| 1B8EA |
| ID: | 1411598976 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 152 (148) | ||
| Sequences: | 1807 (1369.5) | ||
| Seq/Len: | 12.209 | ||
| Nf(neff/√len): | 112.6 |
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: 12.209).
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 |
| 47_K | 55_E | 3.055 | 1.00 |
| 98_D | 101_K | 2.758 | 1.00 |
| 21_S | 24_M | 2.747 | 1.00 |
| 49_T | 53_D | 2.538 | 1.00 |
| 121_C | 136_F | 2.436 | 1.00 |
| 146_H | 149_L | 2.365 | 1.00 |
| 55_E | 70_K | 2.311 | 1.00 |
| 11_D | 14_K | 2.302 | 1.00 |
| 18_T | 45_E | 2.120 | 1.00 |
| 139_A | 143_L | 2.118 | 1.00 |
| 12_I | 54_L | 2.083 | 1.00 |
| 139_A | 142_A | 1.978 | 1.00 |
| 121_C | 128_V | 1.974 | 1.00 |
| 22_L | 123_V | 1.960 | 1.00 |
| 130_D | 134_E | 1.906 | 1.00 |
| 53_D | 74_E | 1.882 | 1.00 |
| 18_T | 43_V | 1.544 | 1.00 |
| 59_Q | 68_Q | 1.535 | 1.00 |
| 136_F | 140_L | 1.526 | 1.00 |
| 59_Q | 66_C | 1.516 | 1.00 |
| 16_A | 48_P | 1.480 | 1.00 |
| 147_I | 150_S | 1.476 | 1.00 |
| 123_V | 128_V | 1.448 | 1.00 |
| 19_W | 124_R | 1.444 | 1.00 |
| 106_C | 145_M | 1.406 | 0.99 |
| 20_Y | 126_P | 1.387 | 0.99 |
| 138_K | 142_A | 1.377 | 0.99 |
| 81_V | 93_L | 1.368 | 0.99 |
| 96_D | 102_Y | 1.349 | 0.99 |
| 130_D | 133_L | 1.340 | 0.99 |
| 44_E | 58_L | 1.331 | 0.99 |
| 5_Q | 8_K | 1.328 | 0.99 |
| 133_L | 137_D | 1.314 | 0.99 |
| 21_S | 120_Q | 1.301 | 0.99 |
| 24_M | 120_Q | 1.300 | 0.99 |
| 128_V | 136_F | 1.299 | 0.99 |
| 53_D | 72_I | 1.288 | 0.99 |
| 58_L | 71_I | 1.269 | 0.99 |
| 15_V | 103_L | 1.254 | 0.99 |
| 134_E | 138_K | 1.248 | 0.99 |
| 14_K | 100_K | 1.245 | 0.98 |
| 119_C | 140_L | 1.243 | 0.98 |
| 102_Y | 132_A | 1.237 | 0.98 |
| 96_D | 135_K | 1.223 | 0.98 |
| 99_Y | 103_L | 1.165 | 0.97 |
| 8_K | 13_Q | 1.163 | 0.97 |
| 136_F | 139_A | 1.150 | 0.97 |
| 119_C | 150_S | 1.137 | 0.97 |
| 15_V | 46_L | 1.137 | 0.97 |
| 10_L | 94_V | 1.131 | 0.97 |
| 21_S | 71_I | 1.123 | 0.97 |
| 131_E | 135_K | 1.114 | 0.96 |
| 80_A | 94_V | 1.111 | 0.96 |
| 94_V | 103_L | 1.100 | 0.96 |
| 47_K | 57_L | 1.096 | 0.96 |
| 61_W | 64_G | 1.089 | 0.96 |
| 26_A | 116_S | 1.086 | 0.96 |
| 16_A | 54_L | 1.081 | 0.95 |
| 132_A | 139_A | 1.062 | 0.95 |
| 129_D | 132_A | 1.062 | 0.95 |
| 104_L | 136_F | 1.043 | 0.94 |
| 141_K | 148_R | 1.042 | 0.94 |
| 137_D | 147_I | 1.042 | 0.94 |
| 5_Q | 9_G | 1.039 | 0.94 |
| 96_D | 136_F | 1.034 | 0.94 |
| 132_A | 135_K | 1.028 | 0.94 |
| 119_C | 145_M | 1.027 | 0.94 |
| 73_A | 84_I | 1.027 | 0.94 |
| 22_L | 128_V | 1.011 | 0.93 |
| 138_K | 141_K | 1.010 | 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 | |
| 3l4rA | 1 | 0.9474 | 100 | 0.095 | Contact Map |
| 4tljA | 2 | 1 | 100 | 0.121 | Contact Map |
| 1exsA | 1 | 0.9934 | 100 | 0.123 | Contact Map |
| 1ew3A | 1 | 0.9671 | 100 | 0.126 | Contact Map |
| 2ra6A | 4 | 0.8947 | 100 | 0.132 | Contact Map |
| 3kffA | 1 | 0.9276 | 100 | 0.138 | Contact Map |
| 1gm6A | 1 | 0.9605 | 100 | 0.139 | Contact Map |
| 3fiqA | 2 | 0.9671 | 100 | 0.143 | Contact Map |
| 2a2uA | 4 | 0.9868 | 100 | 0.146 | Contact Map |
| 3saoA | 2 | 0.9145 | 100 | 0.147 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)