Protein WP_027699309.1 in Weissella oryzae SG25
Annotation: NCBI__GCF_000691805.2:WP_027699309.1
Length: 470 amino acids
Source: GCF_000691805.2 in NCBI
Candidate for 29 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| L-arabinose catabolism | araE | hi | Arabinose/xylose transporter, AraE (characterized) | 72% | 94% | 649.8 | D-xylose transporter; D-xylose-proton symporter | 42% | 365.2 |
| D-xylose catabolism | xylT | hi | Arabinose/xylose transporter, AraE (characterized) | 72% | 94% | 649.8 | Probable metabolite transport protein CsbC | 42% | 339.3 |
| D-cellobiose catabolism | MFS-glucose | lo | Myo-Inositol uptake porter, IolT1 (Km=0.2mM) (characterized) | 38% | 90% | 305.4 | Arabinose/xylose transporter, AraE | 72% | 649.8 |
| D-glucose catabolism | MFS-glucose | lo | Myo-Inositol uptake porter, IolT1 (Km=0.2mM) (characterized) | 38% | 90% | 305.4 | Arabinose/xylose transporter, AraE | 72% | 649.8 |
| lactose catabolism | MFS-glucose | lo | Myo-Inositol uptake porter, IolT1 (Km=0.2mM) (characterized) | 38% | 90% | 305.4 | Arabinose/xylose transporter, AraE | 72% | 649.8 |
| D-maltose catabolism | MFS-glucose | lo | Myo-Inositol uptake porter, IolT1 (Km=0.2mM) (characterized) | 38% | 90% | 305.4 | Arabinose/xylose transporter, AraE | 72% | 649.8 |
| myo-inositol catabolism | iolT | lo | Myo-Inositol uptake porter, IolT1 (Km=0.2mM) (characterized) | 38% | 90% | 305.4 | Arabinose/xylose transporter, AraE | 72% | 649.8 |
| sucrose catabolism | MFS-glucose | lo | Myo-Inositol uptake porter, IolT1 (Km=0.2mM) (characterized) | 38% | 90% | 305.4 | Arabinose/xylose transporter, AraE | 72% | 649.8 |
| trehalose catabolism | MFS-glucose | lo | Myo-Inositol uptake porter, IolT1 (Km=0.2mM) (characterized) | 38% | 90% | 305.4 | Arabinose/xylose transporter, AraE | 72% | 649.8 |
| D-galactose catabolism | galP | lo | Arabinose-proton symporter; Arabinose transporter (characterized) | 33% | 93% | 248.1 | Arabinose/xylose transporter, AraE | 72% | 649.8 |
| D-fructose catabolism | glcP | lo | D-fructose transporter, sugar porter family (characterized) | 34% | 94% | 245 | Arabinose/xylose transporter, AraE | 72% | 649.8 |
| sucrose catabolism | glcP | lo | D-fructose transporter, sugar porter family (characterized) | 34% | 94% | 245 | Arabinose/xylose transporter, AraE | 72% | 649.8 |
| glycerol catabolism | PLT5 | lo | polyol transporter 5 (characterized) | 32% | 88% | 241.9 | Arabinose/xylose transporter, AraE | 72% | 649.8 |
| D-mannitol catabolism | PLT5 | lo | polyol transporter 5 (characterized) | 32% | 88% | 241.9 | Arabinose/xylose transporter, AraE | 72% | 649.8 |
| D-ribose catabolism | PLT5 | lo | polyol transporter 5 (characterized) | 32% | 88% | 241.9 | Arabinose/xylose transporter, AraE | 72% | 649.8 |
| D-sorbitol (glucitol) catabolism | SOT | lo | polyol transporter 5 (characterized) | 32% | 88% | 241.9 | Arabinose/xylose transporter, AraE | 72% | 649.8 |
| xylitol catabolism | PLT5 | lo | polyol transporter 5 (characterized) | 32% | 88% | 241.9 | Arabinose/xylose transporter, AraE | 72% | 649.8 |
| D-fructose catabolism | Slc2a5 | lo | The fructose/xylose:H+ symporter, PMT1 (polyol monosaccharide transporter-1). Also transports other substrates at lower rates. PMT2 is largely of the same sequence and function. Both are present in pollen and young xylem cells (Klepek et al., 2005). A similar ortholog has been identifed in pollen grains of Petunia hybrida (characterized) | 32% | 88% | 227.6 | Arabinose/xylose transporter, AraE | 72% | 649.8 |
