Protein 3607124 in Dinoroseobacter shibae DFL-12
Annotation: FitnessBrowser__Dino:3607124
Length: 338 amino acids
Source: Dino in FitnessBrowser
Candidate for 39 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| xylitol catabolism | Dshi_0546 | hi | ABC transporter for Xylitol, ATPase component (characterized) | 100% | 100% | 666.8 | ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component | 54% | 361.3 |
| D-mannitol catabolism | mtlK | med | ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component (characterized) | 54% | 98% | 361.3 | ABC transporter for Xylitol, ATPase component | 100% | 666.8 |
| D-sorbitol (glucitol) catabolism | mtlK | med | MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized) | 53% | 98% | 359 | ABC transporter for Xylitol, ATPase component | 100% | 666.8 |
| N-acetyl-D-glucosamine catabolism | SMc02869 | med | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 54% | 100% | 350.1 | ABC transporter for Xylitol, ATPase component | 100% | 666.8 |
| D-glucosamine (chitosamine) catabolism | SMc02869 | med | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 54% | 100% | 350.1 | ABC transporter for Xylitol, ATPase component | 100% | 666.8 |
| lactose catabolism | lacK | med | LacK, component of Lactose porter (characterized) | 50% | 100% | 331.6 | ABC transporter for Xylitol, ATPase component | 100% | 666.8 |
| D-maltose catabolism | malK | med | Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 50% | 97% | 318.9 | ABC transporter for Xylitol, ATPase component | 100% | 666.8 |
| D-maltose catabolism | aglK | med | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 50% | 99% | 318.5 | ABC transporter for Xylitol, ATPase component | 100% | 666.8 |
| sucrose catabolism | aglK | med | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 50% | 99% | 318.5 | ABC transporter for Xylitol, ATPase component | 100% | 666.8 |
| trehalose catabolism | aglK | med | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 50% | 99% | 318.5 | ABC transporter for Xylitol, ATPase component | 100% | 666.8 |
| L-fucose catabolism | SM_b21106 | med | ABC transporter for L-Fucose, ATPase component (characterized) | 49% | 99% | 313.9 | ABC transporter for Xylitol, ATPase component | 100% | 666.8 |
| trehalose catabolism | malK | med | MsmK aka SMU.882, component of The raffinose/stachyose transporter, MsmEFGK (MalK (3.A.1.1.27) can probably substitute for MsmK; Webb et al., 2008). This system may also transport melibiose, isomaltotriose and sucrose as well as isomaltosaccharides (characterized) | 48% | 100% | 308.1 | ABC transporter for Xylitol, ATPase component | 100% | 666.8 |
| D-maltose catabolism | malK_Sm | med | MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized) | 47% | 98% | 307.4 | ABC transporter for Xylitol, ATPase component | 100% | 666.8 |
| L-arabinose catabolism | xacK | med | Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) | 47% | 96% | 307 | ABC transporter for Xylitol, ATPase component | 100% | 666.8 |
| D-cellobiose catabolism | msiK | med | MsiK protein, component of The cellobiose/cellotriose (and possibly higher cellooligosaccharides), CebEFGMsiK [MsiK functions to energize several ABC transporters including those for maltose/maltotriose and trehalose] (characterized) | 49% | 95% | 306.6 | ABC transporter for Xylitol, ATPase component | 100% | 666.8 |
| D-maltose catabolism | malK_Aa | med | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 49% | 94% | 300.8 | ABC transporter for Xylitol, ATPase component | 100% | 666.8 |
| D-maltose catabolism | malK_Bb | med | ABC-type maltose transport, ATP binding protein (characterized, see rationale) | 48% | 98% | 300.1 | ABC transporter for Xylitol, ATPase component | 100% | 666.8 |
| D-xylose catabolism | gtsD | med | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 45% | 93% | 298.9 | ABC transporter for Xylitol, ATPase component | 100% | 666.8 |
| D-cellobiose catabolism | SMc04256 | med | ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) | 46% | 98% | 297.7 | ABC transporter for Xylitol, ATPase component | 100% | 666.8 |
