| Perlucin |
| ID: | 1411945864 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 155 (132) | ||
| Sequences: | 3897 (3023) | ||
| Seq/Len: | 29.523 | ||
| Nf(neff/√len): | 263.1 |
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: 29.523).
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 |
| 102_C | 119_C | 4.543 | 1.00 |
| 27_A | 36_H | 3.537 | 1.00 |
| 66_A | 103_L | 3.515 | 1.00 |
| 29_Y | 125_F | 3.164 | 1.00 |
| 2_C | 13_C | 2.766 | 1.00 |
| 104_E | 115_N | 2.407 | 1.00 |
| 12_S | 128_E | 2.383 | 1.00 |
| 66_A | 77_W | 2.326 | 1.00 |
| 23_F | 78_E | 2.237 | 1.00 |
| 46_D | 114_W | 2.186 | 1.00 |
| 9_N | 48_F | 2.131 | 1.00 |
| 100_E | 115_N | 2.092 | 1.00 |
| 43_K | 47_S | 2.057 | 1.00 |
| 21_S | 25_E | 1.955 | 1.00 |
| 104_E | 123_S | 1.939 | 1.00 |
| 68_D | 72_E | 1.870 | 1.00 |
| 22_S | 25_E | 1.804 | 1.00 |
| 45_E | 128_E | 1.757 | 1.00 |
| 75_W | 103_L | 1.620 | 1.00 |
| 3_P | 129_K | 1.555 | 1.00 |
| 6_F | 33_L | 1.505 | 1.00 |
| 40_I | 46_D | 1.482 | 1.00 |
| 42_N | 45_E | 1.451 | 1.00 |
| 39_I | 78_E | 1.451 | 1.00 |
| 38_A | 49_I | 1.409 | 1.00 |
| 29_Y | 33_L | 1.406 | 0.99 |
| 15_W | 33_L | 1.398 | 0.99 |
| 38_A | 64_L | 1.394 | 0.99 |
| 16_F | 62_Y | 1.378 | 0.99 |
| 72_E | 101_H | 1.368 | 0.99 |
| 6_F | 129_K | 1.366 | 0.99 |
| 66_A | 83_M | 1.365 | 0.99 |
| 92_Q | 100_E | 1.337 | 0.99 |
| 14_Y | 38_A | 1.336 | 0.99 |
| 17_S | 125_F | 1.336 | 0.99 |
| 41_S | 128_E | 1.330 | 0.99 |
| 14_Y | 45_E | 1.319 | 0.99 |
| 27_A | 31_R | 1.317 | 0.99 |
| 85_Y | 114_W | 1.316 | 0.99 |
| 21_S | 125_F | 1.300 | 0.99 |
| 93_P | 116_D | 1.297 | 0.99 |
| 68_D | 73_G | 1.296 | 0.99 |
| 7_H | 52_Y | 1.286 | 0.99 |
| 104_E | 117_Y | 1.271 | 0.99 |
| 21_S | 29_Y | 1.257 | 0.99 |
| 31_R | 36_H | 1.255 | 0.99 |
| 37_L | 125_F | 1.252 | 0.99 |
| 68_D | 75_W | 1.248 | 0.99 |
| 25_E | 28_G | 1.244 | 0.98 |
| 94_D | 116_D | 1.233 | 0.98 |
| 6_F | 35_S | 1.214 | 0.98 |
| 23_F | 67_S | 1.209 | 0.98 |
| 14_Y | 128_E | 1.203 | 0.98 |
| 46_D | 87_N | 1.197 | 0.98 |
| 63_W | 117_Y | 1.194 | 0.98 |
| 100_E | 116_D | 1.193 | 0.98 |
| 117_Y | 123_S | 1.191 | 0.98 |
| 68_D | 101_H | 1.191 | 0.98 |
| 26_A | 125_F | 1.184 | 0.98 |
| 39_I | 128_E | 1.171 | 0.98 |
| 64_L | 114_W | 1.137 | 0.97 |
| 40_I | 49_I | 1.133 | 0.97 |
| 88_W | 93_P | 1.111 | 0.96 |
| 95_N | 116_D | 1.083 | 0.96 |
| 9_N | 44_D | 1.067 | 0.95 |
| 87_N | 114_W | 1.064 | 0.95 |
| 12_S | 45_E | 1.057 | 0.95 |
| 75_W | 116_D | 1.049 | 0.94 |
| 83_M | 86_T | 1.044 | 0.94 |
| 94_D | 100_E | 1.043 | 0.94 |
| 89_S | 113_L | 1.031 | 0.94 |
| 41_S | 79_G | 1.026 | 0.94 |
| 36_H | 39_I | 1.015 | 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 | |
| 3aluA | 4 | 0.8774 | 100 | 0.253 | Contact Map |
| 1eggA | 2 | 0.871 | 100 | 0.255 | Contact Map |
| 2py2A | 6 | 0.8194 | 100 | 0.256 | Contact Map |
| 3kqgA | 6 | 0.8387 | 100 | 0.258 | Contact Map |
| 2ls8A | 1 | 0.8968 | 100 | 0.258 | Contact Map |
| 1jznA | 5 | 0.8387 | 100 | 0.263 | Contact Map |
| 1wmzA | 4 | 0.8452 | 100 | 0.266 | Contact Map |
| 2kv3A | 1 | 0.8258 | 100 | 0.27 | Contact Map |
| 1htnA | 1 | 0.8323 | 100 | 0.27 | Contact Map |
| 4mthA | 1 | 0.8387 | 100 | 0.27 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)