Protein GFF4493 in Pseudomonas simiae WCS417
Annotation: FitnessBrowser__WCS417:GFF4493
Length: 836 amino acids
Source: WCS417 in FitnessBrowser
Candidate for 17 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| N-acetyl-D-glucosamine catabolism | nagF | hi | N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) (characterized) | 75% | 100% | 1216.1 | D-trehalose PTS system, I, HPr, and IIA components | 47% | 672.2 |
| D-glucosamine (chitosamine) catabolism | nagF | hi | N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) (characterized) | 75% | 100% | 1216.1 | D-trehalose PTS system, I, HPr, and IIA components | 47% | 672.2 |
| trehalose catabolism | treEIIA | med | D-trehalose PTS system, I, HPr, and IIA components (characterized) | 47% | 98% | 672.2 | N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) | 75% | 1216.1 |
| N-acetyl-D-glucosamine catabolism | crr | med | Putative PTS system sugar phosphotransferase component IIA (characterized, see rationale) | 40% | 97% | 94.4 | N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) | 75% | 1216.1 |
| D-glucosamine (chitosamine) catabolism | crr | med | Putative PTS system sugar phosphotransferase component IIA (characterized, see rationale) | 40% | 97% | 94.4 | N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) | 75% | 1216.1 |
| D-fructose catabolism | fruI | lo | Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) (characterized) | 42% | 70% | 469.5 | N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) | 75% | 1216.1 |
| sucrose catabolism | fruI | lo | Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) (characterized) | 42% | 70% | 469.5 | N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) | 75% | 1216.1 |
| glycerol catabolism | dhaM | lo | PEP-dependent dihydroxyacetone kinase, phosphoryl donor subunit DhaM; Dihydroxyacetone kinase subunit M; EC 2.7.1.121 (characterized) | 31% | 73% | 125.2 | N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) | 75% | 1216.1 |
| D-cellobiose catabolism | crr | lo | glucose-specific phosphotransferase enzyme IIA component; EC 2.7.1.- (characterized) | 40% | 89% | 117.9 | N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) | 75% | 1216.1 |
| D-glucose catabolism | crr | lo | glucose-specific phosphotransferase enzyme IIA component; EC 2.7.1.- (characterized) | 40% | 89% | 117.9 | N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) | 75% | 1216.1 |
| lactose catabolism | crr | lo | glucose-specific phosphotransferase enzyme IIA component; EC 2.7.1.- (characterized) | 40% | 89% | 117.9 | N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) | 75% | 1216.1 |
| D-maltose catabolism | crr | lo | glucose-specific phosphotransferase enzyme IIA component; EC 2.7.1.- (characterized) | 40% | 89% | 117.9 | N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) | 75% | 1216.1 |
| sucrose catabolism | crr | lo | glucose-specific phosphotransferase enzyme IIA component; EC 2.7.1.- (characterized) | 40% | 89% | 117.9 | N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) | 75% | 1216.1 |
| trehalose catabolism | crr | lo | glucose-specific phosphotransferase enzyme IIA component; EC 2.7.1.- (characterized) | 40% | 89% | 117.9 | N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) | 75% | 1216.1 |
| N-acetyl-D-glucosamine catabolism | nagEIIA | lo | Putative phosphotransferase enzyme IIA component YpqE (characterized, see rationale) | 39% | 88% | 112.5 | N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) | 75% | 1216.1 |
| D-glucosamine (chitosamine) catabolism | nagEIIA | lo | Putative phosphotransferase enzyme IIA component YpqE (characterized, see rationale) | 39% | 88% | 112.5 | N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) | 75% | 1216.1 |
| D-maltose catabolism | malEIIA | lo | Putative phosphotransferase enzyme IIA component YpqE (characterized, see rationale) | 39% | 88% | 112.5 | N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) | 75% | 1216.1 |
Sequence Analysis Tools
View GFF4493 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
MSYNNNELTLSAPLSGPVLTLGNVPDEVFASGAMGDGIAIDPLNDCLYAPCDGVIIHVAR
TGHALTIRAENGAEVLMHVGIDTVELNGEGFALLVKDGARVSKGQALVQFDLDRIARQCK
SLVSLIILTNGERFELRAVAGQKVKVGEPLLQIVARSAAAVQTAVDNSEADVSASVRITH
RGGLHARPAALIRKTAQDFSSQAQLHFGDKSASCDSLIGLMGLGIGEGDEVRVTCRGKDA
EAALQALVAALSAVIKEEHHVPVVAPPRRAHTEAGVLQGVCAAPGLVCGPLFRLTGIELP
ADVGNHSADEQLQHLDTALEQVRSEIRSTLAHARQRKNVEEEDIFAAHLALLEDPNLLEA
ATRSIEQGSAATHAWRDAIQAQCAVLLALGKPLFAERANDLRDLQQRVLRALLGEAWHFE
LPAGSIVSAHELTPSDLLQLSAQHAVGICMAEGGATSHVAILARGKGLPCVVALGAEVLD
VPQGQRVVLDAVNGRLELEPTEARHAEVHQIRDAQKLRRQQQQAQAQEPARTTDGVSIEV
AANVASSAEAQVAFENGADGVGLLRTEFLFVDRRTAPDEQEQRHAYQAVLDAMGDKSVII
RTIDVGGDKQLDYLPLPVEANPVLGLRGIRMAQVRPELLDQQLRALLQVSPLERCRILLP
MVSEVDELLQIRQRLDELCVELELTQRPELGVMIEVPAAALMAEHLAKHADFLSIGTNDL
SQYTLAMDRDHAGLAARVDALHPALLRLIAQTCAGATKHGRWVGVCGALASDPLATPVLV
GLGVSELSVSPPQIAEIKDRVRHLDAAQCRQLSQGLLDLSSAKAVRQACQHHWPLS
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