Protein 350322 in Bacteroides thetaiotaomicron VPI-5482
Annotation: FitnessBrowser__Btheta:350322
Length: 484 amino acids
Source: Btheta in FitnessBrowser
Candidate for 14 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| D-xylose catabolism | xylT | hi | D-xylose-proton symporter (characterized) | 49% | 98% | 456.1 | The glucose uptake porter, GluP | 38% | 322.4 |
| D-cellobiose catabolism | MFS-glucose | lo | The glucose uptake porter, GluP (characterized) | 38% | 96% | 322.4 | D-xylose-proton symporter | 49% | 456.1 |
| D-glucose catabolism | MFS-glucose | lo | The glucose uptake porter, GluP (characterized) | 38% | 96% | 322.4 | D-xylose-proton symporter | 49% | 456.1 |
| lactose catabolism | MFS-glucose | lo | The glucose uptake porter, GluP (characterized) | 38% | 96% | 322.4 | D-xylose-proton symporter | 49% | 456.1 |
| D-maltose catabolism | MFS-glucose | lo | The glucose uptake porter, GluP (characterized) | 38% | 96% | 322.4 | D-xylose-proton symporter | 49% | 456.1 |
| sucrose catabolism | MFS-glucose | lo | The glucose uptake porter, GluP (characterized) | 38% | 96% | 322.4 | D-xylose-proton symporter | 49% | 456.1 |
| trehalose catabolism | MFS-glucose | lo | The glucose uptake porter, GluP (characterized) | 38% | 96% | 322.4 | D-xylose-proton symporter | 49% | 456.1 |
| D-fructose catabolism | glcP | lo | Glucose/fructose:H+ symporter, GlcP (characterized) | 39% | 97% | 312 | D-xylose-proton symporter | 49% | 456.1 |
| sucrose catabolism | glcP | lo | Glucose/fructose:H+ symporter, GlcP (characterized) | 39% | 97% | 312 | D-xylose-proton symporter | 49% | 456.1 |
| myo-inositol catabolism | iolT | lo | Major myo-inositol transporter, IolT1, of 456 aas (characterized) | 34% | 97% | 302.4 | D-xylose-proton symporter | 49% | 456.1 |
| xylitol catabolism | PLT5 | lo | Polyol (xylitol):H+ symporter, PLT4 (characterized) | 31% | 90% | 203 | D-xylose-proton symporter | 49% | 456.1 |
| 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% | 95% | 191.8 | D-xylose-proton symporter | 49% | 456.1 |
| trehalose catabolism | TRET1 | lo | Facilitated trehalose transporter Tret1; BmTRET1 (characterized) | 35% | 55% | 162.5 | D-xylose-proton symporter | 49% | 456.1 |
| 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) | 30% | 52% | 150.6 | D-xylose-proton symporter | 49% | 456.1 |
Sequence Analysis Tools
View 350322 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
MNNTTNEGSKLYLYSITSVAILGGLLFGYDTAVISGAEKGLEAFFLSASDFQYNKVMHGI
TSSSALIGCVLGGALSGVFASRLGRRNSLRLAAVLFFLSALGSYYPEVLFFEYGKPNMDL
LIAFNLYRVLGGIGVGLASAVCPMYIAEIAPSNIRGTLVSCNQFAIIFGMLVVYFVNYLI
MGDHQNPIILKDAAGVLSVSAESDMWTVQEGWRYMFGSEAFPAAFFGLLLFFVPKTPRYL
VLVQQEEKAYTILEKINGKKKAQEILNDIKATAQEKTEKLFTYGVTVIVIGILLSVFQQA
IGINAVLYYAPRIFENAGAEGGGMMQTVIMGIVNIIFTLVAIFTVDRFGRKPLLIIGSIG
MAVGAFAVAMCDSMAIKGVLPVLSIIVYAAFFMMSWGPICWVLISEIFPNTIRGKAVAIA
VAFQWIFNYIVSSTFPALYDFSPMFAYSLYGIICVAAAIFVWRWVPETKGKTLEDMSKLW
KKNK
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