Protein GFF1915 in Phaeobacter inhibens BS107
Annotation: FitnessBrowser__Phaeo:GFF1915
Length: 363 amino acids
Source: Phaeo in FitnessBrowser
Candidate for 15 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| D-cellobiose catabolism | SMc04256 | hi | ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) | 57% | 100% | 375.2 | MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) | 50% | 332.0 |
| D-cellobiose catabolism | gtsD | med | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 50% | 99% | 342 | ABC transporter for D-Cellobiose and D-Salicin, ATPase component | 57% | 375.2 |
| D-glucose catabolism | gtsD | med | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 50% | 99% | 342 | ABC transporter for D-Cellobiose and D-Salicin, ATPase component | 57% | 375.2 |
| lactose catabolism | gtsD | med | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 50% | 99% | 342 | ABC transporter for D-Cellobiose and D-Salicin, ATPase component | 57% | 375.2 |
| D-maltose catabolism | gtsD | med | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 50% | 99% | 342 | ABC transporter for D-Cellobiose and D-Salicin, ATPase component | 57% | 375.2 |
| sucrose catabolism | gtsD | med | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 50% | 99% | 342 | ABC transporter for D-Cellobiose and D-Salicin, ATPase component | 57% | 375.2 |
| trehalose catabolism | gtsD | med | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 50% | 99% | 342 | ABC transporter for D-Cellobiose and D-Salicin, ATPase component | 57% | 375.2 |
| D-glucosamine (chitosamine) catabolism | SM_b21216 | med | ABC transporter for D-Glucosamine, ATPase component (characterized) | 51% | 98% | 328.6 | ABC transporter for D-Cellobiose and D-Salicin, ATPase component | 57% | 375.2 |
| D-xylose catabolism | gtsD | med | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 47% | 94% | 323.9 | ABC transporter for D-Cellobiose and D-Salicin, ATPase component | 57% | 375.2 |
| D-maltose catabolism | malK_Aa | med | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 48% | 91% | 318.9 | ABC transporter for D-Cellobiose and D-Salicin, ATPase component | 57% | 375.2 |
| D-galactose catabolism | PfGW456L13_1897 | med | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 47% | 91% | 317 | ABC transporter for D-Cellobiose and D-Salicin, ATPase component | 57% | 375.2 |
| D-maltose catabolism | malK1 | med | MalK; aka Sugar ABC transporter, ATP-binding protein, component of The maltose, maltotriose, mannotetraose (MalE1)/maltose, maltotriose, trehalose (MalE2) porter (Nanavati et al., 2005). For MalG1 (823aas) and MalG2 (833aas), the C-terminal transmembrane domain with 6 putative TMSs is preceded by a single N-terminal TMS and a large (600 residue) hydrophilic region showing sequence similarity to MLP1 and 2 (9.A.14; e-12 & e-7) as well as other proteins (characterized) | 49% | 98% | 315.5 | ABC transporter for D-Cellobiose and D-Salicin, ATPase component | 57% | 375.2 |
| D-maltose catabolism | malK_Bb | med | ABC-type maltose transport, ATP binding protein (characterized, see rationale) | 46% | 99% | 299.3 | ABC transporter for D-Cellobiose and D-Salicin, ATPase component | 57% | 375.2 |
| L-arabinose catabolism | xacJ | med | Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) | 44% | 96% | 287 | ABC transporter for D-Cellobiose and D-Salicin, ATPase component | 57% | 375.2 |
| glycerol catabolism | glpT | lo | GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) | 36% | 91% | 213.8 | ABC transporter for D-Cellobiose and D-Salicin, ATPase component | 57% | 375.2 |
Sequence Analysis Tools
View GFF1915 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
MKQVKIETMTSHVSARDLSVRFGAVEVLKSLNLDIQKGEFLVLLGASGCGKSTLLNTIAG
LQEATEGQIWINDENVTWREPKDRGLAMVFQSYALYPKMTVRGNLAFGLRMNKVPKAEAD
KLVDEAARVLQLEELLDRRPGELSGGQRQRVAIGRALVRKVDVFLFDEPLSNLDAKLRAE
LRVELKRLHQELGATMIYVTHDQVEALTLADRIAVMKDGVVQQLDSPEEIYRRPANRYVA
QFVGLPSMNFVNGVVTESGAIQTEDFELALDQCNLASTPAPGTEVEIGIRPEHVHPANAG
GFMLDVGMVELLGSERLIWGKVGNTSIVMRDDPDTTIRSGDQVRINLKPGAFSVFSAKTG
LRI
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