Protein Ga0059261_2293 in Sphingomonas koreensis DSMZ 15582
Annotation: FitnessBrowser__Korea:Ga0059261_2293
Length: 235 amino acids
Source: Korea in FitnessBrowser
Candidate for 26 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| L-histidine catabolism | PA5503 | lo | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) | 39% | 63% | 147.5 | cell division ATP-binding protein ftsE | 44% | 185.3 |
| L-arginine catabolism | artP | lo | AotP aka PA0892, component of Arginine/ornithine (but not lysine) porter (characterized) | 33% | 93% | 132.1 | cell division ATP-binding protein ftsE | 44% | 185.3 |
| L-citrulline catabolism | AO353_03040 | lo | ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) | 33% | 89% | 129 | cell division ATP-binding protein ftsE | 44% | 185.3 |
| xylitol catabolism | HSERO_RS17020 | lo | ABC-type sugar transport system, ATPase component protein (characterized, see rationale) | 35% | 56% | 127.1 | cell division ATP-binding protein ftsE | 44% | 185.3 |
| L-histidine catabolism | hisP | lo | Histidine transport ATP-binding protein HisP (characterized) | 32% | 90% | 122.5 | cell division ATP-binding protein ftsE | 44% | 185.3 |
| L-lysine catabolism | hisP | lo | Histidine transport ATP-binding protein HisP (characterized) | 32% | 90% | 122.5 | cell division ATP-binding protein ftsE | 44% | 185.3 |
| D-sorbitol (glucitol) catabolism | mtlK | lo | ABC transporter for D-Sorbitol, ATPase component (characterized) | 34% | 57% | 122.5 | cell division ATP-binding protein ftsE | 44% | 185.3 |
| L-arabinose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 32% | 62% | 122.1 | cell division ATP-binding protein ftsE | 44% | 185.3 |
| D-fructose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 32% | 62% | 122.1 | cell division ATP-binding protein ftsE | 44% | 185.3 |
| sucrose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 32% | 62% | 122.1 | cell division ATP-binding protein ftsE | 44% | 185.3 |
| D-xylose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 32% | 62% | 122.1 | cell division ATP-binding protein ftsE | 44% | 185.3 |
| putrescine catabolism | potA | lo | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) | 35% | 53% | 120.2 | cell division ATP-binding protein ftsE | 44% | 185.3 |
| L-proline catabolism | proV | lo | Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized) | 34% | 56% | 115.9 | cell division ATP-binding protein ftsE | 44% | 185.3 |
| 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) | 34% | 51% | 115.2 | cell division ATP-binding protein ftsE | 44% | 185.3 |
| D-cellobiose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 32% | 51% | 112.1 | cell division ATP-binding protein ftsE | 44% | 185.3 |
| D-glucose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 32% | 51% | 112.1 | cell division ATP-binding protein ftsE | 44% | 185.3 |
| lactose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 32% | 51% | 112.1 | cell division ATP-binding protein ftsE | 44% | 185.3 |
| D-maltose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 32% | 51% | 112.1 | cell division ATP-binding protein ftsE | 44% | 185.3 |
| sucrose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 32% | 51% | 112.1 | cell division ATP-binding protein ftsE | 44% | 185.3 |
| trehalose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 32% | 51% | 112.1 | cell division ATP-binding protein ftsE | 44% | 185.3 |
| D-xylose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 32% | 51% | 112.1 | cell division ATP-binding protein ftsE | 44% | 185.3 |
| D-maltose catabolism | musK | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 33% | 51% | 110.5 | cell division ATP-binding protein ftsE | 44% | 185.3 |
| D-maltose catabolism | malK_Aa | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 33% | 51% | 107.1 | cell division ATP-binding protein ftsE | 44% | 185.3 |
| D-mannose catabolism | TT_C0211 | lo | Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized) | 31% | 51% | 107.1 | cell division ATP-binding protein ftsE | 44% | 185.3 |
| trehalose catabolism | thuK | lo | Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized) | 31% | 51% | 107.1 | cell division ATP-binding protein ftsE | 44% | 185.3 |
| D-cellobiose catabolism | cbtF | lo | CbtF, component of Cellobiose and cellooligosaccharide porter (characterized) | 32% | 65% | 90.9 | cell division ATP-binding protein ftsE | 44% | 185.3 |
Sequence Analysis Tools
View Ga0059261_2293 at FitnessBrowser
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Find functional residues: SitesBLAST
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Sequence
MANIVQFENVGLRYGTGAETLSDVSFTLSAGSFYFVTGASGAGKTSLLRLLYLAQRPTRG
IVRLFGEDAGALPRKRLPGFRRRIGVVFQDFRLLPHLSAYDNVALPLRVAGIPEADIEGP
VREMIAWVGLKDRDSAKPPTLSGGEQQRIAIARAVITRPEILIADEPTGNVDPDMAERLL
HLFDSLNRLGTTVVVATHDFQLISRIPDARMMRIEKGRLNDPTGALRYPPGQAPA
This GapMind analysis is from Sep 17 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