Protein Ga0059261_1646 in Sphingomonas koreensis DSMZ 15582
Annotation: FitnessBrowser__Korea:Ga0059261_1646
Length: 830 amino acids
Source: Korea 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-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA (characterized) | 46% | 98% | 654.8 | D-trehalose PTS system, I, HPr, and IIA components | 42% | 603.6 |
| D-glucosamine (chitosamine) catabolism | nagF | hi | N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA (characterized) | 46% | 98% | 654.8 | D-trehalose PTS system, I, HPr, and IIA components | 42% | 603.6 |
| trehalose catabolism | treEIIA | med | D-trehalose PTS system, I, HPr, and IIA components (characterized) | 42% | 98% | 603.6 | N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA | 46% | 654.8 |
| D-fructose catabolism | fruI | med | Multiphosphoryl transfer protein; MTP; Triphosphoryl transfer protein; TTP; EC 2.7.3.9 (characterized) | 43% | 80% | 479.6 | N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA | 46% | 654.8 |
| sucrose catabolism | fruI | med | Multiphosphoryl transfer protein; MTP; Triphosphoryl transfer protein; TTP; EC 2.7.3.9 (characterized) | 43% | 80% | 479.6 | N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA | 46% | 654.8 |
| D-cellobiose catabolism | crr | med | PTS system glucose-specific EIIA component; EIIA-Glc; EIII-Glc; Glucose-specific phosphotransferase enzyme IIA component (characterized) | 42% | 73% | 113.6 | N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA | 46% | 654.8 |
| D-glucose catabolism | crr | med | PTS system glucose-specific EIIA component; EIIA-Glc; EIII-Glc; Glucose-specific phosphotransferase enzyme IIA component (characterized) | 42% | 73% | 113.6 | N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA | 46% | 654.8 |
| lactose catabolism | crr | med | PTS system glucose-specific EIIA component; EIIA-Glc; EIII-Glc; Glucose-specific phosphotransferase enzyme IIA component (characterized) | 42% | 73% | 113.6 | N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA | 46% | 654.8 |
| D-maltose catabolism | crr | med | PTS system glucose-specific EIIA component; EIIA-Glc; EIII-Glc; Glucose-specific phosphotransferase enzyme IIA component (characterized) | 42% | 73% | 113.6 | N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA | 46% | 654.8 |
| sucrose catabolism | crr | med | PTS system glucose-specific EIIA component; EIIA-Glc; EIII-Glc; Glucose-specific phosphotransferase enzyme IIA component (characterized) | 42% | 73% | 113.6 | N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA | 46% | 654.8 |
| trehalose catabolism | crr | med | PTS system glucose-specific EIIA component; EIIA-Glc; EIII-Glc; Glucose-specific phosphotransferase enzyme IIA component (characterized) | 42% | 73% | 113.6 | N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA | 46% | 654.8 |
| N-acetyl-D-glucosamine catabolism | crr | med | Putative PTS system sugar phosphotransferase component IIA (characterized, see rationale) | 44% | 83% | 97.1 | N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA | 46% | 654.8 |
| D-glucosamine (chitosamine) catabolism | crr | med | Putative PTS system sugar phosphotransferase component IIA (characterized, see rationale) | 44% | 83% | 97.1 | N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA | 46% | 654.8 |
| N-acetyl-D-glucosamine catabolism | nagEIIA | lo | Putative phosphotransferase enzyme IIA component YpqE (characterized, see rationale) | 39% | 80% | 118.2 | N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA | 46% | 654.8 |
| D-glucosamine (chitosamine) catabolism | nagEIIA | lo | Putative phosphotransferase enzyme IIA component YpqE (characterized, see rationale) | 39% | 80% | 118.2 | N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA | 46% | 654.8 |
| D-maltose catabolism | malEIIA | lo | Putative phosphotransferase enzyme IIA component YpqE (characterized, see rationale) | 39% | 80% | 118.2 | N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA | 46% | 654.8 |
Sequence Analysis Tools
View Ga0059261_1646 at FitnessBrowser
Find papers: PaperBLAST
Find functional residues: SitesBLAST
Search for conserved domains
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Predict transmenbrane helices: Phobius
Predict protein localization: PSORTb
Find homologs in fast.genomics
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Sequence
MALIITSPLRGWAAPLDSVPDPVFAQRMMGDGVAIQPLADTVCAPFDGEVVTLHEAGHAV
SLRSDEGAEVLIHIGLDTVGLKGRGFTPLVAPGATVARGDPLIRFDMDAVALGATSLITP
VIVTNAEAFTITRRTMGRAIGAHEELMALAPARTQPRRWSDDGTVIEERVTLILPHGIHA
RPAARLGECARQFEAEIHLLHGDKRGDARSTVGLLALGTRLGDELVVQARGSDAEAALAA
IVALLGSDMGEGAPAHAPAIAVPAAPVLQPGQIGGVIASPGLAMGPAARLRQTAIAVERE
GKGVDAERTALDAARTEVRVRIGARADAAGGSVAAVMRAHLALLDDPELAAGAETRIAAG
NSAGYAWRGAVHDQIAALKATGNAHLIERTDDLVDIERQVLGVLTGIPAEADAIAAGAIL
VADDLLPSQLVSIAASKPAGICLVRGGPTSHVAILCAGMGLPALVAMGDAIEAIEDGTAL
LLDAEAGHVTPDPSQADADAFAARLAKREARRDAARAAAGNACQTADGVRIELFANLGTV
EDAKAAAAQGAEGSGLVRSEFLFLDREDAPSEDEQHAAYQGIADALPGKPVIVRLLDVGG
DKPAAYIPFDAEENPALGLRGIRVGLAHRDLLETQIRAILRVQPVGQCRIMLPMVASVSE
IRAVREVVERLRGEMGIETPIEVGVMVETPAAAITADLLAAEADFLSIGTNDLTQYVLAM
DRGNPAVASGVDAMHPAVLRMIAETCRRATAKGRWVGVCGGLASDPAAVPILIGLGATEL
STVPGFVPEAKAIVRSVTLADARDHAERALHCSSAAEVRALARAFEEKNA
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