGRVGAAKLAWDKLQALG
KV

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