| Kristian Davidsen |
| ID: | 1500490834 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 119 (118) | ||
| Sequences: | 5114 (2738.2) | ||
| Seq/Len: | 43.339 | ||
| Nf(neff/√len): | 252.1 |
HHblits Results: (2016_02)
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: 43.339).
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 |
| 110_G | 113_T | 2.606 | 1.00 |
| 12_V | 86_L | 2.340 | 1.00 |
| 12_V | 16_G | 2.317 | 1.00 |
| 48_V | 68_F | 2.190 | 1.00 |
| 68_F | 83_M | 2.126 | 1.00 |
| 62_D | 65_K | 2.105 | 1.00 |
| 13_K | 16_G | 2.089 | 1.00 |
| 38_R | 92_A | 2.050 | 1.00 |
| 109_W | 112_G | 1.927 | 1.00 |
| 36_W | 81_L | 1.767 | 1.00 |
| 19_R | 80_Y | 1.744 | 1.00 |
| 112_G | 115_V | 1.735 | 1.00 |
| 49_T | 70_I | 1.606 | 1.00 |
| 24_A | 34_M | 1.594 | 1.00 |
| 39_Q | 45_L | 1.558 | 1.00 |
| 50_Y | 59_Y | 1.557 | 1.00 |
| 113_T | 117_V | 1.528 | 1.00 |
| 7_S | 10_G | 1.491 | 1.00 |
| 37_I | 47_W | 1.463 | 1.00 |
| 38_R | 46_E | 1.457 | 1.00 |
| 35_N | 47_W | 1.448 | 1.00 |
| 109_W | 115_V | 1.441 | 1.00 |
| 10_G | 18_L | 1.424 | 1.00 |
| 108_V | 111_Q | 1.391 | 0.99 |
| 34_M | 79_L | 1.381 | 0.99 |
| 33_Y | 50_Y | 1.363 | 0.99 |
| 105_G | 111_Q | 1.335 | 0.99 |
| 90_D | 94_Y | 1.329 | 0.99 |
| 19_R | 82_Q | 1.309 | 0.99 |
| 33_Y | 52_S | 1.303 | 0.99 |
| 105_G | 108_V | 1.272 | 0.99 |
| 23_A | 78_S | 1.248 | 0.99 |
| 24_A | 29_F | 1.205 | 0.98 |
| 106_M | 109_W | 1.200 | 0.98 |
| 112_G | 117_V | 1.192 | 0.98 |
| 15_G | 19_R | 1.191 | 0.98 |
| 107_D | 116_T | 1.188 | 0.98 |
| 110_G | 115_V | 1.176 | 0.98 |
| 109_W | 113_T | 1.176 | 0.98 |
| 107_D | 114_T | 1.166 | 0.97 |
| 35_N | 97_A | 1.157 | 0.97 |
| 5_V | 8_G | 1.147 | 0.97 |
| 18_L | 115_V | 1.146 | 0.97 |
| 106_M | 114_T | 1.144 | 0.97 |
| 110_G | 114_T | 1.139 | 0.97 |
| 67_R | 83_M | 1.125 | 0.97 |
| 1_Q | 5_V | 1.125 | 0.97 |
| 109_W | 114_T | 1.116 | 0.96 |
| 42_G | 45_L | 1.098 | 0.96 |
| 114_T | 117_V | 1.094 | 0.96 |
| 94_Y | 97_A | 1.086 | 0.96 |
| 12_V | 18_L | 1.078 | 0.95 |
| 105_G | 114_T | 1.077 | 0.95 |
| 5_V | 9_G | 1.067 | 0.95 |
| 6_E | 9_G | 1.067 | 0.95 |
| 108_V | 114_T | 1.062 | 0.95 |
| 51_I | 79_L | 1.061 | 0.95 |
| 114_T | 118_S | 1.050 | 0.94 |
| 108_V | 116_T | 1.043 | 0.94 |
| 48_V | 64_V | 1.032 | 0.94 |
| 109_W | 118_S | 1.031 | 0.94 |
| 106_M | 115_V | 1.023 | 0.93 |
| 50_Y | 57_T | 1.006 | 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 | |
| 4ut7H | 1 | 0.9916 | 99.9 | 0.164 | Contact Map |
| 4pfeA | 2 | 0 | 99.9 | 0.166 | Contact Map |
| 4qgyA | 2 | 1 | 99.8 | 0.195 | Contact Map |
| 4i13B | 1 | 1 | 99.8 | 0.214 | Contact Map |
| 1yc8A | 2 | 0.9832 | 99.8 | 0.221 | Contact Map |
| 1dqtA | 4 | 0.9496 | 99.8 | 0.222 | Contact Map |
| 3k3qA | 1 | 1 | 99.8 | 0.223 | Contact Map |
| 3j697 | 1 | 1 | 99.8 | 0.223 | Contact Map |
| 3g9aB | 1 | 0.9748 | 99.8 | 0.224 | Contact Map |
| 1zvyA | 1 | 0.9832 | 99.8 | 0.228 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)