Protein AO353_04460 in Pseudomonas fluorescens FW300-N2E3
Annotation: FitnessBrowser__pseudo3_N2E3:AO353_04460
Length: 838 amino acids
Source: pseudo3_N2E3 in FitnessBrowser
Candidate for 16 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) | 100% | 100% | 1629.8 | D-trehalose PTS system, I, HPr, and IIA components | 46% | 669.5 |
| D-glucosamine (chitosamine) catabolism | nagF | hi | N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) (characterized) | 100% | 100% | 1629.8 | D-trehalose PTS system, I, HPr, and IIA components | 46% | 669.5 |
| trehalose catabolism | treEIIA | med | D-trehalose PTS system, I, HPr, and IIA components (characterized) | 46% | 98% | 669.5 | N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) | 100% | 1629.8 |
| D-fructose catabolism | fruI | med | Fructose PTS system (E-I, HPr, and E-IIA components) (characterized) | 40% | 78% | 434.9 | N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) | 100% | 1629.8 |
| sucrose catabolism | fruI | med | Fructose PTS system (E-I, HPr, and E-IIA components) (characterized) | 40% | 78% | 434.9 | N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) | 100% | 1629.8 |
| D-cellobiose catabolism | crr | lo | glucose-specific phosphotransferase enzyme IIA component; EC 2.7.1.- (characterized) | 40% | 93% | 119.8 | N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) | 100% | 1629.8 |
| D-glucose catabolism | crr | lo | glucose-specific phosphotransferase enzyme IIA component; EC 2.7.1.- (characterized) | 40% | 93% | 119.8 | N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) | 100% | 1629.8 |
| lactose catabolism | crr | lo | glucose-specific phosphotransferase enzyme IIA component; EC 2.7.1.- (characterized) | 40% | 93% | 119.8 | N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) | 100% | 1629.8 |
| D-maltose catabolism | crr | lo | glucose-specific phosphotransferase enzyme IIA component; EC 2.7.1.- (characterized) | 40% | 93% | 119.8 | N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) | 100% | 1629.8 |
| sucrose catabolism | crr | lo | glucose-specific phosphotransferase enzyme IIA component; EC 2.7.1.- (characterized) | 40% | 93% | 119.8 | N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) | 100% | 1629.8 |
| trehalose catabolism | crr | lo | glucose-specific phosphotransferase enzyme IIA component; EC 2.7.1.- (characterized) | 40% | 93% | 119.8 | N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) | 100% | 1629.8 |
| N-acetyl-D-glucosamine catabolism | nagEIIA | lo | Putative phosphotransferase enzyme IIA component YpqE (characterized, see rationale) | 37% | 88% | 106.7 | N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) | 100% | 1629.8 |
| D-glucosamine (chitosamine) catabolism | nagEIIA | lo | Putative phosphotransferase enzyme IIA component YpqE (characterized, see rationale) | 37% | 88% | 106.7 | N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) | 100% | 1629.8 |
| D-maltose catabolism | malEIIA | lo | Putative phosphotransferase enzyme IIA component YpqE (characterized, see rationale) | 37% | 88% | 106.7 | N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) | 100% | 1629.8 |
| N-acetyl-D-glucosamine catabolism | crr | lo | Putative PTS system sugar phosphotransferase component IIA (characterized, see rationale) | 38% | 97% | 90.9 | N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) | 100% | 1629.8 |
| D-glucosamine (chitosamine) catabolism | crr | lo | Putative PTS system sugar phosphotransferase component IIA (characterized, see rationale) | 38% | 97% | 90.9 | N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) | 100% | 1629.8 |
Sequence Analysis Tools
View AO353_04460 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
MHNNNKDLTLSAPLSGPVLTLAKVPDPVFASGAMGDGIAIDPLNNTLHAPCAGVVVHVAR
TGHAVTLRADNGAELLLHLGLDTVELQGEGFSMLVKEGTRVSNGQALLRFDLDQVAQGCK
SLVSLLVLTNSEDFQVLPITLKSVKVGEPLLHIVPRTTHSAQVEADSSGAEVHGHIRIIH
RGGLHARPAALIRQTAHLFNSKSQLHFAGKSASCDSLIGLMGLGIGEQDEVQVSCKGADA
KAALQALLNALSTAVNDDSHAAAPTPIAQRTRTAEAGVLNGVCAAPGLVGGPLFQLAAIP
LPEDTGKHNAEEQLQALDRALEQVRSEIRETLSHAKKHKHTEEEQIFAAHLALLEDPALL
EAAIQSIDQGSAATHAWSQSIEAQCEVLQQLGNPLLAERANDLRDLRQRVLRALLGQDWH
YDVPAGAIVAAHELTPSDLLQLSQQGVAGLCMAEGGATSHVAILARGKGLPCLVALSASL
LQQPQGQSVVLDADGGRLELTPDSQRLEQVAQAQREHLQRRERQQAQAHTPAHTRDGLRI
EVAANVASSNEAADALKGGADGVGLLRTEFLFVDRQTAPDEQEQRQAYQAVLDAMGDKSV
IIRTIDVGGDKQLDYLPLPAEANPVLGLRGIRMAQVRPELLDQQLRALLQVSPLQRCRIL
LPMVTEVDELLYIRQRLDALCAELALTQRLELGVMIEVPAAALLAEQLAEHADFLSIGTN
DLSQYTLAMDRDHAGLAARVDALHPALLRLIAQTCIGAAKHQRWVGVCGALASDPLATPV
LIGLGISELSVSPPQVGEIKERVRQLDAADCRRFSATLLNLSSATAVRHACHQHWPLS
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:
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