| scpB |
| ID: | 1498926570 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 221 (176) | ||
| Sequences: | 1905 (1179.8) | ||
| Seq/Len: | 10.824 | ||
| Nf(neff/√len): | 88.9 |
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: 10.824).
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 |
| 133_R | 146_G | 4.744 | 1.00 |
| 10_E | 49_R | 4.722 | 1.00 |
| 10_E | 45_A | 3.139 | 1.00 |
| 15_A | 72_L | 2.861 | 1.00 |
| 12_C | 75_L | 2.597 | 1.00 |
| 11_R | 72_L | 2.379 | 1.00 |
| 49_R | 53_R | 2.373 | 1.00 |
| 10_E | 42_G | 2.205 | 1.00 |
| 59_C | 158_A | 2.177 | 1.00 |
| 109_E | 116_A | 2.068 | 1.00 |
| 57_L | 66_F | 2.029 | 1.00 |
| 135_R | 143_V | 2.021 | 1.00 |
| 9_V | 42_G | 2.007 | 1.00 |
| 158_A | 162_D | 1.955 | 1.00 |
| 87_S | 90_A | 1.938 | 1.00 |
| 46_L | 50_Y | 1.926 | 1.00 |
| 16_L | 24_L | 1.904 | 1.00 |
| 139_P | 142_P | 1.866 | 1.00 |
| 103_V | 107_E | 1.815 | 1.00 |
| 13_I | 42_G | 1.800 | 1.00 |
| 159_T | 162_D | 1.781 | 1.00 |
| 132_M | 143_V | 1.773 | 1.00 |
| 56_E | 69_A | 1.671 | 1.00 |
| 43_I | 57_L | 1.667 | 1.00 |
| 29_L | 39_I | 1.666 | 1.00 |
| 26_D | 39_I | 1.664 | 1.00 |
| 99_Y | 164_P | 1.647 | 1.00 |
| 96_I | 103_V | 1.642 | 1.00 |
| 28_D | 31_K | 1.634 | 1.00 |
| 14_E | 53_R | 1.571 | 1.00 |
| 101_Q | 160_L | 1.548 | 1.00 |
| 125_L | 130_I | 1.542 | 1.00 |
| 22_E | 28_D | 1.536 | 1.00 |
| 128_G | 150_A | 1.517 | 1.00 |
| 48_V | 51_E | 1.503 | 1.00 |
| 65_R | 153_E | 1.502 | 1.00 |
| 44_D | 47_R | 1.492 | 1.00 |
| 93_T | 114_V | 1.489 | 1.00 |
| 96_I | 111_V | 1.488 | 1.00 |
| 17_L | 66_F | 1.487 | 1.00 |
| 42_G | 45_A | 1.480 | 1.00 |
| 59_C | 64_W | 1.469 | 1.00 |
| 98_A | 151_F | 1.444 | 1.00 |
| 101_Q | 147_T | 1.438 | 1.00 |
| 97_V | 130_I | 1.429 | 1.00 |
| 97_V | 121_I | 1.404 | 0.99 |
| 26_D | 40_A | 1.387 | 0.99 |
| 107_E | 136_R | 1.376 | 0.99 |
| 150_A | 153_E | 1.370 | 0.99 |
| 23_P | 63_R | 1.338 | 0.99 |
| 47_R | 57_L | 1.325 | 0.99 |
| 40_A | 59_C | 1.322 | 0.99 |
| 147_T | 152_M | 1.281 | 0.99 |
| 138_T | 142_P | 1.257 | 0.99 |
| 44_D | 48_V | 1.252 | 0.99 |
| 123_V | 127_L | 1.246 | 0.98 |
| 38_D | 41_A | 1.243 | 0.98 |
| 25_S | 28_D | 1.241 | 0.98 |
| 58_A | 67_Q | 1.238 | 0.98 |
| 60_V | 63_R | 1.238 | 0.98 |
| 14_E | 50_Y | 1.235 | 0.98 |
| 15_A | 76_M | 1.206 | 0.98 |
| 41_A | 44_D | 1.190 | 0.98 |
| 33_L | 39_I | 1.189 | 0.98 |
| 165_G | 168_E | 1.179 | 0.98 |
| 59_C | 62_G | 1.174 | 0.98 |
| 26_D | 64_W | 1.170 | 0.97 |
| 134_G | 144_T | 1.164 | 0.97 |
| 65_R | 148_T | 1.157 | 0.97 |
| 137_R | 141_R | 1.151 | 0.97 |
| 5_D | 162_D | 1.111 | 0.96 |
| 6_P | 38_D | 1.110 | 0.96 |
| 52_G | 69_A | 1.097 | 0.96 |
| 56_E | 70_A | 1.067 | 0.95 |
| 16_L | 79_E | 1.064 | 0.95 |
| 134_G | 146_G | 1.055 | 0.95 |
| 131_R | 146_G | 1.053 | 0.95 |
| 21_A | 66_F | 1.042 | 0.94 |
| 30_A | 39_I | 1.038 | 0.94 |
| 147_T | 151_F | 1.025 | 0.93 |
| 69_A | 72_L | 1.023 | 0.93 |
| 17_L | 24_L | 1.020 | 0.93 |
| 100_H | 107_E | 1.018 | 0.93 |
| 13_I | 29_L | 1.015 | 0.93 |
| 35_E | 38_D | 1.000 | 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 | |
| 3w6jB | 4 | 0.7421 | 100 | 0.272 | Contact Map |
| 4i98B | 2 | 0.724 | 100 | 0.292 | Contact Map |
| 2z99A | 1 | 0.7014 | 100 | 0.294 | Contact Map |
| 1t6sA | 2 | 0.7014 | 100 | 0.332 | Contact Map |
| 3w6kB | 4 | 0.3846 | 99.7 | 0.761 | Contact Map |
| 2k4bA | 1 | 0.2805 | 92.3 | 0.929 | Contact Map |
| 1okrA | 2 | 0.4887 | 91.3 | 0.93 | Contact Map |
| 4asnA | 3 | 0.362 | 89.8 | 0.933 | Contact Map |
| 1p6rA | 1 | 0.3439 | 89.7 | 0.933 | Contact Map |
| 1sd4A | 2 | 0.4072 | 89 | 0.934 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)