GapMind for catabolism of small carbon sources

 

Protein 17782 in Escherichia coli BW25113

Annotation: b3722 fused beta-glucoside-specific PTS enzymes: IIA component/IIB component/IIC component (NCBI)

Length: 625 amino acids

Source: Keio 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-cellobiose catabolism bglF hi β-Glucoside (salicin, arbutin, cellobiose, etc) group translocator, BglF (characterized) 100% 100% 1236.1 PTS beta-glucoside transporter, EIIBCA of 672 aas and 12 predicted TMSs 40% 517.7
D-cellobiose catabolism bglG hi β-Glucoside (salicin, arbutin, cellobiose, etc) group translocator, BglF (characterized) 100% 100% 1236.1 β-glucoside (Aesculin/arbutin) porter, BglP 39% 445.7
D-glucose catabolism bglF hi β-Glucoside (salicin, arbutin, cellobiose, etc) group translocator, BglF (characterized) 100% 100% 1236.1 PTS beta-glucoside transporter, EIIBCA of 672 aas and 12 predicted TMSs 40% 517.7
lactose catabolism bglF hi β-Glucoside (salicin, arbutin, cellobiose, etc) group translocator, BglF (characterized) 100% 100% 1236.1 PTS beta-glucoside transporter, EIIBCA of 672 aas and 12 predicted TMSs 40% 517.7
D-maltose catabolism bglF hi β-Glucoside (salicin, arbutin, cellobiose, etc) group translocator, BglF (characterized) 100% 100% 1236.1 PTS beta-glucoside transporter, EIIBCA of 672 aas and 12 predicted TMSs 40% 517.7
sucrose catabolism bglF hi β-Glucoside (salicin, arbutin, cellobiose, etc) group translocator, BglF (characterized) 100% 100% 1236.1 PTS beta-glucoside transporter, EIIBCA of 672 aas and 12 predicted TMSs 40% 517.7
trehalose catabolism bglF hi β-Glucoside (salicin, arbutin, cellobiose, etc) group translocator, BglF (characterized) 100% 100% 1236.1 PTS beta-glucoside transporter, EIIBCA of 672 aas and 12 predicted TMSs 40% 517.7
sucrose catabolism ptsS lo protein-Npi-phosphohistidine-sucrose phosphotransferase (EC 2.7.1.211) (characterized) 33% 99% 323.9 β-Glucoside (salicin, arbutin, cellobiose, etc) group translocator, BglF 100% 1236.1
sucrose catabolism sacP lo Sucrose porter, IIBC (SacP) (55% identical to 4.A.1.2.1) (characterized) 31% 97% 240.7 β-Glucoside (salicin, arbutin, cellobiose, etc) group translocator, BglF 100% 1236.1
trehalose catabolism treB lo Trehalose permease IIC protein (characterized, see rationale) 31% 96% 226.5 β-Glucoside (salicin, arbutin, cellobiose, etc) group translocator, BglF 100% 1236.1
N-acetyl-D-glucosamine catabolism nagEIIA lo Putative phosphotransferase enzyme IIA component YpqE (characterized, see rationale) 37% 98% 119.8 β-Glucoside (salicin, arbutin, cellobiose, etc) group translocator, BglF 100% 1236.1
D-glucosamine (chitosamine) catabolism nagEIIA lo Putative phosphotransferase enzyme IIA component YpqE (characterized, see rationale) 37% 98% 119.8 β-Glucoside (salicin, arbutin, cellobiose, etc) group translocator, BglF 100% 1236.1
D-maltose catabolism malEIIA lo Putative phosphotransferase enzyme IIA component YpqE (characterized, see rationale) 37% 98% 119.8 β-Glucoside (salicin, arbutin, cellobiose, etc) group translocator, BglF 100% 1236.1

Sequence Analysis Tools

View 17782 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

MTELARKIVAGVGGADNIVSLMHCATRLRFKLKDESKAQAEVLKKTPGIIMVVESGGQFQ
VVIGNHVADVFLAVNSVAGLDEKAQQAPENDDKGNLLNRFVYVISGIFTPLIGLMAATGI
LKGMLALALTFQWTTEQSGTYLILFSASDALFWFFPIILGYTAGKRFGGNPFTAMVIGGA
LVHPLILTAFENGQKADALGLDFLGIPVTLLNYSSSVIPIIFSAWLCSILERRLNAWLPS
AIKNFFTPLLCLMVITPVTFLLVGPLSTWISELIAAGYLWLYQAVPAFAGAVMGGFWQIF
VMFGLHWGLVPLCINNFTVLGYDTMIPLLMPAIMAQVGAALGVFLCERDAQKKVVAGSAA
LTSLFGITEPAVYGVNLPRKYPFVIACISGALGATIIGYAQTKVYSFGLPSIFTFMQTIP
STGIDFTVWASVIGGVIAIGCAFVGTVMLHFITAKRQPAQGAPQEKTPEVITPPEQGGIC
SPMTGEIVPLIHVADTTFASGLLGKGIAILPSVGEVRSPVAGRIASLFATLHAIGIESDD
GVEILIHVGIDTVKLDGKFFSAHVNVGDKVNTGDRLISFDIPAIREAGFDLTTPVLISNS
DDFTDVLPHGTAQISAGEPLLSIIR

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