Protein N515DRAFT_0382 in Dyella japonica UNC79MFTsu3.2
Annotation: FitnessBrowser__Dyella79:N515DRAFT_0382
Length: 472 amino acids
Source: Dyella79 in FitnessBrowser
Candidate for 23 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 glucose uptake porter, GluP (characterized) | 59% | 95% | 526.9 | D-xylose-proton symporter | 38% | 306.6 |
| D-glucose catabolism | MFS-glucose | hi | The glucose uptake porter, GluP (characterized) | 59% | 95% | 526.9 | D-xylose-proton symporter | 38% | 306.6 |
| lactose catabolism | MFS-glucose | hi | The glucose uptake porter, GluP (characterized) | 59% | 95% | 526.9 | D-xylose-proton symporter | 38% | 306.6 |
| D-maltose catabolism | MFS-glucose | hi | The glucose uptake porter, GluP (characterized) | 59% | 95% | 526.9 | D-xylose-proton symporter | 38% | 306.6 |
| sucrose catabolism | MFS-glucose | hi | The glucose uptake porter, GluP (characterized) | 59% | 95% | 526.9 | D-xylose-proton symporter | 38% | 306.6 |
| trehalose catabolism | MFS-glucose | hi | The glucose uptake porter, GluP (characterized) | 59% | 95% | 526.9 | D-xylose-proton symporter | 38% | 306.6 |
| D-fructose catabolism | glcP | med | Glucose/fructose:H+ symporter, GlcP (characterized) | 56% | 97% | 488.4 | The glucose uptake porter, GluP | 59% | 526.9 |
| sucrose catabolism | glcP | med | Glucose/fructose:H+ symporter, GlcP (characterized) | 56% | 97% | 488.4 | The glucose uptake porter, GluP | 59% | 526.9 |
| D-xylose catabolism | xylT | med | Glucose/fructose transport protein (characterized, see rationale) | 48% | 95% | 445.7 | The glucose uptake porter, GluP | 59% | 526.9 |
| L-arabinose catabolism | araE | lo | Arabinose-proton symporter; Arabinose transporter (characterized) | 35% | 94% | 281.6 | The glucose uptake porter, GluP | 59% | 526.9 |
| D-galactose catabolism | galP | lo | Arabinose-proton symporter; Arabinose transporter (characterized) | 35% | 94% | 281.6 | The glucose uptake porter, GluP | 59% | 526.9 |
| myo-inositol catabolism | iolT | lo | Major myo-inositol transporter, IolT1, of 456 aas (characterized) | 33% | 95% | 274.6 | The glucose uptake porter, GluP | 59% | 526.9 |
| myo-inositol catabolism | HMIT | lo | inositol transporter 4 (characterized) | 34% | 59% | 192.2 | The glucose uptake porter, GluP | 59% | 526.9 |
| D-fructose catabolism | STP6 | lo | sugar transport protein 6 (characterized) | 32% | 78% | 189.9 | The glucose uptake porter, GluP | 59% | 526.9 |
| D-mannose catabolism | STP6 | lo | sugar transport protein 6 (characterized) | 32% | 78% | 189.9 | The glucose uptake porter, GluP | 59% | 526.9 |
| sucrose catabolism | STP6 | lo | sugar transport protein 6 (characterized) | 32% | 78% | 189.9 | The glucose uptake porter, GluP | 59% | 526.9 |
| 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) | 30% | 92% | 185.7 | The glucose uptake porter, GluP | 59% | 526.9 |
| D-fructose catabolism | Slc2a5 | lo | sugar transport protein 13 (characterized) | 32% | 76% | 185.3 | The glucose uptake porter, GluP | 59% | 526.9 |
| sucrose catabolism | Slc2a5 | lo | sugar transport protein 13 (characterized) | 32% | 76% | 185.3 | The glucose uptake porter, GluP | 59% | 526.9 |
| glycerol catabolism | PLT5 | lo | polyol transporter 5 (characterized) | 31% | 84% | 183.7 | The glucose uptake porter, GluP | 59% | 526.9 |
| D-mannitol catabolism | PLT5 | lo | polyol transporter 5 (characterized) | 31% | 84% | 183.7 | The glucose uptake porter, GluP | 59% | 526.9 |
| D-ribose catabolism | PLT5 | lo | polyol transporter 5 (characterized) | 31% | 84% | 183.7 | The glucose uptake porter, GluP | 59% | 526.9 |
| xylitol catabolism | PLT5 | lo | polyol transporter 5 (characterized) | 31% | 84% | 183.7 | The glucose uptake porter, GluP | 59% | 526.9 |
Sequence Analysis Tools
View N515DRAFT_0382 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
MNAVEIVEGEGRATARVVLIAAAAALGGFLFGFDTAVINGAVDAVRGSFGLGAGRIGFAV
SCALLGSALGAWYAGPLADRWGRVRTMQVAAVLLAISALGSGLVAGVWDLVLWRLVGGIG
VGVASVIAPTYIAEVSPARVRGRLGSLQQLAIVLGIFAALLSDAWLAGTAGGASQKLWLG
LEAWRWMFLVAVVPALIYGSLVLGVPESPRHLVAKGRMDEAKQVLRQVLDLQDEHALQHK
LGDIAQSLRSEYRPGLRDLRGSMAGLLPVVWVGILLSVFQQFVGINVIFYYSSTLWHSVG
FSESDAFSISVVTSVVNVLVTLVAIALVDRIGRKPLLAIGSAGMTVTLGLMAWCFSQAAG
SGAALSLPAPWGMVALVAANAYVVFFGLSWGPMVWVLLGEMFPNRIRAIALAVAAAAQWV
ANFIITSSFPALSELGLSFAYGVYAFFALVSLVFVVKAVRETKGMELEEMGR
This GapMind analysis is from Apr 09 2024. 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