Protein Ga0059261_3668 in Sphingomonas koreensis DSMZ 15582
Annotation: Ga0059261_3668 ABC transporter
Length: 201 amino acids
Source: Korea in FitnessBrowser
Candidate for 29 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| D-maltose catabolism | malK | lo | Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 41% | 52% | 137.5 | ABC-type molybdate transporter (EC 7.3.2.5) | 46% | 169.1 |
| D-cellobiose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 40% | 58% | 137.1 | ABC-type molybdate transporter (EC 7.3.2.5) | 46% | 169.1 |
| D-glucose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 40% | 58% | 137.1 | ABC-type molybdate transporter (EC 7.3.2.5) | 46% | 169.1 |
| lactose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 40% | 58% | 137.1 | ABC-type molybdate transporter (EC 7.3.2.5) | 46% | 169.1 |
| D-maltose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 40% | 58% | 137.1 | ABC-type molybdate transporter (EC 7.3.2.5) | 46% | 169.1 |
| sucrose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 40% | 58% | 137.1 | ABC-type molybdate transporter (EC 7.3.2.5) | 46% | 169.1 |
| trehalose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 40% | 58% | 137.1 | ABC-type molybdate transporter (EC 7.3.2.5) | 46% | 169.1 |
| D-maltose catabolism | thuK | lo | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 38% | 51% | 131.7 | ABC-type molybdate transporter (EC 7.3.2.5) | 46% | 169.1 |
| trehalose catabolism | thuK | lo | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 38% | 51% | 131.7 | ABC-type molybdate transporter (EC 7.3.2.5) | 46% | 169.1 |
| N-acetyl-D-glucosamine catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 37% | 56% | 128.3 | ABC-type molybdate transporter (EC 7.3.2.5) | 46% | 169.1 |
| D-glucosamine (chitosamine) catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 37% | 56% | 128.3 | ABC-type molybdate transporter (EC 7.3.2.5) | 46% | 169.1 |
| L-arabinose catabolism | xacJ | lo | Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) | 39% | 51% | 127.5 | ABC-type molybdate transporter (EC 7.3.2.5) | 46% | 169.1 |
| D-sorbitol (glucitol) catabolism | mtlK | lo | ABC transporter for D-Sorbitol, ATPase component (characterized) | 40% | 51% | 126.7 | ABC-type molybdate transporter (EC 7.3.2.5) | 46% | 169.1 |
| D-glucosamine (chitosamine) catabolism | SM_b21216 | lo | ABC transporter for D-Glucosamine, ATPase component (characterized) | 38% | 54% | 126.3 | ABC-type molybdate transporter (EC 7.3.2.5) | 46% | 169.1 |
| D-cellobiose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 38% | 54% | 125.2 | ABC-type molybdate transporter (EC 7.3.2.5) | 46% | 169.1 |
| D-glucose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 38% | 54% | 125.2 | ABC-type molybdate transporter (EC 7.3.2.5) | 46% | 169.1 |
| lactose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 38% | 54% | 125.2 | ABC-type molybdate transporter (EC 7.3.2.5) | 46% | 169.1 |
| D-maltose catabolism | aglK | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 38% | 54% | 125.2 | ABC-type molybdate transporter (EC 7.3.2.5) | 46% | 169.1 |
| D-maltose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 38% | 54% | 125.2 | ABC-type molybdate transporter (EC 7.3.2.5) | 46% | 169.1 |
| sucrose catabolism | aglK | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 38% | 54% | 125.2 | ABC-type molybdate transporter (EC 7.3.2.5) | 46% | 169.1 |
| sucrose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 38% | 54% | 125.2 | ABC-type molybdate transporter (EC 7.3.2.5) | 46% | 169.1 |
| trehalose catabolism | aglK | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 38% | 54% | 125.2 | ABC-type molybdate transporter (EC 7.3.2.5) | 46% | 169.1 |
| trehalose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 38% | 54% | 125.2 | ABC-type molybdate transporter (EC 7.3.2.5) | 46% | 169.1 |
| D-maltose catabolism | malK_Bb | lo | ABC-type maltose transport, ATP binding protein (characterized, see rationale) | 37% | 56% | 124.8 | ABC-type molybdate transporter (EC 7.3.2.5) | 46% | 169.1 |
| sucrose catabolism | thuK | lo | ABC transporter (characterized, see rationale) | 38% | 52% | 124 | ABC-type molybdate transporter (EC 7.3.2.5) | 46% | 169.1 |
| lactose catabolism | lacK | lo | ABC transporter for Lactose, ATPase component (characterized) | 39% | 51% | 123.2 | ABC-type molybdate transporter (EC 7.3.2.5) | 46% | 169.1 |
| D-mannitol catabolism | mtlK | lo | SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) | 35% | 60% | 120.9 | ABC-type molybdate transporter (EC 7.3.2.5) | 46% | 169.1 |
| trehalose catabolism | treV | lo | TreV, component of Trehalose porter (characterized) | 35% | 56% | 109 | ABC-type molybdate transporter (EC 7.3.2.5) | 46% | 169.1 |
| D-cellobiose catabolism | SMc04256 | lo | ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) | 37% | 51% | 104.4 | ABC-type molybdate transporter (EC 7.3.2.5) | 46% | 169.1 |
Sequence Analysis Tools
View Ga0059261_3668 at FitnessBrowser
Find papers: PaperBLAST
Find functional residues: SitesBLAST
Search for conserved domains
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Predict transmenbrane helices: Phobius
Predict protein localization: PSORTb
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Sequence
MSFDIAIEKRRGDAQISCRIEGGEGIIVLFGPSGVGKTSVLDMVAGLLEPDTGHVRVGGE
TLFDAAIGEDVPPERRRAGYVFQDARLFPHLSVRANLLYGAGGDPSGLGDLAARFDIAHL
LDRWPRSLSGGEARRVAIGRALLAKPRFLLLDEPLSSLDRARREEVTRVIERLRDEAALP
ILMVTHDPVEAERLGQRIIEI
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