Protein 3607949 in Dinoroseobacter shibae DFL-12
Annotation: FitnessBrowser__Dino:3607949
Length: 349 amino acids
Source: Dino in FitnessBrowser
Candidate for 34 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 | SMc02869 | med | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 57% | 95% | 372.9 | SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter | 58% | 372.1 |
| D-glucosamine (chitosamine) catabolism | SMc02869 | med | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 57% | 95% | 372.9 | SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter | 58% | 372.1 |
| D-mannitol catabolism | mtlK | med | SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) | 58% | 100% | 372.1 | N-Acetyl-D-glucosamine ABC transport system, ATPase component | 57% | 372.9 |
| D-sorbitol (glucitol) catabolism | mtlK | med | ABC transporter for D-Sorbitol, ATPase component (characterized) | 57% | 100% | 365.2 | N-Acetyl-D-glucosamine ABC transport system, ATPase component | 57% | 372.9 |
| lactose catabolism | lacK | med | ABC transporter for Lactose, ATPase component (characterized) | 55% | 100% | 355.9 | N-Acetyl-D-glucosamine ABC transport system, ATPase component | 57% | 372.9 |
| D-maltose catabolism | aglK | med | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 54% | 100% | 346.3 | N-Acetyl-D-glucosamine ABC transport system, ATPase component | 57% | 372.9 |
| D-maltose catabolism | thuK | med | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 54% | 100% | 346.3 | N-Acetyl-D-glucosamine ABC transport system, ATPase component | 57% | 372.9 |
| sucrose catabolism | aglK | med | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 54% | 100% | 346.3 | N-Acetyl-D-glucosamine ABC transport system, ATPase component | 57% | 372.9 |
| trehalose catabolism | aglK | med | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 54% | 100% | 346.3 | N-Acetyl-D-glucosamine ABC transport system, ATPase component | 57% | 372.9 |
| xylitol catabolism | Dshi_0546 | med | ABC transporter for Xylitol, ATPase component (characterized) | 54% | 100% | 339.7 | N-Acetyl-D-glucosamine ABC transport system, ATPase component | 57% | 372.9 |
| D-cellobiose catabolism | aglK' | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 54% | 97% | 337 | N-Acetyl-D-glucosamine ABC transport system, ATPase component | 57% | 372.9 |
| D-glucose catabolism | aglK' | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 54% | 97% | 337 | N-Acetyl-D-glucosamine ABC transport system, ATPase component | 57% | 372.9 |
| lactose catabolism | aglK' | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 54% | 97% | 337 | N-Acetyl-D-glucosamine ABC transport system, ATPase component | 57% | 372.9 |
| D-maltose catabolism | aglK' | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 54% | 97% | 337 | N-Acetyl-D-glucosamine ABC transport system, ATPase component | 57% | 372.9 |
| sucrose catabolism | aglK' | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 54% | 97% | 337 | N-Acetyl-D-glucosamine ABC transport system, ATPase component | 57% | 372.9 |
| trehalose catabolism | aglK' | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 54% | 97% | 337 | N-Acetyl-D-glucosamine ABC transport system, ATPase component | 57% | 372.9 |
| sucrose catabolism | thuK | med | ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) | 54% | 97% | 335.9 | N-Acetyl-D-glucosamine ABC transport system, ATPase component | 57% | 372.9 |
| trehalose catabolism | thuK | med | ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) | 54% | 97% | 335.9 | N-Acetyl-D-glucosamine ABC transport system, ATPase component | 57% | 372.9 |
| L-fucose catabolism | SM_b21106 | med | ABC transporter for L-Fucose, ATPase component (characterized) | 51% | 99% | 331.6 | N-Acetyl-D-glucosamine ABC transport system, ATPase component | 57% | 372.9 |
| D-maltose catabolism | malK | med | Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 52% | 98% | 327.8 | N-Acetyl-D-glucosamine ABC transport system, ATPase component | 57% | 372.9 |
| D-cellobiose catabolism | gtsD | med | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 47% | 98% | 306.6 | N-Acetyl-D-glucosamine ABC transport system, ATPase component | 57% | 372.9 |
| D-glucose catabolism | gtsD | med | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 47% | 98% | 306.6 | N-Acetyl-D-glucosamine ABC transport system, ATPase component | 57% | 372.9 |
| lactose catabolism | gtsD | med | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 47% | 98% | 306.6 | N-Acetyl-D-glucosamine ABC transport system, ATPase component | 57% | 372.9 |
| D-maltose catabolism | gtsD | med | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 47% | 98% | 306.6 | N-Acetyl-D-glucosamine ABC transport system, ATPase component | 57% | 372.9 |
| sucrose catabolism | gtsD | med | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 47% | 98% | 306.6 | N-Acetyl-D-glucosamine ABC transport system, ATPase component | 57% | 372.9 |
| trehalose catabolism | gtsD | med | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 47% | 98% | 306.6 | N-Acetyl-D-glucosamine ABC transport system, ATPase component | 57% | 372.9 |
| xylitol catabolism | HSERO_RS17020 | med | ABC-type sugar transport system, ATPase component protein (characterized, see rationale) | 47% | 86% | 305.1 | N-Acetyl-D-glucosamine ABC transport system, ATPase component | 57% | 372.9 |
| D-galactose catabolism | PfGW456L13_1897 | med | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 46% | 93% | 299.7 | N-Acetyl-D-glucosamine ABC transport system, ATPase component | 57% | 372.9 |
| D-cellobiose catabolism | SMc04256 | med | ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) | 48% | 99% | 294.3 | N-Acetyl-D-glucosamine ABC transport system, ATPase component | 57% | 372.9 |
| trehalose catabolism | treV | med | TreV, component of Trehalose porter (characterized) | 45% | 88% | 246.9 | N-Acetyl-D-glucosamine ABC transport system, ATPase component | 57% | 372.9 |
| glycerol catabolism | glpT | lo | ABC transporter for Glycerol, ATPase component 2 (characterized) | 38% | 92% | 212.6 | N-Acetyl-D-glucosamine ABC transport system, ATPase component | 57% | 372.9 |
| L-proline catabolism | proV | lo | Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized) | 39% | 65% | 172.2 | N-Acetyl-D-glucosamine ABC transport system, ATPase component | 57% | 372.9 |
| L-asparagine catabolism | aatP | lo | ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) | 35% | 91% | 146.4 | N-Acetyl-D-glucosamine ABC transport system, ATPase component | 57% | 372.9 |
| L-aspartate catabolism | aatP | lo | ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) | 35% | 91% | 146.4 | N-Acetyl-D-glucosamine ABC transport system, ATPase component | 57% | 372.9 |
Sequence Analysis Tools
View 3607949 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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Sequence
MGAITLSKVEKWFGDVQVIKGVDLEIRDGEFVVFVGPSGCGKSTLLRMIGGLEDTSRGAM
LIDGVDVTDHPPAKRGLTMVFQSYALYPHMSVRENMGFSLKTAGAPAAEIAEKVEAAAAV
LKLEPYLDRRPKDLSGGQRQRVAIGRSIVRAPTAFLFDEPLSNLDAALRVEMRYEIAKLH
QSLDTTMIYVTHDQVEAMTLADRIVVLEFGKIAQVGTPRELYETPANLFVAQFIGSPKMN
VMPCTTDAGRYRLSAGRGGVFSGDRPAVQLGIRPEHITPGAPGTGACDGRVDVVEYLGAD
TLLVLDCGPEGRVTVRVIGDTDLTPGDAVGLSFNPDRLSFFDTDGLAIR
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