| L-arabinose catabolism | xacJ | med | Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) | 48% | 96% | 297 | ABC transporter for Xylitol, ATPase component | 100% | 666.8 |
| D-glucosamine (chitosamine) catabolism | SM_b21216 | med | ABC transporter for D-Glucosamine, ATPase component (characterized) | 46% | 99% | 295 | ABC transporter for Xylitol, ATPase component | 100% | 666.8 |
| D-galactose catabolism | PfGW456L13_1897 | med | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 44% | 93% | 292 | ABC transporter for Xylitol, ATPase component | 100% | 666.8 |
| D-maltose catabolism | musK | med | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 47% | 95% | 291.2 | ABC transporter for Xylitol, ATPase component | 100% | 666.8 |
| xylitol catabolism | HSERO_RS17020 | med | ABC-type sugar transport system, ATPase component protein (characterized, see rationale) | 45% | 89% | 283.1 | ABC transporter for Xylitol, ATPase component | 100% | 666.8 |
| trehalose catabolism | treV | med | TreV, component of Trehalose porter (characterized) | 41% | 97% | 248.4 | ABC transporter for Xylitol, ATPase component | 100% | 666.8 |
| L-arginine catabolism | artP | med | Arginine transport ATP-binding protein ArtP; EC 7.4.2.- (characterized) | 42% | 92% | 154.1 | ABC transporter for Xylitol, ATPase component | 100% | 666.8 |
| D-cellobiose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 35% | 96% | 196.4 | ABC transporter for Xylitol, ATPase component | 100% | 666.8 |
| D-galactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 35% | 96% | 196.4 | ABC transporter for Xylitol, ATPase component | 100% | 666.8 |
| D-glucose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 35% | 96% | 196.4 | ABC transporter for Xylitol, ATPase component | 100% | 666.8 |
| lactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 35% | 96% | 196.4 | ABC transporter for Xylitol, ATPase component | 100% | 666.8 |
| D-maltose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 35% | 96% | 196.4 | ABC transporter for Xylitol, ATPase component | 100% | 666.8 |
| D-mannose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 35% | 96% | 196.4 | ABC transporter for Xylitol, ATPase component | 100% | 666.8 |
| sucrose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 35% | 96% | 196.4 | ABC transporter for Xylitol, ATPase component | 100% | 666.8 |
| trehalose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 35% | 96% | 196.4 | ABC transporter for Xylitol, ATPase component | 100% | 666.8 |
| glycerol catabolism | glpS | lo | ABC transporter for Glycerol, ATPase component 1 (characterized) | 32% | 95% | 191 | ABC transporter for Xylitol, ATPase component | 100% | 666.8 |
| L-proline catabolism | proV | lo | glycine betaine/l-proline transport atp-binding protein prov (characterized) | 38% | 62% | 172.6 | ABC transporter for Xylitol, ATPase component | 100% | 666.8 |
| D-alanine catabolism | Pf6N2E2_5405 | lo | ABC transporter for D-Alanine, ATPase component (characterized) | 37% | 94% | 154.5 | ABC transporter for Xylitol, ATPase component | 100% | 666.8 |
| D-glucosamine (chitosamine) catabolism | AO353_21725 | lo | ABC transporter for D-glucosamine, ATPase component (characterized) | 38% | 94% | 154.1 | ABC transporter for Xylitol, ATPase component | 100% | 666.8 |
| L-tryptophan catabolism | ecfA1 | lo | Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) | 37% | 77% | 129 | ABC transporter for Xylitol, ATPase component | 100% | 666.8 |
Sequence Analysis Tools
View 3607124 at FitnessBrowser
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Find functional residues: SitesBLAST
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Predict transmenbrane helices: Phobius
Predict protein localization: PSORTb
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Fitness BLAST: loading...
Sequence
MAGIKIDKINKFYGTTQALFDINLDIEDGEFVVFVGPSGCGKSTLLRTLAGLEGVSSGRI
EIGGRDVTTVEPADRDLAMVFQSYALYPHMTVRENMEFGMKVNGFEPDLRKERIAEAARV
LQLEDYLDRKPGQLSGGQRQRVAIGRAIVKNPSVFLFDEPLSNLDAKLRVQMRVELEGLH
KQLGATMIYVTHDQVEAMTMADKIVVLNRGRIEQVGSPMDLYHKPNSRFVAEFIGSPAMN
VFSSDVGLQDISLDASAAFVGCRPEHIEIVPDGDGHIAATVHVKERLGGESLLYLGLKGG
GQIVARVGGDDETKVGAAVSLRFSRHRLHQFDEAGRAI
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