| GS13232A 40-167 |
| ID: | 1387402449 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 128 (111) | ||
| Sequences: | 1384 (945.9) | ||
| Seq/Len: | 12.468 | ||
| Nf(neff/√len): | 89.8 |
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: 12.468).
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 |
| 34_M | 45_I | 3.667 | 1.00 |
| 12_I | 93_A | 2.862 | 1.00 |
| 85_P | 97_M | 2.601 | 1.00 |
| 13_I | 96_K | 2.584 | 1.00 |
| 81_G | 99_V | 2.434 | 1.00 |
| 11_N | 96_K | 2.350 | 1.00 |
| 109_Q | 115_V | 2.313 | 1.00 |
| 101_F | 118_E | 2.273 | 1.00 |
| 42_I | 53_N | 2.201 | 1.00 |
| 89_V | 95_V | 2.061 | 1.00 |
| 98_I | 118_E | 1.922 | 1.00 |
| 100_P | 103_R | 1.869 | 1.00 |
| 107_N | 116_Y | 1.840 | 1.00 |
| 88_Y | 95_V | 1.828 | 1.00 |
| 21_A | 88_Y | 1.813 | 1.00 |
| 109_Q | 117_Y | 1.769 | 1.00 |
| 14_D | 94_K | 1.764 | 1.00 |
| 35_S | 42_I | 1.758 | 1.00 |
| 114_P | 117_Y | 1.729 | 1.00 |
| 101_F | 116_Y | 1.705 | 1.00 |
| 104_G | 119_I | 1.701 | 1.00 |
| 20_R | 90_G | 1.635 | 1.00 |
| 29_L | 59_A | 1.530 | 1.00 |
| 15_K | 90_G | 1.529 | 1.00 |
| 12_I | 95_V | 1.524 | 1.00 |
| 8_V | 103_R | 1.487 | 1.00 |
| 51_H | 54_G | 1.477 | 1.00 |
| 32_C | 46_E | 1.429 | 1.00 |
| 15_K | 93_A | 1.403 | 0.99 |
| 6_N | 84_E | 1.383 | 0.99 |
| 16_G | 93_A | 1.373 | 0.99 |
| 82_M | 97_M | 1.298 | 0.99 |
| 33_K | 52_S | 1.294 | 0.99 |
| 33_K | 42_I | 1.293 | 0.99 |
| 82_M | 105_A | 1.247 | 0.99 |
| 8_V | 84_E | 1.218 | 0.98 |
| 90_G | 93_A | 1.211 | 0.98 |
| 94_K | 123_I | 1.179 | 0.98 |
| 62_Y | 87_K | 1.153 | 0.97 |
| 10_L | 95_V | 1.144 | 0.97 |
| 10_L | 93_A | 1.144 | 0.97 |
| 12_I | 15_K | 1.130 | 0.97 |
| 67_K | 83_Q | 1.117 | 0.96 |
| 36_Y | 40_S | 1.086 | 0.96 |
| 65_Y | 83_Q | 1.082 | 0.96 |
| 34_M | 82_M | 1.064 | 0.95 |
| 61_T | 77_Y | 1.062 | 0.95 |
| 30_Y | 82_M | 1.029 | 0.94 |
| 105_A | 119_I | 1.004 | 0.93 |
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 | |
| 1fd9A | 1 | 0.8359 | 99.9 | 0.245 | Contact Map |
| 1q6hA | 2 | 0.8359 | 99.9 | 0.246 | Contact Map |
| 3oe2A | 1 | 0.8125 | 99.9 | 0.264 | Contact Map |
| 3uf8A | 1 | 0.8516 | 99.9 | 0.271 | Contact Map |
| 2y78A | 1 | 0.8516 | 99.9 | 0.295 | Contact Map |
| 1jvwA | 1 | 0.8359 | 99.9 | 0.296 | Contact Map |
| 1u79A | 5 | 0.8516 | 99.8 | 0.301 | Contact Map |
| 4bf8A | 1 | 0.8438 | 99.8 | 0.302 | Contact Map |
| 1kt0A | 1 | 0.6562 | 99.8 | 0.311 | Contact Map |
| 2f4eA | 2 | 0.8594 | 99.8 | 0.319 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)