Protein WP_108909017.1 in Bacillus safensis FO-36b
Annotation: NCBI__GCF_000691165.1:WP_108909017.1
Length: 454 amino acids
Source: GCF_000691165.1 in NCBI
Candidate for 34 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| D-cellobiose catabolism | MFS-glucose | med | Glucose transporter GlcP; Glucose/H(+) symporter (characterized) | 49% | 100% | 448 | Probable metabolite transport protein CsbC | 51% | 458.8 |
| D-glucose catabolism | MFS-glucose | med | Glucose transporter GlcP; Glucose/H(+) symporter (characterized) | 49% | 100% | 448 | Probable metabolite transport protein CsbC | 51% | 458.8 |
| lactose catabolism | MFS-glucose | med | Glucose transporter GlcP; Glucose/H(+) symporter (characterized) | 49% | 100% | 448 | Probable metabolite transport protein CsbC | 51% | 458.8 |
| D-maltose catabolism | MFS-glucose | med | Glucose transporter GlcP; Glucose/H(+) symporter (characterized) | 49% | 100% | 448 | Probable metabolite transport protein CsbC | 51% | 458.8 |
| sucrose catabolism | MFS-glucose | med | Glucose transporter GlcP; Glucose/H(+) symporter (characterized) | 49% | 100% | 448 | Probable metabolite transport protein CsbC | 51% | 458.8 |
| trehalose catabolism | MFS-glucose | med | Glucose transporter GlcP; Glucose/H(+) symporter (characterized) | 49% | 100% | 448 | Probable metabolite transport protein CsbC | 51% | 458.8 |
| D-xylose catabolism | xylT | med | D-xylose transporter; D-xylose-proton symporter (characterized) | 47% | 97% | 420.6 | Probable metabolite transport protein CsbC | 51% | 458.8 |
| myo-inositol catabolism | iolT | med | Major myo-inositol transporter IolT (characterized) | 43% | 94% | 359.8 | Probable metabolite transport protein CsbC | 51% | 458.8 |
| L-arabinose catabolism | araE | med | Arabinose-proton symporter; Arabinose transporter (characterized) | 41% | 93% | 325.5 | Probable metabolite transport protein CsbC | 51% | 458.8 |
| D-galactose catabolism | galP | med | Arabinose-proton symporter; Arabinose transporter (characterized) | 41% | 93% | 325.5 | Probable metabolite transport protein CsbC | 51% | 458.8 |
| D-sorbitol (glucitol) catabolism | SOT | lo | Sorbitol (glucitol):H+ co-transporter, SOT2 (Km for sorbitol of 0.81 mM) of 491 aas and 12 TMSs (Gao et al. 2003). SOT2 of Prunus cerasus is mainly expressed only early in fruit development and not in leaves (characterized) | 35% | 97% | 285.8 | Probable metabolite transport protein CsbC | 51% | 458.8 |
| D-fructose catabolism | glcP | lo | Glucose/fructose:H+ symporter, GlcP (characterized) | 37% | 95% | 282.7 | Probable metabolite transport protein CsbC | 51% | 458.8 |
| sucrose catabolism | glcP | lo | Glucose/fructose:H+ symporter, GlcP (characterized) | 37% | 95% | 282.7 | Probable metabolite transport protein CsbC | 51% | 458.8 |
| glycerol catabolism | PLT5 | lo | polyol transporter 5 (characterized) | 32% | 86% | 267.3 | Probable metabolite transport protein CsbC | 51% | 458.8 |
| D-mannitol catabolism | PLT5 | lo | polyol transporter 5 (characterized) | 32% | 86% | 267.3 | Probable metabolite transport protein CsbC | 51% | 458.8 |
| D-ribose catabolism | PLT5 | lo | polyol transporter 5 (characterized) | 32% | 86% | 267.3 | Probable metabolite transport protein CsbC | 51% | 458.8 |
| xylitol catabolism | PLT5 | lo | polyol transporter 5 (characterized) | 32% | 86% | 267.3 | Probable metabolite transport protein CsbC | 51% | 458.8 |
| D-fructose catabolism | Slc2a5 | lo | The fructose/xylose:H+ symporter, PMT1 (polyol monosaccharide transporter-1). Also transports other substrates at lower rates. PMT2 is largely of the same sequence and function. Both are present in pollen and young xylem cells (Klepek et al., 2005). A similar ortholog has been identifed in pollen grains of Petunia hybrida (characterized) | 34% | 91% | 266.2 | Probable metabolite transport protein CsbC | 51% | 458.8 |
