| 2iqy |
| ID: | 1453737313 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 190 (170) | ||
| Sequences: | 1085 (853.2) | ||
| Seq/Len: | 6.382 | ||
| Nf(neff/√len): | 65.4 |
HHblits Results: (2015_06)
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: 6.382).
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 |
| 88_H | 107_S | 3.395 | 1.00 |
| 73_D | 121_H | 3.072 | 1.00 |
| 153_K | 156_S | 2.989 | 1.00 |
| 112_S | 172_F | 2.884 | 1.00 |
| 70_V | 154_V | 2.843 | 1.00 |
| 32_Y | 125_W | 2.677 | 1.00 |
| 56_I | 69_L | 2.675 | 1.00 |
| 44_L | 49_V | 2.659 | 1.00 |
| 118_T | 121_H | 2.503 | 1.00 |
| 65_K | 129_E | 2.341 | 1.00 |
| 46_P | 174_A | 2.112 | 1.00 |
| 94_N | 130_Q | 2.065 | 1.00 |
| 43_V | 175_E | 1.979 | 1.00 |
| 89_H | 123_Y | 1.882 | 1.00 |
| 70_V | 91_L | 1.878 | 1.00 |
| 28_L | 127_V | 1.857 | 1.00 |
| 76_A | 115_P | 1.846 | 1.00 |
| 75_D | 122_R | 1.815 | 1.00 |
| 182_K | 185_D | 1.814 | 1.00 |
| 74_P | 124_V | 1.775 | 1.00 |
| 49_V | 112_S | 1.723 | 1.00 |
| 152_F | 157_F | 1.692 | 1.00 |
| 96_K | 102_S | 1.653 | 1.00 |
| 66_L | 94_N | 1.649 | 1.00 |
| 73_D | 123_Y | 1.632 | 1.00 |
| 71_L | 109_Y | 1.572 | 0.99 |
| 90_F | 105_V | 1.542 | 0.99 |
| 71_L | 125_W | 1.520 | 0.99 |
| 78_S | 85_R | 1.514 | 0.99 |
| 72_T | 86_E | 1.508 | 0.99 |
| 90_F | 109_Y | 1.488 | 0.99 |
| 93_V | 136_C | 1.487 | 0.99 |
| 90_F | 125_W | 1.453 | 0.99 |
| 69_L | 95_M | 1.431 | 0.99 |
| 69_L | 127_V | 1.413 | 0.99 |
| 94_N | 97_G | 1.407 | 0.99 |
| 73_D | 76_A | 1.387 | 0.98 |
| 32_Y | 109_Y | 1.386 | 0.98 |
| 120_L | 175_E | 1.378 | 0.98 |
| 92_V | 95_M | 1.367 | 0.98 |
| 33_G | 51_N | 1.356 | 0.98 |
| 78_S | 81_D | 1.342 | 0.98 |
| 132_Q | 135_N | 1.336 | 0.98 |
| 86_E | 153_K | 1.310 | 0.97 |
| 29_R | 57_S | 1.249 | 0.96 |
| 86_E | 154_V | 1.225 | 0.96 |
| 88_H | 91_L | 1.213 | 0.95 |
| 92_V | 105_V | 1.209 | 0.95 |
| 156_S | 159_K | 1.206 | 0.95 |
| 88_H | 152_F | 1.204 | 0.95 |
| 66_L | 96_K | 1.197 | 0.95 |
| 137_D | 160_K | 1.184 | 0.94 |
| 66_L | 130_Q | 1.180 | 0.94 |
| 39_E | 42_K | 1.166 | 0.94 |
| 76_A | 87_W | 1.165 | 0.94 |
| 45_T | 48_Q | 1.161 | 0.94 |
| 96_K | 103_G | 1.159 | 0.94 |
| 71_L | 90_F | 1.141 | 0.93 |
| 121_H | 149_R | 1.139 | 0.93 |
| 58_W | 127_V | 1.137 | 0.93 |
| 87_W | 150_G | 1.129 | 0.92 |
| 123_Y | 174_A | 1.111 | 0.92 |
| 94_N | 104_T | 1.106 | 0.91 |
| 177_D | 180_V | 1.102 | 0.91 |
| 158_R | 163_L | 1.102 | 0.91 |
| 182_K | 186_Q | 1.073 | 0.90 |
| 91_L | 106_L | 1.058 | 0.89 |
| 30_V | 125_W | 1.049 | 0.88 |
| 28_L | 168_A | 1.033 | 0.87 |
| 134_L | 137_D | 1.028 | 0.87 |
| 82_P | 85_R | 1.020 | 0.86 |
| 58_W | 97_G | 1.008 | 0.85 |
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 | |
| 2iqyA | 1 | 1 | 100 | 0.151 | Contact Map |
| 3j7y6 | 1 | 0.9421 | 100 | 0.241 | Contact Map |
| 2jyzA | 1 | 0.9211 | 100 | 0.247 | Contact Map |
| 1vw41 | 1 | 0.9737 | 100 | 0.251 | Contact Map |
| 1wkoA | 2 | 0.8526 | 100 | 0.315 | Contact Map |
| 3axyA | 4 | 0.8526 | 100 | 0.317 | Contact Map |
| 1wpxB | 1 | 0.9105 | 100 | 0.321 | Contact Map |
| 2gzqA | 1 | 0.9211 | 100 | 0.34 | Contact Map |
| 4begA | 2 | 0.7737 | 99.8 | 0.621 | Contact Map |
| 1fuxA | 2 | 0.7053 | 99.8 | 0.63 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)