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- Task 1: Database OPM.
- 5ctg >> Bidirectional sugar transporter SWEET2b
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- The thickness of the hydrophobic part of the protein in the membrane: 33 angstrom
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- Coordinates of transmembrane spirals:
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- A - Tilt: 5° - Segments: 1( 7- 28), 2( 46- 63), 3( 71- 92),
4( 102- 125), 5( 131- 155), 6( 168- 188), 7( 191- 213)
- B - Tilt: 8° - Segments: 1( 8- 29), 2( 46- 63), 3( 71- 93),
4( 102- 125), 5( 131- 155), 6( 168- 188), 7( 191- 213)
- C - Tilt: 5° - Segments: 1( 7- 28), 2( 46- 63), 3( 71- 90),
4( 103- 125), 5( 131- 155), 6( 168- 188), 7( 191- 213)
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- The average number of residues in one transmembrane helix protein
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- 21
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- Location
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- The protein locates in cell membrane
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- Bidirectional sugar transporter SWEET2b
- It is a protein involved in the transport of glucose in Oryza sativa. Also, a gene encoding this protein uses some pathogenic bacteria, linking to a promoter and enhancing its expression for its own nutrition. [source: Pfam]
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- The thickness of the hydrophobic part of the protein in the membrane: 23,4 angstrom
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- Coordinates of transmembrane spirals:
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- X - Tilt: 4° - Segments:
1( 14- 21), 2( 28- 33), 3( 40- 46), 4( 55- 62),
5( 70- 74), 6( 81- 87), 7( 95- 102), 8( 111- 119),
9( 123- 130), 10( 137- 145), 11( 149- 156), 12( 166- 173),
13( 180- 184), 14( 191- 197), 15( 204- 209), 16( 218- 226),
17( 243- 249), 18( 257- 263), 19( 274- 281)
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- The average number of residues in one transmembrane helix protein
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- 6
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- Location
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- The protein locates in external mitochondrial membrane
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- TheVDAC-2 channel protein plays the role of a pore for the diffuse exchange of small hydrophilic molecules between the mitochondria and the cytosol. [source: Pfam]
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- Task 2: Analysis of the prediction of transmembrane spirals.
- This protein consists of 3 identical chains, therefore, predictions for only one of the chains will be considered below.
TMHMM
- axis Ox - № of amino acids in the protein sequence
- axis Oy - probability of finding a transmembrane spiral
- red lines - transmembrane sites
- blue lines - areas of the protein that enter the cytoplasm
- crimson lines - areas of the protein that go out from the cytoplasm
Phobius
- axis Ox - № of amino acids in the protein sequence
- axis Oy - probability of finding a transmembrane spiral
- grey lines - transmembrane sites
- green lines - areas that go into the cytoplasm
- blue lines - areas that are not in the cytoplasm
- red lines - a signal sequence (in this protein such areas were not found)
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- The output of both programs is the same in terms of the number of spirals, and the coordinates of their transmembrane sites. There are no superfluous and missed predictions, the results of both algorithms fully correspond to the real structural information from the ORM DB.
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- Task 3:TCDB Database
- TCDB (Transporter Classification Database) contains information on transmembrane proteins.
- Of the 2 proteins of task 1, information in the TCDB exists only for the protein SWEET2b sugar transporter
- TC-code: 2.A.123.1.18
- 2. - Proteins-transporters, acting due to the electrochemical potential
- 2. A. - Protein-porters (uniporters, symporters, anti-porters)
- 2.A.123. - proteins of the SWEET family :З
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