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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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