GapMind for catabolism of small carbon sources

 

Protein BWI76_RS19725 in Klebsiella michiganensis M5al

Annotation: BWI76_RS19725 PTS fructose transporter subunit EIIBC

Length: 558 amino acids

Source: Koxy in FitnessBrowser

Candidate for 11 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-fructose catabolism fruA hi PTS system fructose-specific EIIB'BC component; EIIB'BC-Fru; EC 2.7.1.202 (characterized) 89% 99% 974.5 The fructose porter, FruA (fructose-1-P forming IIABC) (Delobbe et al. 1975) FruA is 39% identical to 4.A.2.1.1). fructose can be metabolized to Fru-1-P via this system as well as Fru-6-P by another PTS system 47% 426.4
sucrose catabolism fruA hi PTS system fructose-specific EIIB'BC component; EIIB'BC-Fru; EC 2.7.1.202 (characterized) 89% 99% 974.5 The fructose porter, FruA (fructose-1-P forming IIABC) (Delobbe et al. 1975) FruA is 39% identical to 4.A.2.1.1). fructose can be metabolized to Fru-1-P via this system as well as Fru-6-P by another PTS system 47% 426.4
D-fructose catabolism fruII-ABC med The fructose porter, FruA (fructose-1-P forming IIABC) (Delobbe et al. 1975) FruA is 39% identical to 4.A.2.1.1). fructose can be metabolized to Fru-1-P via this system as well as Fru-6-P by another PTS system (characterized) 47% 74% 426.4 PTS system fructose-specific EIIB'BC component; EIIB'BC-Fru; EC 2.7.1.202 89% 974.5
sucrose catabolism fruII-ABC med The fructose porter, FruA (fructose-1-P forming IIABC) (Delobbe et al. 1975) FruA is 39% identical to 4.A.2.1.1). fructose can be metabolized to Fru-1-P via this system as well as Fru-6-P by another PTS system (characterized) 47% 74% 426.4 PTS system fructose-specific EIIB'BC component; EIIB'BC-Fru; EC 2.7.1.202 89% 974.5
D-mannose catabolism manP med protein-Npi-phosphohistidine-D-mannose phosphotransferase (EC 2.7.1.191) (characterized) 44% 70% 377.1 PTS system fructose-specific EIIB'BC component; EIIB'BC-Fru; EC 2.7.1.202 89% 974.5
D-fructose catabolism fruII-C med Sugar phosphotransferase system IIC component, component of Fructose-specific Enzyme I-HPr-Enzyme IIABC complex, all encoded within a single operon with genes in the order: ptsC (IIC), ptsA (IIA), ptsH (HPr), ptsI (Enzyme I) and ptsB (IIB) (characterized) 44% 89% 284.3 PTS system fructose-specific EIIB'BC component; EIIB'BC-Fru; EC 2.7.1.202 89% 974.5
sucrose catabolism fruII-C med Sugar phosphotransferase system IIC component, component of Fructose-specific Enzyme I-HPr-Enzyme IIABC complex, all encoded within a single operon with genes in the order: ptsC (IIC), ptsA (IIA), ptsH (HPr), ptsI (Enzyme I) and ptsB (IIB) (characterized) 44% 89% 284.3 PTS system fructose-specific EIIB'BC component; EIIB'BC-Fru; EC 2.7.1.202 89% 974.5
xylitol catabolism fruI lo The fructose inducible fructose/xylitol porter, FruI (characterized) 39% 84% 347.8 PTS system fructose-specific EIIB'BC component; EIIB'BC-Fru; EC 2.7.1.202 89% 974.5
D-ribose catabolism fru2-IIC lo PTS system, fructose-specific, IIC component, component of D-allose/D-ribose transporting Enzyme II complex (Fru2; IIA/IIB/IIC) (Patron et al. 2017). This system is similar to Frz of E. coli (TC#4.A.2.1.9) which is involved in environmental sensing, host adaptation and virulence (characterized) 37% 90% 221.5 PTS system fructose-specific EIIB'BC component; EIIB'BC-Fru; EC 2.7.1.202 89% 974.5
D-fructose catabolism fruII-B lo Phosphotransferase system IIB component, component of Fructose-specific Enzyme I-HPr-Enzyme IIABC complex, all encoded within a single operon with genes in the order: ptsC (IIC), ptsA (IIA), ptsH (HPr), ptsI (Enzyme I) and ptsB (IIB) (characterized) 38% 82% 81.3 PTS system fructose-specific EIIB'BC component; EIIB'BC-Fru; EC 2.7.1.202 89% 974.5
sucrose catabolism fruII-B lo Phosphotransferase system IIB component, component of Fructose-specific Enzyme I-HPr-Enzyme IIABC complex, all encoded within a single operon with genes in the order: ptsC (IIC), ptsA (IIA), ptsH (HPr), ptsI (Enzyme I) and ptsB (IIB) (characterized) 38% 82% 81.3 PTS system fructose-specific EIIB'BC component; EIIB'BC-Fru; EC 2.7.1.202 89% 974.5

Sequence Analysis Tools

View BWI76_RS19725 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

MKTLLIIDAGLGQARAYMAKTLLSTAAQKAQLELIDNPNDAELAIVLGTALPADSALNGK
KVYLGDINRAVAHPELFLGEAKSHATPYAAPTAAALPTAANGPKRIVAVTACPTGVAHTF
MAAEAIETEAKKRGWWVKVETRGSVGAGNAITPEEVEQADLVVVAADIEVDLAKFAGKPM
YRTTTGLALKKTAQELDKAVVEAKPYQPAGKSQAAAEGKKESAGAYRHLLTGVSYMLPMV
VAGGLCIALSFAFGIKAFEVKDTLAAALMQIGGGSAFALMVPVLAGFIAFSIADRPGLTP
GLIGGMLAVSTGSGFIGGIIAGFLAGYVAKAISTKLKLPQSMEALKPILIIPLVSSLIVG
LAMIYLIGKPVAGILEGLTHWLQTMGTANAVLLGAILGGMMCTDMGGPVNKAAYAFGVGL
LSTQTYAPMAAIMAAGMVPPLALGLATLIARKKFDKAQQEGGKAALVLGLCFITEGAIPF
AARDPMRVLPCCIVGGAVTGAMSMWVGAKLMAPHGGLFVLLIPGAITPVLGYLMAIVVGT
LVAGLSYAVLKRPEVQAA

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