Protein WP_089136844.1 in Lactobacillus silagei IWT126
Annotation: NCBI__GCF_002217945.1:WP_089136844.1
Length: 464 amino acids
Source: GCF_002217945.1 in NCBI
Candidate for 22 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| D-cellobiose catabolism | MFS-glucose | hi | The D-glucose:H+ symporter, GlcP (glucose uptake is inhibited by 2-deoxyglucose, mannose and galactose) (characterized) | 69% | 87% | 610.9 | D-xylose transporter; D-xylose-proton symporter | 45% | 395.2 |
| D-glucose catabolism | MFS-glucose | hi | The D-glucose:H+ symporter, GlcP (glucose uptake is inhibited by 2-deoxyglucose, mannose and galactose) (characterized) | 69% | 87% | 610.9 | D-xylose transporter; D-xylose-proton symporter | 45% | 395.2 |
| lactose catabolism | MFS-glucose | hi | The D-glucose:H+ symporter, GlcP (glucose uptake is inhibited by 2-deoxyglucose, mannose and galactose) (characterized) | 69% | 87% | 610.9 | D-xylose transporter; D-xylose-proton symporter | 45% | 395.2 |
| D-maltose catabolism | MFS-glucose | hi | The D-glucose:H+ symporter, GlcP (glucose uptake is inhibited by 2-deoxyglucose, mannose and galactose) (characterized) | 69% | 87% | 610.9 | D-xylose transporter; D-xylose-proton symporter | 45% | 395.2 |
| sucrose catabolism | MFS-glucose | hi | The D-glucose:H+ symporter, GlcP (glucose uptake is inhibited by 2-deoxyglucose, mannose and galactose) (characterized) | 69% | 87% | 610.9 | D-xylose transporter; D-xylose-proton symporter | 45% | 395.2 |
| trehalose catabolism | MFS-glucose | hi | The D-glucose:H+ symporter, GlcP (glucose uptake is inhibited by 2-deoxyglucose, mannose and galactose) (characterized) | 69% | 87% | 610.9 | D-xylose transporter; D-xylose-proton symporter | 45% | 395.2 |
| D-xylose catabolism | xylT | med | D-xylose transporter; D-xylose-proton symporter (characterized) | 45% | 100% | 395.2 | The D-glucose:H+ symporter, GlcP (glucose uptake is inhibited by 2-deoxyglucose, mannose and galactose) | 69% | 610.9 |
| L-arabinose catabolism | araE | lo | Arabinose/xylose transporter, AraE (characterized) | 38% | 92% | 309.3 | The D-glucose:H+ symporter, GlcP (glucose uptake is inhibited by 2-deoxyglucose, mannose and galactose) | 69% | 610.9 |
| myo-inositol catabolism | iolT | lo | Myo-Inositol uptake porter, IolT1 (Km=0.2mM) (characterized) | 37% | 91% | 283.9 | The D-glucose:H+ symporter, GlcP (glucose uptake is inhibited by 2-deoxyglucose, mannose and galactose) | 69% | 610.9 |
| D-galactose catabolism | galP | lo | Galactose-proton symporter; Galactose transporter (characterized) | 36% | 95% | 279.3 | The D-glucose:H+ symporter, GlcP (glucose uptake is inhibited by 2-deoxyglucose, mannose and galactose) | 69% | 610.9 |
| D-fructose catabolism | glcP | lo | Glucose/fructose:H+ symporter, GlcP (characterized) | 36% | 95% | 276.6 | The D-glucose:H+ symporter, GlcP (glucose uptake is inhibited by 2-deoxyglucose, mannose and galactose) | 69% | 610.9 |
| sucrose catabolism | glcP | lo | Glucose/fructose:H+ symporter, GlcP (characterized) | 36% | 95% | 276.6 | The D-glucose:H+ symporter, GlcP (glucose uptake is inhibited by 2-deoxyglucose, mannose and galactose) | 69% | 610.9 |