| sucrose catabolism | Slc2a5 | lo | The fructose/xylose:H+ symporter, PMT1 (polyol monosaccharide transporter-1). Also transports other substrates at lower rates. PMT2 is largely of the same sequence and function. Both are present in pollen and young xylem cells (Klepek et al., 2005). A similar ortholog has been identifed in pollen grains of Petunia hybrida (characterized) | 32% | 88% | 227.6 | Arabinose/xylose transporter, AraE | 72% | 649.8 |
| D-galacturonate catabolism | gatA | lo | The galacturonic acid (galacturonate) uptake porter, GatA, of 518 aas and 12 TMSs (characterized) | 31% | 87% | 221.1 | Arabinose/xylose transporter, AraE | 72% | 649.8 |
| 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) | 30% | 89% | 219.9 | Arabinose/xylose transporter, AraE | 72% | 649.8 |
| D-fructose catabolism | STP6 | lo | sugar transport protein 6 (characterized) | 31% | 92% | 213.8 | Arabinose/xylose transporter, AraE | 72% | 649.8 |
| sucrose catabolism | STP6 | lo | sugar transport protein 6 (characterized) | 31% | 92% | 213.8 | Arabinose/xylose transporter, AraE | 72% | 649.8 |
| D-galactose catabolism | gal2 | lo | galactose transporter (characterized) | 30% | 79% | 211.1 | Arabinose/xylose transporter, AraE | 72% | 649.8 |
| D-xylose catabolism | gal2 | lo | galactose transporter (characterized) | 30% | 79% | 211.1 | Arabinose/xylose transporter, AraE | 72% | 649.8 |
| myo-inositol catabolism | HMIT | lo | Probable inositol transporter 2 (characterized) | 37% | 57% | 208.4 | Arabinose/xylose transporter, AraE | 72% | 649.8 |
| trehalose catabolism | TRET1 | lo | Facilitated trehalose transporter Tret1-2 homolog; DmTret1-2 (characterized) | 32% | 81% | 196.8 | Arabinose/xylose transporter, AraE | 72% | 649.8 |
| D-galactose catabolism | MST1 | lo | The monosaccharide (MST) (glucose > mannose > galactose > fructose):H+ symporter, MST1 (characterized) | 30% | 80% | 194.1 | Arabinose/xylose transporter, AraE | 72% | 649.8 |
| D-mannose catabolism | MST1 | lo | The monosaccharide (MST) (glucose > mannose > galactose > fructose):H+ symporter, MST1 (characterized) | 30% | 80% | 194.1 | Arabinose/xylose transporter, AraE | 72% | 649.8 |
Sequence Analysis Tools
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Find functional residues: SitesBLAST
Search for conserved domains
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Compare to protein structures
Predict transmenbrane helices: Phobius
Predict protein localization: PSORTb
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Sequence
MMAKKKISSNFIYFFGAFGGILFGYDIGVMTGALPFLQTDWNLAGNASITGWITSSLMLG
AIFGGALAGQLSDRLGRRRMILMSAVVFAVFALASAFAPTHGGAMFLIAMRVFLGLGVGA
ASALVPAFMSEMAPAKVRGRLSGINQVMIVSGMLISYIVDYLLQGLPTGISWRMMIGMAA
VPAVILFLGVLRLPESPRFLVKQGKLDEARQVLSWIRPADEVASELADIQATATIEKKAT
SSTNWGSLLSGRYRYLVIAGIGVAAFQQFQGANAIFYYIPLIVQSATGKAATSALMWPII
QGVILVAGSLFFLVIADRFNRRTLLTVGGTIMGLSFLLPAILNMISPSLMKSQPMLLVVF
LSIYVTLYSCTWAPLTWVIVGEVFPLAIRGRASGLASSFNWIGSFLVGLLFPIMTAAMSQ
AAVFGIFGLICLLGVVFIRTRVPETRGHSLEEIEEAGAQKAGIDTSAEIA
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