Protein WP_014265448.1 in Granulicella mallensis MP5ACTX8
Annotation: NCBI__GCF_000178955.2:WP_014265448.1
Length: 468 amino acids
Source: GCF_000178955.2 in NCBI
Candidate for 22 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 | Galactose-proton symporter; Galactose transporter (characterized) | 39% | 93% | 309.3 | D-xylose transporter; D-xylose-proton symporter | 39% | 302.8 |
| D-galactose catabolism | galP | med | Galactose-proton symporter; Galactose transporter (characterized) | 39% | 93% | 309.3 | D-xylose transporter; D-xylose-proton symporter | 39% | 302.8 |
| D-glucose catabolism | MFS-glucose | med | Galactose-proton symporter; Galactose transporter (characterized) | 39% | 93% | 309.3 | D-xylose transporter; D-xylose-proton symporter | 39% | 302.8 |
| lactose catabolism | MFS-glucose | med | Galactose-proton symporter; Galactose transporter (characterized) | 39% | 93% | 309.3 | D-xylose transporter; D-xylose-proton symporter | 39% | 302.8 |
| D-maltose catabolism | MFS-glucose | med | Galactose-proton symporter; Galactose transporter (characterized) | 39% | 93% | 309.3 | D-xylose transporter; D-xylose-proton symporter | 39% | 302.8 |
| sucrose catabolism | MFS-glucose | med | Galactose-proton symporter; Galactose transporter (characterized) | 39% | 93% | 309.3 | D-xylose transporter; D-xylose-proton symporter | 39% | 302.8 |
| trehalose catabolism | MFS-glucose | med | Galactose-proton symporter; Galactose transporter (characterized) | 39% | 93% | 309.3 | D-xylose transporter; D-xylose-proton symporter | 39% | 302.8 |
| D-xylose catabolism | xylT | lo | D-xylose transporter; D-xylose-proton symporter (characterized) | 39% | 95% | 302.8 | Galactose-proton symporter; Galactose transporter | 39% | 309.3 |
| myo-inositol catabolism | iolT | lo | Inositol transporter 1 (characterized) | 36% | 90% | 294.7 | Galactose-proton symporter; Galactose transporter | 39% | 309.3 |
| L-arabinose catabolism | araE | lo | Arabinose-proton symporter; Arabinose transporter (characterized) | 37% | 96% | 286.6 | Galactose-proton symporter; Galactose transporter | 39% | 309.3 |
| D-sorbitol (glucitol) catabolism | SOT | lo | Sorbitol (D-Glucitol):H+ co-transporter, SOT1 (Km for sorbitol of 0.64 mM) of 509 aas and 12 TMSs (Gao et al. 2003). SOT1 of P. cerasus is expressed throughout fruit development, but especially when growth and sorbitol accumulation rates are highest. In leaves, PcSOT1 expression is highest in young, expanding tissues, but substantially less in mature leaves (characterized) | 34% | 95% | 283.1 | Galactose-proton symporter; Galactose transporter | 39% | 309.3 |
| glycerol catabolism | PLT5 | lo | polyol transporter 5 (characterized) | 32% | 86% | 263.1 | Galactose-proton symporter; Galactose transporter | 39% | 309.3 |
| D-mannitol catabolism | PLT5 | lo | polyol transporter 5 (characterized) | 32% | 86% | 263.1 | Galactose-proton symporter; Galactose transporter | 39% | 309.3 |
| D-ribose catabolism | PLT5 | lo | polyol transporter 5 (characterized) | 32% | 86% | 263.1 | Galactose-proton symporter; Galactose transporter | 39% | 309.3 |
| xylitol catabolism | PLT5 | lo | polyol transporter 5 (characterized) | 32% | 86% | 263.1 | Galactose-proton symporter; Galactose transporter | 39% | 309.3 |
| D-fructose catabolism | glcP | lo | Glucose/fructose:H+ symporter, GlcP (characterized) | 35% | 98% | 256.5 | Galactose-proton symporter; Galactose transporter | 39% | 309.3 |
| sucrose catabolism | glcP | lo | Glucose/fructose:H+ symporter, GlcP (characterized) | 35% | 98% | 256.5 | Galactose-proton symporter; Galactose transporter | 39% | 309.3 |
| 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) | 31% | 92% | 243.4 | Galactose-proton symporter; Galactose transporter | 39% | 309.3 |
| 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) | 31% | 92% | 243.4 | Galactose-proton symporter; Galactose transporter | 39% | 309.3 |
| myo-inositol catabolism | HMIT | lo | Probable inositol transporter 2 (characterized) | 34% | 64% | 236.9 | Galactose-proton symporter; Galactose transporter | 39% | 309.3 |
| trehalose catabolism | TRET1 | lo | Facilitated trehalose transporter Tret1; BmTRET1 (characterized) | 31% | 92% | 219.2 | Galactose-proton symporter; Galactose transporter | 39% | 309.3 |
| D-galacturonate catabolism | gatA | lo | The galacturonic acid (galacturonate) uptake porter, GatA, of 518 aas and 12 TMSs (characterized) | 31% | 92% | 211.8 | Galactose-proton symporter; Galactose transporter | 39% | 309.3 |
Sequence Analysis Tools
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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
MSTFVSREEILPNTETVLQTYVRRNFIWKVSFIAGLGGILYGFDMGIIAAALIFVRESFS
LSTRMEEVVVSIVLVGAMLGAIAGGSIADRIGRRATLLWGGGIFLIASLLAPASPNAATL
IVARALLGIAIGFTSVTAPVYISELAPPQSRGRLIGLYQFALTVGIALADLVGYWFAGQH
AWRLMFGLGAAPAALFVVLLLTLPESPRWLFAQNRVAEAQSVLSSYTDEAGARLLIEDIH
SALDLKVEKRWSALWSPAVRLSLLIAVGFTVLQQVTGINTIIYYGPRIFSLAGITSNRSA
IFATLLVAVTNVLATIIALVLVDRVGRKPLLYAGISGMTASLFLLAYSFHNPAAFGAAPG
IIATICLMVYITCFAFSMGPIAWILVSEVFPLQLRGRGVAAASLGSGAANFLVSITFLSL
IKVAGNSVTFIIYGAFCIVTLLFVRFIVPETKGRELESISAGHGASVS
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