| cus-tm |
| ID: | 1419257780 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 100 (97) | ||
| Sequences: | 393 (290.6) | ||
| Seq/Len: | 4.052 | ||
| Nf(neff/√len): | 29.5 |
HHblits Results: (2013_03)
Sequences per length for each position, BEFORE the coverage/gap filter was applied
Legend: Dots above the red line, indicates positions where there is > 5 sequences per length (if visible, green bar = 20 seq/len). Point of this graphic is to give you an idea if resubmitting a sub-portion of your sequence might help increase the overall Seq/Len (which after applying the coverage filter is at: 4.052).
Sequences per length for each position, AFTER the coverage/gap filter was applied
Residue pairs sorted by coevolution strength:
Legend: The darker and larger the blue dots, the higher strength in covariance. Below we provide the list of the top [1.5 x length] covarying residues with sequence seperation > 3. The i and j are positions as given in the input sequence.
| i | j | Scaled score | Prob |
| 32_H | 37_D | 2.126 | 1.00 |
| 3_A | 21_F | 1.838 | 1.00 |
| 7_T | 17_A | 1.763 | 0.99 |
| 82_D | 86_K | 1.692 | 0.99 |
| 32_H | 35_E | 1.657 | 0.99 |
| 10_I | 22_A | 1.651 | 0.99 |
| 2_L | 15_I | 1.601 | 0.99 |
| 40_D | 71_S | 1.563 | 0.98 |
| 33_F | 37_D | 1.543 | 0.98 |
| 25_M | 29_V | 1.542 | 0.98 |
| 75_N | 80_L | 1.503 | 0.98 |
| 12_L | 27_H | 1.413 | 0.96 |
| 18_F | 37_D | 1.392 | 0.96 |
| 18_F | 73_Y | 1.376 | 0.95 |
| 45_S | 60_A | 1.360 | 0.95 |
| 28_S | 36_Q | 1.307 | 0.94 |
| 59_Q | 86_K | 1.294 | 0.93 |
| 92_P | 95_P | 1.291 | 0.93 |
| 32_H | 36_Q | 1.279 | 0.93 |
| 80_L | 88_V | 1.269 | 0.92 |
| 85_G | 88_V | 1.264 | 0.92 |
| 33_F | 41_L | 1.244 | 0.91 |
| 82_D | 85_G | 1.234 | 0.91 |
| 14_T | 18_F | 1.220 | 0.90 |
| 92_P | 96_D | 1.211 | 0.90 |
| 18_F | 45_S | 1.166 | 0.87 |
| 15_I | 19_F | 1.155 | 0.86 |
| 10_I | 25_M | 1.137 | 0.85 |
| 29_V | 32_H | 1.119 | 0.84 |
| 21_F | 41_L | 1.101 | 0.83 |
| 93_G | 96_D | 1.098 | 0.82 |
| 65_T | 68_D | 1.087 | 0.82 |
| 7_T | 64_M | 1.080 | 0.81 |
| 26_I | 32_H | 1.078 | 0.81 |
| 69_I | 77_L | 1.077 | 0.81 |
| 10_I | 44_I | 1.069 | 0.80 |
| 4_T | 87_T | 1.063 | 0.80 |
| 66_L | 80_L | 1.055 | 0.79 |
| 47_T | 66_L | 1.054 | 0.79 |
| 44_I | 73_Y | 1.042 | 0.78 |
| 81_A | 86_K | 1.041 | 0.78 |
| 32_H | 47_T | 1.040 | 0.77 |
| 38_I | 66_L | 1.036 | 0.77 |
| 2_L | 16_A | 1.036 | 0.77 |
| 93_G | 97_I | 1.035 | 0.77 |
| 14_T | 29_V | 1.026 | 0.76 |
| 40_D | 72_G | 1.026 | 0.76 |
| 3_A | 48_L | 1.010 | 0.75 |
| 36_Q | 44_I | 1.008 | 0.74 |
| 13_A | 36_Q | 1.004 | 0.74 |
Prob = P(contact | scaled_score, seq/len).
Scaled Score = (raw_score/average(raw_scores)).
- Text file of contact predictions (all 3L/2 predictions)
- Generate restraints for ROSETTA Structure Modeling
- Import to GREMLIN BETA - features includes ability to upload PDB and latest P(contact) calculation based on eLife 2015 fitting to PDB data.
GREMLIN results overlayed on top 10 PDB hits:
Legend: Blue filled circles are GREMLIN results (Scaled Score > 1). The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on 10 HHsearch results which uses the overall probability and per-position alignment confidence. Inter oligomeric contacts in the pdb are in shades of red.
| PDB | M | Cov | P(%) | HHΔ | |
| 2kseA | 1 | 0.32 | 98.2 | 0.543 | Contact Map |
| 3e4oA | 2 | 0.69 | 78.8 | 0.783 | Contact Map |
| 4i5sA | 2 | 0.8 | 50.1 | 0.821 | Contact Map |
| 3cwfA | 2 | 0.69 | 48.9 | 0.822 | Contact Map |
| 4u65A | 4 | 0.8 | 28.4 | 0.844 | Contact Map |
| 4onxA | 6 | 0.72 | 21.1 | 0.854 | Contact Map |
| 2wadA | 3 | 0.33 | 16.2 | 0.861 | Contact Map |
| 3pjvD | 2 | 0.76 | 16 | 0.861 | Contact Map |
| 4p02B | 1 | 0.32 | 13.2 | 0.867 | Contact Map |
| 4twkA | 2 | 0.88 | 12.2 | 0.868 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)