| roko |
| ID: | 1399115759 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 235 (226) | ||
| Sequences: | 29116 (21652.2) | ||
| Seq/Len: | 128.832 | ||
| Nf(neff/√len): | 1440.3 |
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: 128.832).
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 |
| 14_S | 30_V | 3.525 | 1.00 |
| 14_S | 32_A | 2.825 | 1.00 |
| 7_V | 37_A | 2.554 | 1.00 |
| 35_E | 57_K | 2.514 | 1.00 |
| 33_D | 57_K | 2.469 | 1.00 |
| 18_K | 30_V | 2.428 | 1.00 |
| 161_R | 164_E | 2.413 | 1.00 |
| 29_H | 46_P | 2.408 | 1.00 |
| 196_R | 199_D | 2.391 | 1.00 |
| 179_R | 199_D | 2.311 | 1.00 |
| 58_M | 66_Q | 2.285 | 1.00 |
| 84_E | 104_S | 2.212 | 1.00 |
| 18_K | 22_T | 2.199 | 1.00 |
| 162_E | 208_K | 2.148 | 1.00 |
| 87_K | 107_E | 2.120 | 1.00 |
| 34_G | 58_M | 2.115 | 1.00 |
| 20_N | 105_N | 2.091 | 1.00 |
| 38_L | 66_Q | 2.031 | 1.00 |
| 33_D | 36_E | 2.026 | 1.00 |
| 42_D | 70_N | 2.015 | 1.00 |
| 220_V | 230_R | 1.921 | 1.00 |
| 59_D | 62_E | 1.889 | 1.00 |
| 3_K | 27_E | 1.883 | 1.00 |
| 139_D | 152_R | 1.867 | 1.00 |
| 32_A | 36_E | 1.864 | 1.00 |
| 167_H | 171_Q | 1.811 | 1.00 |
| 77_M | 90_G | 1.805 | 1.00 |
| 31_A | 40_K | 1.805 | 1.00 |
| 220_V | 228_Y | 1.794 | 1.00 |
| 201_T | 204_R | 1.739 | 1.00 |
| 3_K | 29_H | 1.731 | 1.00 |
| 21_L | 112_V | 1.715 | 1.00 |
| 51_L | 63_V | 1.697 | 1.00 |
| 136_E | 141_V | 1.687 | 1.00 |
| 64_A | 75_I | 1.685 | 1.00 |
| 76_I | 115_N | 1.684 | 1.00 |
| 48_L | 112_V | 1.680 | 1.00 |
| 54_M | 81_K | 1.660 | 1.00 |
| 5_L | 31_A | 1.651 | 1.00 |
| 142_I | 170_A | 1.609 | 1.00 |
| 148_M | 155_N | 1.607 | 1.00 |
| 64_A | 77_M | 1.606 | 1.00 |
| 53_L | 77_M | 1.586 | 1.00 |
| 96_D | 118_R | 1.567 | 1.00 |
| 172_H | 175_Q | 1.559 | 1.00 |
| 51_L | 64_A | 1.530 | 1.00 |
| 92_E | 113_K | 1.521 | 1.00 |
| 97_D | 111_R | 1.512 | 1.00 |
| 66_Q | 69_K | 1.510 | 1.00 |
| 24_E | 109_V | 1.507 | 1.00 |
| 168_Y | 182_L | 1.504 | 1.00 |
| 81_K | 86_D | 1.502 | 1.00 |
| 141_V | 150_S | 1.491 | 1.00 |
| 77_M | 95_A | 1.482 | 1.00 |
| 68_R | 96_D | 1.481 | 1.00 |
| 49_I | 73_M | 1.465 | 1.00 |
| 168_Y | 185_T | 1.448 | 1.00 |
| 7_V | 55_L | 1.447 | 1.00 |
| 8_D | 14_S | 1.445 | 1.00 |
| 34_G | 63_V | 1.402 | 0.99 |
| 202_V | 206_R | 1.393 | 0.99 |
| 29_H | 40_K | 1.392 | 0.99 |
| 58_M | 62_E | 1.377 | 0.99 |
| 38_L | 63_V | 1.360 | 0.99 |
| 178_T | 181_H | 1.355 | 0.99 |
| 66_Q | 70_N | 1.341 | 0.99 |
| 173_I | 177_M | 1.323 | 0.99 |
| 143_H | 146_A | 1.310 | 0.99 |
