| normal prot |
| ID: | 1417291784 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 213 (176) | ||
| Sequences: | 6439 (4055.4) | ||
| Seq/Len: | 36.585 | ||
| Nf(neff/√len): | 305.7 |
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: 36.585).
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 |
| 16_D | 99_N | 4.542 | 1.00 |
| 94_R | 137_E | 3.518 | 1.00 |
| 89_F | 149_Y | 3.278 | 1.00 |
| 87_L | 100_V | 2.705 | 1.00 |
| 93_N | 96_S | 2.543 | 1.00 |
| 24_L | 160_V | 2.537 | 1.00 |
| 139_E | 143_A | 2.522 | 1.00 |
| 24_L | 88_L | 2.499 | 1.00 |
| 138_A | 142_A | 2.466 | 1.00 |
| 88_L | 123_H | 2.432 | 1.00 |
| 135_R | 139_E | 2.422 | 1.00 |
| 121_V | 163_A | 2.419 | 1.00 |
| 84_G | 167_L | 2.416 | 1.00 |
| 91_I | 125_C | 2.340 | 1.00 |
| 141_L | 145_Y | 2.316 | 1.00 |
| 150_I | 166_D | 2.287 | 1.00 |
| 138_A | 149_Y | 2.140 | 1.00 |
| 131_R | 151_E | 2.119 | 1.00 |
| 13_V | 25_I | 2.006 | 1.00 |
| 89_F | 138_A | 1.938 | 1.00 |
| 27_R | 31_G | 1.903 | 1.00 |
| 91_I | 122_G | 1.897 | 1.00 |
| 27_R | 157_A | 1.874 | 1.00 |
| 140_K | 144_A | 1.839 | 1.00 |
| 9_F | 171_I | 1.836 | 1.00 |
| 123_H | 154_A | 1.800 | 1.00 |
| 104_L | 108_K | 1.784 | 1.00 |
| 54_P | 169_R | 1.771 | 1.00 |
| 84_G | 171_I | 1.750 | 1.00 |
| 125_C | 158_I | 1.726 | 1.00 |
| 101_H | 144_A | 1.718 | 1.00 |
| 170_D | 173_E | 1.704 | 1.00 |
| 159_N | 162_K | 1.686 | 1.00 |
| 120_L | 147_M | 1.661 | 1.00 |
| 119_V | 150_I | 1.611 | 1.00 |
| 100_V | 120_L | 1.601 | 1.00 |
| 94_R | 98_Q | 1.570 | 1.00 |
| 101_H | 141_L | 1.566 | 1.00 |
| 60_L | 168_T | 1.510 | 1.00 |
| 33_F | 155_R | 1.466 | 1.00 |
| 28_F | 48_R | 1.460 | 1.00 |
| 79_Y | 106_E | 1.460 | 1.00 |
| 66_A | 69_E | 1.406 | 0.99 |
| 152_T | 163_A | 1.397 | 0.99 |
| 134_T | 137_E | 1.373 | 0.99 |
| 85_G | 107_T | 1.370 | 0.99 |
| 27_R | 33_F | 1.369 | 0.99 |
| 89_F | 122_G | 1.361 | 0.99 |
| 97_F | 141_L | 1.325 | 0.99 |
| 90_D | 124_K | 1.301 | 0.99 |
| 40_T | 67_G | 1.292 | 0.99 |
| 62_I | 164_F | 1.275 | 0.99 |
| 122_G | 138_A | 1.273 | 0.99 |
| 161_E | 165_T | 1.257 | 0.99 |
| 51_E | 57_R | 1.249 | 0.99 |
| 148_K | 166_D | 1.212 | 0.98 |
| 97_F | 133_V | 1.197 | 0.98 |
| 91_I | 131_R | 1.192 | 0.98 |
| 5_W | 8_Q | 1.184 | 0.98 |
| 104_L | 145_Y | 1.183 | 0.98 |
| 94_R | 132_Q | 1.175 | 0.98 |
| 150_I | 159_N | 1.173 | 0.98 |
| 12_I | 82_S | 1.161 | 0.97 |
| 118_F | 147_M | 1.149 | 0.97 |
| 10_R | 81_N | 1.146 | 0.97 |
| 51_E | 55_G | 1.144 | 0.97 |
| 86_L | 121_V | 1.119 | 0.96 |
| 90_D | 93_N | 1.117 | 0.96 |
| 121_V | 150_I | 1.115 | 0.96 |
| 26_R | 30_E | 1.114 | 0.96 |
| 16_D | 103_W | 1.112 | 0.96 |
| 108_K | 118_F | 1.109 | 0.96 |
| 15_G | 21_K | 1.101 | 0.96 |
| 166_D | 169_R | 1.100 | 0.96 |
| 119_V | 163_A | 1.097 | 0.96 |
| 64_D | 67_G | 1.095 | 0.96 |
| 15_G | 20_G | 1.093 | 0.96 |
| 30_E | 46_F | 1.093 | 0.96 |
| 104_L | 118_F | 1.084 | 0.96 |
| 105_E | 109_V | 1.080 | 0.95 |
| 128_D | 131_R | 1.079 | 0.95 |
| 28_F | 164_F | 1.074 | 0.95 |
| 84_G | 163_A | 1.057 | 0.95 |
| 35_Q | 155_R | 1.047 | 0.94 |
| 100_V | 141_L | 1.031 | 0.94 |
| 8_Q | 61_Q | 1.030 | 0.94 |
| 65_T | 69_E | 1.020 | 0.93 |
| 11_L | 84_G | 1.011 | 0.93 |
| 31_G | 48_R | 1.004 | 0.93 |
| 135_R | 151_E | 1.003 | 0.93 |
| 166_D | 170_D | 1.003 | 0.93 |
| 87_L | 104_L | 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 | |
| 3cpjB | 1 | 0.77 | 100 | 0.348 | Contact Map |
| 4dkxA | 2 | 0.7324 | 100 | 0.367 | Contact Map |
| 3dz8A | 1 | 0.8122 | 100 | 0.37 | Contact Map |
| 2bcgY | 1 | 0.9108 | 100 | 0.37 | Contact Map |
| 2bmeA | 4 | 0.8263 | 100 | 0.371 | Contact Map |
| 2g3yA | 1 | 0.784 | 100 | 0.375 | Contact Map |
| 4lhwA | 5 | 0.8169 | 100 | 0.376 | Contact Map |
| 2a5jA | 1 | 0.8122 | 100 | 0.379 | Contact Map |
| 1zbdA | 1 | 0.831 | 100 | 0.38 | Contact Map |
| 3tklA | 1 | 0.8028 | 100 | 0.384 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)