Protein WP_041597293.1 in Granulicella tundricola MP5ACTX9
Annotation: NCBI__GCF_000178975.2:WP_041597293.1
Length: 225 amino acids
Source: GCF_000178975.2 in NCBI
Candidate for 33 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| D-cellobiose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 38% | 55% | 144.1 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 201.4 |
| D-glucose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 38% | 55% | 144.1 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 201.4 |
| lactose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 38% | 55% | 144.1 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 201.4 |
| D-maltose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 38% | 55% | 144.1 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 201.4 |
| sucrose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 38% | 55% | 144.1 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 201.4 |
| trehalose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 38% | 55% | 144.1 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 201.4 |
| D-xylose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 38% | 55% | 144.1 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 201.4 |
| D-glucosamine (chitosamine) catabolism | SM_b21216 | lo | ABC transporter for D-Glucosamine, ATPase component (characterized) | 39% | 58% | 142.1 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 201.4 |
| D-galactose catabolism | PfGW456L13_1897 | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 37% | 55% | 141 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 201.4 |
| xylitol catabolism | HSERO_RS17020 | lo | ABC-type sugar transport system, ATPase component protein (characterized, see rationale) | 39% | 52% | 139.8 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 201.4 |
| L-arabinose catabolism | xacJ | lo | Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) | 39% | 55% | 138.3 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 201.4 |
| D-cellobiose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 37% | 61% | 137.5 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 201.4 |
| D-galactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 37% | 61% | 137.5 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 201.4 |
| D-glucose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 37% | 61% | 137.5 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 201.4 |
| lactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 37% | 61% | 137.5 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 201.4 |
| D-maltose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 37% | 61% | 137.5 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 201.4 |
| D-mannose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 37% | 61% | 137.5 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 201.4 |
| sucrose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 37% | 61% | 137.5 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 201.4 |
| trehalose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 37% | 61% | 137.5 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 201.4 |
| N-acetyl-D-glucosamine catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 37% | 59% | 135.2 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 201.4 |
| D-glucosamine (chitosamine) catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 37% | 59% | 135.2 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 201.4 |
| D-maltose catabolism | musK | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 38% | 52% | 135.2 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 201.4 |
| lactose catabolism | lacK | lo | LacK, component of Lactose porter (characterized) | 40% | 58% | 133.7 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 201.4 |
| putrescine catabolism | potA | lo | Spermidine/putrescine import ATP-binding protein PotA, component of The spermidine/putrescine uptake porter, PotABCD (characterized) | 36% | 56% | 133.3 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 201.4 |
| D-mannitol catabolism | mtlK | lo | ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component (characterized) | 36% | 57% | 132.9 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 201.4 |
| D-cellobiose catabolism | msiK | lo | MsiK protein, component of The cellobiose/cellotriose (and possibly higher cellooligosaccharides), CebEFGMsiK [MsiK functions to energize several ABC transporters including those for maltose/maltotriose and trehalose] (characterized) | 37% | 52% | 132.1 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 201.4 |
| D-sorbitol (glucitol) catabolism | mtlK | lo | ABC transporter for D-Sorbitol, ATPase component (characterized) | 35% | 57% | 132.1 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 201.4 |
| D-maltose catabolism | malK | lo | Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 36% | 57% | 131 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 201.4 |
| sucrose catabolism | thuK | lo | ABC transporter (characterized, see rationale) | 38% | 52% | 127.9 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 201.4 |
| D-cellobiose catabolism | SMc04256 | lo | ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) | 35% | 58% | 127.5 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 201.4 |
| D-maltose catabolism | malK_Aa | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 36% | 55% | 124 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 201.4 |
| L-arabinose catabolism | xylGsa | lo | Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale) | 32% | 87% | 110.2 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 201.4 |
| glycerol catabolism | glpS | lo | GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized) | 30% | 59% | 100.1 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 201.4 |
Sequence Analysis Tools
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Find functional residues: SitesBLAST
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Predict protein localization: PSORTb
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Sequence
MVNAPIIEVRNLIKTYRAGEVDVNALNGVSLDVARGEFLSIVGTSGSGKSTLFNILGGLT
PPTSGSVSINGRDLSHMTDTQRNDLRKRTVGFVFQKYNLLPTLTAEQNIQIVRDVAGRPT
AFDDQFREILAMLGIDKRMSHKPRALSGGEQQRVAIARAIVNGPAILLADEPTGNLDSKN
SDVVLTLLRDLNKRLGQTILMITHNPEAAAYADRTIQMRDGKVVA
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