Protein Ga0059261_1777 in Sphingomonas koreensis DSMZ 15582
Annotation: FitnessBrowser__Korea:Ga0059261_1777
Length: 458 amino acids
Source: Korea in FitnessBrowser
Candidate for 21 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| D-fructose catabolism | glcP | hi | D-fructose transporter, sugar porter family (characterized) | 100% | 100% | 885.9 | D-xylose-proton symporter | 36% | 303.5 |
| sucrose catabolism | glcP | hi | D-fructose transporter, sugar porter family (characterized) | 100% | 100% | 885.9 | D-xylose-proton symporter | 36% | 303.5 |
| D-xylose catabolism | xylT | lo | D-xylose-proton symporter (characterized) | 36% | 93% | 303.5 | D-fructose transporter, sugar porter family | 100% | 885.9 |
| D-cellobiose catabolism | MFS-glucose | lo | The glucose uptake porter, GluP (characterized) | 37% | 98% | 285.8 | D-fructose transporter, sugar porter family | 100% | 885.9 |
| D-glucose catabolism | MFS-glucose | lo | The glucose uptake porter, GluP (characterized) | 37% | 98% | 285.8 | D-fructose transporter, sugar porter family | 100% | 885.9 |
| lactose catabolism | MFS-glucose | lo | The glucose uptake porter, GluP (characterized) | 37% | 98% | 285.8 | D-fructose transporter, sugar porter family | 100% | 885.9 |
| D-maltose catabolism | MFS-glucose | lo | The glucose uptake porter, GluP (characterized) | 37% | 98% | 285.8 | D-fructose transporter, sugar porter family | 100% | 885.9 |
| sucrose catabolism | MFS-glucose | lo | The glucose uptake porter, GluP (characterized) | 37% | 98% | 285.8 | D-fructose transporter, sugar porter family | 100% | 885.9 |
| trehalose catabolism | MFS-glucose | lo | The glucose uptake porter, GluP (characterized) | 37% | 98% | 285.8 | D-fructose transporter, sugar porter family | 100% | 885.9 |
| L-arabinose catabolism | araE | lo | Arabinose-proton symporter; Arabinose transporter (characterized) | 35% | 94% | 282 | D-fructose transporter, sugar porter family | 100% | 885.9 |
| D-galactose catabolism | galP | lo | Arabinose-proton symporter; Arabinose transporter (characterized) | 35% | 94% | 282 | D-fructose transporter, sugar porter family | 100% | 885.9 |
| myo-inositol catabolism | iolT | lo | Major myo-inositol transporter, IolT1, of 456 aas (characterized) | 33% | 95% | 261.5 | D-fructose transporter, sugar porter family | 100% | 885.9 |
| 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) | 33% | 92% | 237.3 | D-fructose transporter, sugar porter family | 100% | 885.9 |
| glycerol catabolism | PLT5 | lo | polyol transporter 5 (characterized) | 33% | 84% | 226.5 | D-fructose transporter, sugar porter family | 100% | 885.9 |
| D-mannitol catabolism | PLT5 | lo | polyol transporter 5 (characterized) | 33% | 84% | 226.5 | D-fructose transporter, sugar porter family | 100% | 885.9 |
| D-ribose catabolism | PLT5 | lo | polyol transporter 5 (characterized) | 33% | 84% | 226.5 | D-fructose transporter, sugar porter family | 100% | 885.9 |
| xylitol catabolism | PLT5 | lo | polyol transporter 5 (characterized) | 33% | 84% | 226.5 | D-fructose transporter, sugar porter family | 100% | 885.9 |
| 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) | 30% | 90% | 209.5 | D-fructose transporter, sugar porter family | 100% | 885.9 |
| 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) | 30% | 90% | 209.5 | D-fructose transporter, sugar porter family | 100% | 885.9 |
| trehalose catabolism | TRET1 | lo | Facilitated trehalose transporter Tret1; PvTret1 (characterized) | 30% | 88% | 193.7 | D-fructose transporter, sugar porter family | 100% | 885.9 |
| 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) | 34% | 57% | 183.3 | D-fructose transporter, sugar porter family | 100% | 885.9 |
Sequence Analysis Tools
View Ga0059261_1777 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
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Sequence
MHSVSASFAGAPDEEARATVAIILSAAGAALGGLLFGFDTAVISGATQALQLQFGLTDAM
LGFTVASALIGTVLGSLIAGAPADRFGRKGVMLTVAIAYVVSSLGTGLAPDLNAFLVFRF
MGGLAIGAASVVTPIYIAEVSPARFRGRLVAMNQLNIVLGILIAFLSNYIIAGLVQYDVA
WRWMFGIVAVPSTIFLLVTLLLPESPRWLAIHGQADRARDVMQRLGFADPRAELARIELA
EAREEAAGKPRLFQRSHFTPVACAIAIAMFNQLSGINALLYYAPRIFELAGAGADSALLQ
SIAVGGTNLVFTVAALFLIDRFGRRPLLFVGSVICAATLLLVGWQLESAKPDGTLILFGL
LGFIAAFAMSQGAVIWVFISEVFPSAVRGKGQALGSTTHWVMAAAITWAFPVFAASVGGW
VFAFFGAMMLLQLLWTWKFMPETNGIALEDMNLGSARA
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