Protein WP_012385446.1 in Beijerinckia indica ATCC 9039
Annotation: NCBI__GCF_000019845.1:WP_012385446.1
Length: 509 amino acids
Source: GCF_000019845.1 in NCBI
Candidate for 17 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 | lo | Myo-Inositol uptake porter, IolT1 (Km=0.2mM) (characterized) | 35% | 93% | 273.1 | Probable metabolite transport protein CsbC | 36% | 291.2 |
| D-glucose catabolism | MFS-glucose | lo | Myo-Inositol uptake porter, IolT1 (Km=0.2mM) (characterized) | 35% | 93% | 273.1 | Probable metabolite transport protein CsbC | 36% | 291.2 |
| lactose catabolism | MFS-glucose | lo | Myo-Inositol uptake porter, IolT1 (Km=0.2mM) (characterized) | 35% | 93% | 273.1 | Probable metabolite transport protein CsbC | 36% | 291.2 |
| D-maltose catabolism | MFS-glucose | lo | Myo-Inositol uptake porter, IolT1 (Km=0.2mM) (characterized) | 35% | 93% | 273.1 | Probable metabolite transport protein CsbC | 36% | 291.2 |
| myo-inositol catabolism | iolT | lo | Myo-Inositol uptake porter, IolT1 (Km=0.2mM) (characterized) | 35% | 93% | 273.1 | Probable metabolite transport protein CsbC | 36% | 291.2 |
| sucrose catabolism | MFS-glucose | lo | Myo-Inositol uptake porter, IolT1 (Km=0.2mM) (characterized) | 35% | 93% | 273.1 | Probable metabolite transport protein CsbC | 36% | 291.2 |
| trehalose catabolism | MFS-glucose | lo | Myo-Inositol uptake porter, IolT1 (Km=0.2mM) (characterized) | 35% | 93% | 273.1 | Probable metabolite transport protein CsbC | 36% | 291.2 |
| L-arabinose catabolism | araE | lo | Arabinose-proton symporter; Arabinose transporter (characterized) | 33% | 97% | 251.1 | Probable metabolite transport protein CsbC | 36% | 291.2 |
| D-galactose catabolism | galP | lo | Arabinose-proton symporter; Arabinose transporter (characterized) | 33% | 97% | 251.1 | Probable metabolite transport protein CsbC | 36% | 291.2 |
| D-xylose catabolism | xylT | lo | Arabinose-proton symporter; Arabinose transporter (characterized) | 33% | 97% | 251.1 | Probable metabolite transport protein CsbC | 36% | 291.2 |
| D-fructose catabolism | glcP | lo | D-fructose transporter, sugar porter family (characterized) | 35% | 95% | 216.5 | Probable metabolite transport protein CsbC | 36% | 291.2 |
| sucrose catabolism | glcP | lo | D-fructose transporter, sugar porter family (characterized) | 35% | 95% | 216.5 | Probable metabolite transport protein CsbC | 36% | 291.2 |
| D-mannose catabolism | STP6 | lo | The high affinity sugar:H+ symporter (sugar uptake) porter of 514 aas and 12 TMSs, STP10. It transports glucose, galactose and mannose, and is therefore a hexose transporter (Rottmann et al. 2016). The 2.4 (characterized) | 31% | 93% | 210.3 | Probable metabolite transport protein CsbC | 36% | 291.2 |
| myo-inositol catabolism | HMIT | lo | Probable inositol transporter 2 (characterized) | 35% | 62% | 208.8 | Probable metabolite transport protein CsbC | 36% | 291.2 |
| D-fructose catabolism | STP6 | lo | sugar transport protein 6 (characterized) | 30% | 92% | 207.2 | Probable metabolite transport protein CsbC | 36% | 291.2 |
| sucrose catabolism | STP6 | lo | sugar transport protein 6 (characterized) | 30% | 92% | 207.2 | Probable metabolite transport protein CsbC | 36% | 291.2 |
| trehalose catabolism | TRET1 | lo | Facilitated trehalose transporter Tret1; PvTret1 (characterized) | 31% | 92% | 187.6 | Probable metabolite transport protein CsbC | 36% | 291.2 |
Sequence Analysis Tools
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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
MISETRGGGSSRPGVDEAVSASKPNPFADRILMVAGLTAAVCGGLYGYDTGIISGALFSM
TREFDLSHQMQETVAASILAGAVLGALITSWFSERYGRKATVLIVAGLFAVGAGACALAP
KVGSLIAARLFLGFAVGGSTQVVPMYISELAPPERRGQLVTMFNVAIGIGIVIANLVGYG
LRDSWTWREMVAVAAVPAAIVFFVMLFMPSSPRWIAERRRLGEAAKILQSIRTSHAEIRD
ELNQIYDVSNAAAQEDAGWKGICKPWVRPALIAALGVAFFTQCGGLEMMIYYSPTFLADA
GFGRNSALLASVGVALVYALVTFLGCLFVDRIGRRRLMLIMIPGSVISLIGLGIMFAFGR
HEGWEATLTVVFLLLFMMFNSAGIQICGWLLGSEMFPLAMRGPATALHAAMLWGSNLLVT
GTALSVVNAVGLGATMWIYAAVNLASLVFVYFFVPETAGASLEDIEGALREGRFKPSRTS
SSVLRIAANSEPMFITKPEPGVAPLKVVE
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