Protein WP_085218060.1 in Sphingomonas indica Dd16
Annotation: NCBI__GCF_900177405.1:WP_085218060.1
Length: 229 amino acids
Source: GCF_900177405.1 in NCBI
Candidate for 27 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| L-glutamate catabolism | gltL | med | GluA aka CGL1950, component of Glutamate porter (characterized) | 42% | 83% | 141 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 44% | 189.1 |
| L-lysine catabolism | hisP | med | Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) | 40% | 78% | 137.1 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 44% | 189.1 |
| L-histidine catabolism | PA5503 | lo | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) | 40% | 66% | 145.6 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 44% | 189.1 |
| L-fucose catabolism | SM_b21106 | lo | ABC transporter for L-Fucose, ATPase component (characterized) | 39% | 58% | 130.2 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 44% | 189.1 |
| N-acetyl-D-glucosamine catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 40% | 56% | 128.6 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 44% | 189.1 |
| D-glucosamine (chitosamine) catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 40% | 56% | 128.6 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 44% | 189.1 |
| D-mannitol catabolism | mtlK | lo | ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component (characterized) | 39% | 56% | 128.3 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 44% | 189.1 |
| D-cellobiose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 39% | 52% | 125.6 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 44% | 189.1 |
| D-glucose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 39% | 52% | 125.6 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 44% | 189.1 |
| lactose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 39% | 52% | 125.6 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 44% | 189.1 |
| D-maltose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 39% | 52% | 125.6 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 44% | 189.1 |
| sucrose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 39% | 52% | 125.6 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 44% | 189.1 |
| trehalose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 39% | 52% | 125.6 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 44% | 189.1 |
| D-xylose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 39% | 52% | 125.6 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 44% | 189.1 |
| D-sorbitol (glucitol) catabolism | mtlK | lo | ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component (characterized) | 37% | 56% | 122.5 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 44% | 189.1 |
| D-galactose catabolism | PfGW456L13_1897 | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 35% | 55% | 118.2 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 44% | 189.1 |
| D-cellobiose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 36% | 53% | 117.1 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 44% | 189.1 |
| D-glucose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 36% | 53% | 117.1 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 44% | 189.1 |
| lactose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 36% | 53% | 117.1 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 44% | 189.1 |
| D-maltose catabolism | aglK | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 36% | 53% | 117.1 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 44% | 189.1 |
| D-maltose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 36% | 53% | 117.1 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 44% | 189.1 |
| sucrose catabolism | aglK | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 36% | 53% | 117.1 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 44% | 189.1 |
| sucrose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 36% | 53% | 117.1 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 44% | 189.1 |
| trehalose catabolism | aglK | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 36% | 53% | 117.1 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 44% | 189.1 |
| trehalose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 36% | 53% | 117.1 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 44% | 189.1 |
| trehalose catabolism | treV | lo | TreV, component of Trehalose porter (characterized) | 32% | 68% | 115.5 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 44% | 189.1 |
| D-cellobiose catabolism | cbtF | lo | CbtF, component of Cellobiose and cellooligosaccharide porter (characterized) | 32% | 59% | 82.8 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 44% | 189.1 |
Sequence Analysis Tools
View WP_085218060.1 at NCBI
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
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Sequence
MLSPNIVIDAADVTLALGSGASRVEILRGIDLSVSKGDSVALLGPSGSGKSSLMAVLAGL
ERATGGSIRIAGADFAALDEDGLARARRGRVGIVLQAFHLLPTMTAHENVAVPLELAGVA
DAFAIAAGELEAVGLGHRLTHYPAQLSGGEQQRVAIARATAPRPELIFADEPTGNLDAAT
GTAILDLLFARQKDTGATLFVITHDPALAARCDRVLEMQDGRIVTDKRT
This GapMind analysis is from Sep 24 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