Protein Dsui_2799 in Dechlorosoma suillum PS
Annotation: FitnessBrowser__PS:Dsui_2799
Length: 670 amino acids
Source: PS in FitnessBrowser
Candidate for 7 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| D-mannose catabolism | TM1750 | med | TM1750, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized) | 48% | 95% | 309.3 | Uncharacterized ABC transporter ATP-binding protein Rv1281c/MT1318, component of The glutathione transporter, OppA (Dasgupta et al., 2010). OppA binds glutathione and the nanopeptide, bradykinin. Also regulates cytokine release, apoptosis and the innate immune response of macrophages infected with M. tuberculosis | 48% | 517.3 |
| D-mannose catabolism | TM1749 | med | TM1749, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized) | 48% | 98% | 296.2 | Uncharacterized ABC transporter ATP-binding protein Rv1281c/MT1318, component of The glutathione transporter, OppA (Dasgupta et al., 2010). OppA binds glutathione and the nanopeptide, bradykinin. Also regulates cytokine release, apoptosis and the innate immune response of macrophages infected with M. tuberculosis | 48% | 517.3 |
| D-cellobiose catabolism | TM0027 | med | TM0027, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized) | 40% | 96% | 181 | Uncharacterized ABC transporter ATP-binding protein Rv1281c/MT1318, component of The glutathione transporter, OppA (Dasgupta et al., 2010). OppA binds glutathione and the nanopeptide, bradykinin. Also regulates cytokine release, apoptosis and the innate immune response of macrophages infected with M. tuberculosis | 48% | 517.3 |
| D-maltose catabolism | malK_Ss | lo | MalK, component of Maltose and maltooligosaccharide porter (characterized) | 39% | 99% | 404.4 | Uncharacterized ABC transporter ATP-binding protein Rv1281c/MT1318, component of The glutathione transporter, OppA (Dasgupta et al., 2010). OppA binds glutathione and the nanopeptide, bradykinin. Also regulates cytokine release, apoptosis and the innate immune response of macrophages infected with M. tuberculosis | 48% | 517.3 |
| D-cellobiose catabolism | TM0028 | lo | TM0028, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized) | 37% | 98% | 198.4 | Uncharacterized ABC transporter ATP-binding protein Rv1281c/MT1318, component of The glutathione transporter, OppA (Dasgupta et al., 2010). OppA binds glutathione and the nanopeptide, bradykinin. Also regulates cytokine release, apoptosis and the innate immune response of macrophages infected with M. tuberculosis | 48% | 517.3 |
| D-cellobiose catabolism | cbtD | lo | CbtD, component of Cellobiose and cellooligosaccharide porter (characterized) | 36% | 86% | 185.7 | Uncharacterized ABC transporter ATP-binding protein Rv1281c/MT1318, component of The glutathione transporter, OppA (Dasgupta et al., 2010). OppA binds glutathione and the nanopeptide, bradykinin. Also regulates cytokine release, apoptosis and the innate immune response of macrophages infected with M. tuberculosis | 48% | 517.3 |
| D-cellobiose catabolism | cbtF | lo | CbtF, component of Cellobiose and cellooligosaccharide porter (characterized) | 36% | 98% | 183.7 | Uncharacterized ABC transporter ATP-binding protein Rv1281c/MT1318, component of The glutathione transporter, OppA (Dasgupta et al., 2010). OppA binds glutathione and the nanopeptide, bradykinin. Also regulates cytokine release, apoptosis and the innate immune response of macrophages infected with M. tuberculosis | 48% | 517.3 |
Sequence Analysis Tools
View Dsui_2799 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
MSDLLSVRNLKAGFLAGGRVLTAVDGVSFAVAPGETFALLGESGCGKSATALALLRLLPN
AGRIQGGEVWLEGEEILALPEAAMRDRRGSAAAMIFQEPATSLNPVLTIGRQIGESLERH
RGMKGEAARREALALLTAVGIADPERRLEEYPFQLSGGMKQRAMIAIALAGEPRLLIADE
PTTALDVTIQAQILDLLARLQAERAMGMLLITHDLGVVARSAHRVGVMYAGEIVETAPRQ
EFFASPRHPYTQKLFAALPDLGQRGAQLATIPGQVPGLAAMPAGCRFAPRCPVAMDRCRL
ESPGWTELEAGHQVRCHWVAQQLPGGEQRLPDLPAAPPAAAAAADAARENLLAVGELKVH
FPIRKGLFKRTVGHVKAVDGVSLELQRGRTLALVGESGCGKTTAGKAVLRLLPATGSVRL
DGRELLGLPERELKPLRRRMQMVFQDPFASLNPRLTVGEIIEEGMTALRVAASRDERRAA
LAALLESVGLPAEALGRYPHEFSGGQRQRIAIARALAVQPELLVCDEPTSALDVSVQAQI
LNLLRRLQEELGLAYLFITHNFAVVEYLAHDVAVMYLGRIVEQGPVQQVLAAPCHPYTRA
LLSAVPEPRLAGQREMVRLPGETPSPARPPQGCHFHPRCAQASERCRQEYPAPSTQAGGV
VVRCHLYPAD
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