| D-mannose catabolism | STP6 | lo | The high affinity sugar:H+ symporter (sugar uptake) porter of 514 aas and 12 TMSs, STP10. It transports glucose, galactose and mannose, and is therefore a hexose transporter (Rottmann et al. 2016). The 2.4 (characterized) | 32% | 88% | 238.8 | The D-glucose:H+ symporter, GlcP (glucose uptake is inhibited by 2-deoxyglucose, mannose and galactose) | 69% | 610.9 |
| D-fructose catabolism | STP6 | lo | sugar transport protein 6 (characterized) | 32% | 91% | 237.3 | The D-glucose:H+ symporter, GlcP (glucose uptake is inhibited by 2-deoxyglucose, mannose and galactose) | 69% | 610.9 |
| sucrose catabolism | STP6 | lo | sugar transport protein 6 (characterized) | 32% | 91% | 237.3 | The D-glucose:H+ symporter, GlcP (glucose uptake is inhibited by 2-deoxyglucose, mannose and galactose) | 69% | 610.9 |
| D-fructose catabolism | Slc2a5 | lo | sugar transport protein 13 (characterized) | 31% | 87% | 232.6 | The D-glucose:H+ symporter, GlcP (glucose uptake is inhibited by 2-deoxyglucose, mannose and galactose) | 69% | 610.9 |
| sucrose catabolism | Slc2a5 | lo | sugar transport protein 13 (characterized) | 31% | 87% | 232.6 | The D-glucose:H+ symporter, GlcP (glucose uptake is inhibited by 2-deoxyglucose, mannose and galactose) | 69% | 610.9 |
| trehalose catabolism | TRET1 | lo | Facilitated trehalose transporter Tret1; BmTRET1 (characterized) | 32% | 87% | 220.7 | The D-glucose:H+ symporter, GlcP (glucose uptake is inhibited by 2-deoxyglucose, mannose and galactose) | 69% | 610.9 |
| D-sorbitol (glucitol) catabolism | SOT | lo | Sorbitol (glucitol):H+ co-transporter, SOT2 (Km for sorbitol of 0.81 mM) of 491 aas and 12 TMSs (Gao et al. 2003). SOT2 of Prunus cerasus is mainly expressed only early in fruit development and not in leaves (characterized) | 31% | 96% | 219.5 | The D-glucose:H+ symporter, GlcP (glucose uptake is inhibited by 2-deoxyglucose, mannose and galactose) | 69% | 610.9 |
| D-galactose catabolism | gal2 | lo | galactose transporter (characterized) | 30% | 79% | 203 | The D-glucose:H+ symporter, GlcP (glucose uptake is inhibited by 2-deoxyglucose, mannose and galactose) | 69% | 610.9 |
| D-xylose catabolism | gal2 | lo | galactose transporter (characterized) | 30% | 79% | 203 | The D-glucose:H+ symporter, GlcP (glucose uptake is inhibited by 2-deoxyglucose, mannose and galactose) | 69% | 610.9 |
| myo-inositol catabolism | HMIT | lo | Proton myo-inositol cotransporter; H(+)-myo-inositol cotransporter; Hmit; H(+)-myo-inositol symporter; Solute carrier family 2 member 13 (characterized) | 35% | 54% | 186.8 | The D-glucose:H+ symporter, GlcP (glucose uptake is inhibited by 2-deoxyglucose, mannose and galactose) | 69% | 610.9 |
Sequence Analysis Tools
View WP_089136844.1 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
MRVRHLSTWFIFTFGALGGLLFGFDTGIISGASPLIESSFHLNIEQTGFITSSVLIGSSV
GALSIGSLSDKFGRKRLLLVASILFLLGSGLSMTASGFVSMVVARIILGFAVGSASALTP
AYLAELADAPHRGSLGTMFQLMVTLGILLAYVSNLGFLGHNLLGLQDWRWMLGSALIPAA
ALFFGSLVLPESPRYLVEMGKIDEAKEVLHDLRAKTNEDPDKELADIQSVANQPKGGLHE
LFTFARPAVLVAIGLMLLQQLVGINSVIYFLPQVFIKGFGFAEGDAIWISVGIGIVNFLC
TVLAYNIMDKFNRRTILLFGSIVMAVAIIILSILNFTLSVKAAAVPTMILIAIYIFGFAV
SWGPICWLMIGEIFPLNVRGIGNSIGSAANWIGNFIVSQFFLVLLNAFHNNVGGPFAVFG
FFAIVSIFFVIYAVPETRGKTLEEIEMEMRHKEANKEAAKKTAN
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:
- 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:
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