| sucrose catabolism | Slc2a5 | lo | The fructose/xylose:H+ symporter, PMT1 (polyol monosaccharide transporter-1). Also transports other substrates at lower rates. PMT2 is largely of the same sequence and function. Both are present in pollen and young xylem cells (Klepek et al., 2005). A similar ortholog has been identifed in pollen grains of Petunia hybrida (characterized) | 34% | 91% | 266.2 | Probable metabolite transport protein CsbC | 51% | 458.8 |
| D-fructose catabolism | STP6 | lo | sugar transport protein 6 (characterized) | 34% | 91% | 247.3 | Probable metabolite transport protein CsbC | 51% | 458.8 |
| D-mannose catabolism | STP6 | lo | sugar transport protein 6 (characterized) | 34% | 91% | 247.3 | Probable metabolite transport protein CsbC | 51% | 458.8 |
| sucrose catabolism | STP6 | lo | sugar transport protein 6 (characterized) | 34% | 91% | 247.3 | Probable metabolite transport protein CsbC | 51% | 458.8 |
| myo-inositol catabolism | HMIT | lo | Probable inositol transporter 2 (characterized) | 39% | 58% | 237.7 | Probable metabolite transport protein CsbC | 51% | 458.8 |
| trehalose catabolism | TRET1 | lo | Facilitated trehalose transporter Tret1; BmTRET1 (characterized) | 34% | 87% | 231.1 | Probable metabolite transport protein CsbC | 51% | 458.8 |
| D-glucosamine (chitosamine) catabolism | SLC2A2 | lo | Solute carrier family 2, facilitated glucose transporter member 2; Glucose transporter type 2, liver; GLUT-2 (characterized) | 34% | 77% | 221.1 | Probable metabolite transport protein CsbC | 51% | 458.8 |
| D-galactose catabolism | MST1 | lo | The monosaccharide (MST) (glucose > mannose > galactose > fructose):H+ symporter, MST1 (characterized) | 32% | 78% | 210.3 | Probable metabolite transport protein CsbC | 51% | 458.8 |
| D-mannose catabolism | MST1 | lo | The monosaccharide (MST) (glucose > mannose > galactose > fructose):H+ symporter, MST1 (characterized) | 32% | 78% | 210.3 | Probable metabolite transport protein CsbC | 51% | 458.8 |
| D-galactose catabolism | gal2 | lo | galactose transporter (characterized) | 33% | 79% | 204.5 | Probable metabolite transport protein CsbC | 51% | 458.8 |
| D-xylose catabolism | gal2 | lo | galactose transporter (characterized) | 33% | 79% | 204.5 | Probable metabolite transport protein CsbC | 51% | 458.8 |
| D-gluconate catabolism | ght3 | lo | high-affinity gluconate transporter ght3 (characterized) | 31% | 83% | 195.7 | Probable metabolite transport protein CsbC | 51% | 458.8 |
| D-fructose catabolism | frt1 | lo | Fructose:H+ symporter, Frt1 (characterized) | 30% | 83% | 191.4 | Probable metabolite transport protein CsbC | 51% | 458.8 |
| sucrose catabolism | frt1 | lo | Fructose:H+ symporter, Frt1 (characterized) | 30% | 83% | 191.4 | Probable metabolite transport protein CsbC | 51% | 458.8 |
| D-fructose catabolism | ght6 | lo | high-affinity fructose transporter ght6 (characterized) | 30% | 86% | 189.5 | Probable metabolite transport protein CsbC | 51% | 458.8 |
| sucrose catabolism | ght6 | lo | high-affinity fructose transporter ght6 (characterized) | 30% | 86% | 189.5 | Probable metabolite transport protein CsbC | 51% | 458.8 |
Sequence Analysis Tools
View WP_108909017.1 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
Fitness BLAST: loading...
Sequence
MKNRNGWLYFFGALGGALYGYDTGVISGAILFMKEDLGLNAFTEGLVVSSILIGAMLGSS
LSGKLTDQFGRKKAIIAAAILFIIGGFGTALAPNTEVMILFRIVLGLAVGCSTTIVPLYL
SELAPKESRGALSSLNQLMITFGILLAYIVNYALADAEAWRLMLGIAVVPSVLLLFGILF
MPESPRWLFVHGQADRAKEILSKLRKSKQEVAEEISDIQKAESEEKGGFKELFEPWVRPA
LIAGVGLAFLQQFIGTNTIIYYAPKTFTSVGFGNSAAILGTVGIGAVNVIMTFVAIKIID
RVGRKALLLFGNAGMVLSLIVLSVVNRFFEGSTAAGWTTVICLGLFIVIFAVSWGPVVWV
MLPELFPVHVRGIGTGVSTFLLHTGNLIISLTFPALLSAIGISNLFLIYAFIGVVAFLFV
KYLVTETKGKSLEEIEEDLKKRNRAVTSGEGKTV
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