| 61_L | 93_L | 1.286 | 0.99 |
| 172_H | 176_V | 1.280 | 0.99 |
| 53_L | 61_L | 1.274 | 0.99 |
| 40_K | 44_V | 1.268 | 0.99 |
| 62_E | 65_R | 1.262 | 0.99 |
| 83_S | 86_D | 1.252 | 0.99 |
| 35_E | 58_M | 1.241 | 0.98 |
| 222_R | 228_Y | 1.236 | 0.98 |
| 41_V | 67_V | 1.200 | 0.98 |
| 147_Y | 225_V | 1.198 | 0.98 |
| 40_K | 43_E | 1.197 | 0.98 |
| 39_Q | 43_E | 1.191 | 0.98 |
| 147_Y | 164_E | 1.183 | 0.98 |
| 48_L | 116_L | 1.179 | 0.98 |
| 26_Y | 113_K | 1.176 | 0.98 |
| 177_M | 185_T | 1.172 | 0.98 |
| 168_Y | 177_M | 1.170 | 0.97 |
| 31_A | 37_A | 1.164 | 0.97 |
| 65_R | 89_L | 1.164 | 0.97 |
| 200_V | 203_R | 1.163 | 0.97 |
| 11_K | 32_A | 1.160 | 0.97 |
| 115_N | 118_R | 1.159 | 0.97 |
| 197_T | 201_T | 1.155 | 0.97 |
| 35_E | 39_Q | 1.153 | 0.97 |
| 38_L | 58_M | 1.150 | 0.97 |
| 29_H | 44_V | 1.138 | 0.97 |
| 36_E | 39_Q | 1.118 | 0.96 |
| 144_P | 167_H | 1.117 | 0.96 |
| 4_I | 26_Y | 1.115 | 0.96 |
| 161_R | 187_W | 1.110 | 0.96 |
| 54_M | 80_A | 1.105 | 0.96 |
| 159_T | 208_K | 1.104 | 0.96 |
| 175_Q | 181_H | 1.093 | 0.96 |
| 5_L | 46_P | 1.081 | 0.95 |
| 17_M | 78_V | 1.080 | 0.95 |
| 186_V | 191_Y | 1.076 | 0.95 |
| 84_E | 88_V | 1.076 | 0.95 |
| 180_E | 195_V | 1.076 | 0.95 |
| 37_A | 41_V | 1.076 | 0.95 |
| 9_D | 52_D | 1.070 | 0.95 |
| 5_L | 37_A | 1.065 | 0.95 |
| 85_L | 89_L | 1.063 | 0.95 |
| 7_V | 49_I | 1.061 | 0.95 |
| 137_I | 229_L | 1.059 | 0.95 |
| 24_E | 113_K | 1.058 | 0.95 |
| 196_R | 200_V | 1.051 | 0.94 |
| 145_E | 175_Q | 1.050 | 0.94 |
| 142_I | 163_F | 1.050 | 0.94 |
| 61_L | 89_L | 1.049 | 0.94 |
| 6_V | 28_V | 1.032 | 0.94 |
| 40_K | 46_P | 1.030 | 0.94 |
| 150_S | 155_N | 1.025 | 0.93 |
| 36_E | 40_K | 1.025 | 0.93 |
| 8_D | 55_L | 1.021 | 0.93 |
| 195_V | 199_D | 1.020 | 0.93 |
| 180_E | 184_Q | 1.012 | 0.93 |
| 88_V | 106_R | 1.008 | 0.93 |
| 87_K | 100_T | 1.002 | 0.92 |
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 | |
| 4kfcA | 2 | 0.9532 | 100 | 0.149 | Contact Map |
| 2gwrA | 1 | 0.9447 | 100 | 0.155 | Contact Map |
| 2oqrA | 1 | 0.9617 | 100 | 0.159 | Contact Map |
| 3r0jA | 2 | 0.9319 | 100 | 0.16 | Contact Map |
| 1ys7A | 2 | 0.9574 | 100 | 0.169 | Contact Map |
| 4b09A | 12 | 0.9064 | 100 | 0.184 | Contact Map |
| 1kgsA | 1 | 0.9277 | 100 | 0.19 | Contact Map |
| 1p2fA | 1 | 0.9149 | 100 | 0.205 | Contact Map |
| 2hqrA | 2 | 0.9277 | 100 | 0.215 | Contact Map |
| 3q9sA | 1 | 0.8936 | 100 | 0.231 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)