Protein BWI76_RS27570 in Klebsiella michiganensis M5al
Annotation: FitnessBrowser__Koxy:BWI76_RS27570
Length: 363 amino acids
Source: Koxy in FitnessBrowser
Candidate for 9 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 | lo | PTS system fructose-specific EIIB'BC component; EIIB'BC-Fru; EC 2.7.1.202 (characterized) | 47% | 57% | 302 | Putative PTS enzyme-II fructose, component of The FrzABC PTS putative transporter (promotes bacterial fitness under stress conditions and promotes fimbrial (fim) gene expression indirectly (Rouquet et al., 2009). Might transport D-tagatose, D-psicose and/or D-sorbose, or a disaccharide of these (Rouquet et al. 2009); involved in environmental sensing, host adaptation and virulence | 95% | 694.9 |
| sucrose catabolism | fruA | lo | PTS system fructose-specific EIIB'BC component; EIIB'BC-Fru; EC 2.7.1.202 (characterized) | 47% | 57% | 302 | Putative PTS enzyme-II fructose, component of The FrzABC PTS putative transporter (promotes bacterial fitness under stress conditions and promotes fimbrial (fim) gene expression indirectly (Rouquet et al., 2009). Might transport D-tagatose, D-psicose and/or D-sorbose, or a disaccharide of these (Rouquet et al. 2009); involved in environmental sensing, host adaptation and virulence | 95% | 694.9 |
| D-fructose catabolism | fruII-ABC | lo | 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) | 41% | 53% | 268.1 | Putative PTS enzyme-II fructose, component of The FrzABC PTS putative transporter (promotes bacterial fitness under stress conditions and promotes fimbrial (fim) gene expression indirectly (Rouquet et al., 2009). Might transport D-tagatose, D-psicose and/or D-sorbose, or a disaccharide of these (Rouquet et al. 2009); involved in environmental sensing, host adaptation and virulence | 95% | 694.9 |
| sucrose catabolism | fruII-ABC | lo | 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) | 41% | 53% | 268.1 | Putative PTS enzyme-II fructose, component of The FrzABC PTS putative transporter (promotes bacterial fitness under stress conditions and promotes fimbrial (fim) gene expression indirectly (Rouquet et al., 2009). Might transport D-tagatose, D-psicose and/or D-sorbose, or a disaccharide of these (Rouquet et al. 2009); involved in environmental sensing, host adaptation and virulence | 95% | 694.9 |
| D-fructose catabolism | fruII-C | lo | 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) | 37% | 95% | 256.9 | Putative PTS enzyme-II fructose, component of The FrzABC PTS putative transporter (promotes bacterial fitness under stress conditions and promotes fimbrial (fim) gene expression indirectly (Rouquet et al., 2009). Might transport D-tagatose, D-psicose and/or D-sorbose, or a disaccharide of these (Rouquet et al. 2009); involved in environmental sensing, host adaptation and virulence | 95% | 694.9 |
| sucrose catabolism | fruII-C | lo | 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) | 37% | 95% | 256.9 | Putative PTS enzyme-II fructose, component of The FrzABC PTS putative transporter (promotes bacterial fitness under stress conditions and promotes fimbrial (fim) gene expression indirectly (Rouquet et al., 2009). Might transport D-tagatose, D-psicose and/or D-sorbose, or a disaccharide of these (Rouquet et al. 2009); involved in environmental sensing, host adaptation and virulence | 95% | 694.9 |
| D-mannose catabolism | manP | lo | protein-Npi-phosphohistidine-D-mannose phosphotransferase (EC 2.7.1.191) (characterized) | 39% | 52% | 236.5 | Putative PTS enzyme-II fructose, component of The FrzABC PTS putative transporter (promotes bacterial fitness under stress conditions and promotes fimbrial (fim) gene expression indirectly (Rouquet et al., 2009). Might transport D-tagatose, D-psicose and/or D-sorbose, or a disaccharide of these (Rouquet et al. 2009); involved in environmental sensing, host adaptation and virulence | 95% | 694.9 |
| 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% | 98% | 232.3 | Putative PTS enzyme-II fructose, component of The FrzABC PTS putative transporter (promotes bacterial fitness under stress conditions and promotes fimbrial (fim) gene expression indirectly (Rouquet et al., 2009). Might transport D-tagatose, D-psicose and/or D-sorbose, or a disaccharide of these (Rouquet et al. 2009); involved in environmental sensing, host adaptation and virulence | 95% | 694.9 |
| xylitol catabolism | fruI | lo | The fructose inducible fructose/xylitol porter, FruI (characterized) | 34% | 57% | 216.5 | Putative PTS enzyme-II fructose, component of The FrzABC PTS putative transporter (promotes bacterial fitness under stress conditions and promotes fimbrial (fim) gene expression indirectly (Rouquet et al., 2009). Might transport D-tagatose, D-psicose and/or D-sorbose, or a disaccharide of these (Rouquet et al. 2009); involved in environmental sensing, host adaptation and virulence | 95% | 694.9 |
Sequence Analysis Tools
View BWI76_RS27570 at FitnessBrowser
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
MSENKTPVSQEIKKHLLTGISWMIPLIVAAGICIALGQVLGGTNVGEKTGTIPWMLNQIG
GWGMGLIVPLICAAIAYSIADRPGFAPGLIVGFVCGQIHTGFIGGMLGGFLVGYTVLALK
HYIRLPKSMQGLMPIMVLPVLSTIISGLLMMTLIGKPIAWLQDALIHLLESMQGGSRFLL
GAILGAMATFDFGGPVNKTMSLFADGLLVSGVYGPEAVKFVGSIIPPFGITLSFLLTRHK
YTRAEREALKAAFPMGICMITEGVIPIAARDLLRVVGSCVVASAVAGGLIMTWGVESPVP
HGGMFVVPLFTHPLLFCLSLAIGTVICGVMLSLWKKPVTERDEEFDELNDQKVKDDEITF
TLE
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:
- ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
- HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.
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:
- ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
- ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
- HMMer finds a hit (regardless of coverage or other bits).
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:
- our ignorance of proteins' functions,
- omissions in the gene models,
- frame-shift errors in the genome sequence, or
- the organism lacks the pathway.
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