| 2opi |
| ID: | 1458975527 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 203 (195) | ||
| Sequences: | 5159 (2994.7) | ||
| Seq/Len: | 26.456 | ||
| Nf(neff/√len): | 214.5 |
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: 26.456).
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 |
| 59_N | 64_T | 4.935 | 1.00 |
| 182_R | 186_Q | 3.005 | 1.00 |
| 98_Y | 186_Q | 2.968 | 1.00 |
| 165_K | 169_Q | 2.855 | 1.00 |
| 9_L | 168_D | 2.459 | 1.00 |
| 38_A | 79_L | 2.453 | 1.00 |
| 39_L | 55_V | 2.377 | 1.00 |
| 6_H | 32_W | 2.261 | 1.00 |
| 39_L | 57_I | 2.221 | 1.00 |
| 88_V | 163_C | 2.215 | 1.00 |
| 137_P | 141_K | 2.077 | 1.00 |
| 34_I | 39_L | 2.065 | 1.00 |
| 152_S | 177_F | 2.058 | 1.00 |
| 130_P | 156_T | 1.937 | 1.00 |
| 107_N | 188_G | 1.929 | 1.00 |
| 98_Y | 182_R | 1.902 | 1.00 |
| 80_G | 141_K | 1.885 | 1.00 |
| 90_V | 167_F | 1.854 | 1.00 |
| 195_T | 198_E | 1.821 | 1.00 |
| 4_D | 8_E | 1.809 | 1.00 |
| 51_A | 54_K | 1.804 | 1.00 |
| 80_G | 83_R | 1.774 | 1.00 |
| 92_L | 170_V | 1.730 | 1.00 |
| 101_A | 186_Q | 1.706 | 1.00 |
| 97_E | 182_R | 1.695 | 1.00 |
| 106_K | 156_T | 1.646 | 1.00 |
| 61_A | 64_T | 1.640 | 1.00 |
| 127_P | 150_H | 1.634 | 1.00 |
| 98_Y | 185_V | 1.621 | 1.00 |
| 11_L | 52_K | 1.616 | 1.00 |
| 160_Q | 177_F | 1.613 | 1.00 |
| 89_N | 166_D | 1.605 | 1.00 |
| 8_E | 52_K | 1.596 | 1.00 |
| 166_D | 169_Q | 1.577 | 1.00 |
| 132_Y | 142_A | 1.563 | 1.00 |
| 95_Q | 158_H | 1.502 | 1.00 |
| 58_C | 75_S | 1.486 | 1.00 |
| 8_E | 12_A | 1.477 | 1.00 |
| 32_W | 167_F | 1.472 | 1.00 |
| 20_A | 175_T | 1.470 | 1.00 |
| 164_G | 169_Q | 1.462 | 1.00 |
| 97_E | 101_A | 1.456 | 1.00 |
| 162_V | 174_A | 1.448 | 1.00 |
| 102_I | 188_G | 1.444 | 1.00 |
| 10_F | 30_L | 1.429 | 1.00 |
| 34_I | 57_I | 1.421 | 1.00 |
| 10_F | 55_V | 1.417 | 1.00 |
| 94_F | 174_A | 1.401 | 0.99 |
| 80_G | 84_E | 1.385 | 0.99 |
| 13_Q | 171_Y | 1.381 | 0.99 |
| 61_A | 83_R | 1.368 | 0.99 |
| 98_Y | 178_E | 1.353 | 0.99 |
| 142_A | 145_E | 1.350 | 0.99 |
| 151_N | 173_R | 1.343 | 0.99 |
| 85_R | 88_V | 1.328 | 0.99 |
| 17_Y | 92_L | 1.279 | 0.99 |
| 130_P | 145_E | 1.273 | 0.99 |
| 38_A | 60_I | 1.263 | 0.99 |
| 9_L | 12_A | 1.258 | 0.99 |
| 93_H | 158_H | 1.258 | 0.99 |
| 31_S | 82_L | 1.257 | 0.99 |
| 40_I | 72_S | 1.257 | 0.99 |
| 108_K | 181_C | 1.252 | 0.99 |
| 15_H | 19_D | 1.248 | 0.99 |
| 32_W | 90_V | 1.231 | 0.98 |
| 77_F | 161_V | 1.219 | 0.98 |
| 147_M | 163_C | 1.214 | 0.98 |
| 184_I | 188_G | 1.196 | 0.98 |
| 13_Q | 167_F | 1.195 | 0.98 |
| 82_L | 91_V | 1.195 | 0.98 |
| 5_E | 9_L | 1.191 | 0.98 |
| 196_P | 200_E | 1.187 | 0.98 |
| 100_T | 103_S | 1.185 | 0.98 |
| 178_E | 182_R | 1.182 | 0.98 |
| 45_S | 54_K | 1.182 | 0.98 |
| 79_L | 83_R | 1.180 | 0.98 |
| 99_A | 160_Q | 1.180 | 0.98 |
| 84_E | 148_L | 1.173 | 0.98 |
| 33_R | 89_N | 1.169 | 0.97 |
| 17_Y | 30_L | 1.163 | 0.97 |
| 77_F | 143_V | 1.149 | 0.97 |
| 84_E | 144_V | 1.139 | 0.97 |
| 54_K | 69_V | 1.135 | 0.97 |
| 97_E | 179_M | 1.133 | 0.97 |
| 14_A | 30_L | 1.125 | 0.97 |
| 160_Q | 174_A | 1.107 | 0.96 |
| 42_G | 45_S | 1.105 | 0.96 |
| 11_L | 55_V | 1.084 | 0.96 |
| 109_P | 184_I | 1.076 | 0.95 |
| 122_V | 196_P | 1.076 | 0.95 |
| 16_R | 20_A | 1.070 | 0.95 |
| 31_S | 91_V | 1.057 | 0.95 |
| 143_V | 155_L | 1.054 | 0.95 |
| 38_A | 75_S | 1.045 | 0.94 |
| 81_V | 147_M | 1.020 | 0.93 |
| 85_R | 163_C | 1.018 | 0.93 |
| 94_F | 160_Q | 1.007 | 0.93 |
| 155_L | 161_V | 1.001 | 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 | |
| 2opiA | 2 | 0.9606 | 100 | 0.086 | Contact Map |
| 4c24A | 1 | 0.9803 | 100 | 0.092 | Contact Map |
| 1e4cP | 1 | 0.9754 | 100 | 0.093 | Contact Map |
| 3ocrA | 2 | 0.9754 | 100 | 0.119 | Contact Map |
| 2v9lA | 1 | 0.9951 | 100 | 0.135 | Contact Map |
| 4m6rA | 4 | 0.9655 | 100 | 0.148 | Contact Map |
| 4xxfA | 1 | 0.9409 | 100 | 0.153 | Contact Map |
| 2fk5A | 2 | 0.9113 | 100 | 0.153 | Contact Map |
| 1pvtA | 1 | 0.9458 | 100 | 0.157 | Contact Map |
| 2z7bA | 1 | 0.9655 | 100 | 0.157 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)