| MSJ_Rv1401_200 |
| ID: | 1490819926 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 200 (189) | ||
| Sequences: | 1292 (925.1) | ||
| Seq/Len: | 6.836 | ||
| Nf(neff/√len): | 67.3 |
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: 6.836).
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 |
| 37_S | 63_A | 5.661 | 1.00 |
| 67_F | 177_E | 3.952 | 1.00 |
| 61_L | 121_A | 3.166 | 1.00 |
| 126_V | 147_A | 3.100 | 1.00 |
| 30_L | 70_A | 2.510 | 1.00 |
| 57_L | 61_L | 2.268 | 1.00 |
| 145_C | 175_A | 2.245 | 1.00 |
| 36_L | 62_L | 2.208 | 1.00 |
| 153_I | 169_I | 2.194 | 1.00 |
| 65_L | 69_G | 2.116 | 1.00 |
| 139_T | 183_G | 1.987 | 1.00 |
| 8_A | 45_A | 1.975 | 1.00 |
| 152_M | 168_P | 1.957 | 1.00 |
| 43_L | 59_A | 1.941 | 1.00 |
| 39_T | 59_A | 1.932 | 1.00 |
| 172_S | 176_A | 1.779 | 1.00 |
| 62_L | 66_C | 1.736 | 1.00 |
| 8_A | 42_W | 1.730 | 1.00 |
| 44_L | 56_G | 1.708 | 1.00 |
| 64_H | 153_I | 1.646 | 1.00 |
| 118_Y | 150_D | 1.603 | 1.00 |
| 57_L | 158_F | 1.580 | 1.00 |
| 122_L | 143_A | 1.571 | 1.00 |
| 119_I | 122_L | 1.564 | 1.00 |
| 60_F | 118_Y | 1.508 | 0.99 |
| 11_A | 14_L | 1.499 | 0.99 |
| 10_M | 174_A | 1.479 | 0.99 |
| 33_A | 70_A | 1.474 | 0.99 |
| 32_P | 66_C | 1.468 | 0.99 |
| 125_M | 143_A | 1.443 | 0.99 |
| 118_Y | 146_F | 1.432 | 0.99 |
| 169_I | 172_S | 1.426 | 0.99 |
| 29_W | 69_G | 1.411 | 0.99 |
| 15_A | 38_A | 1.410 | 0.99 |
| 36_L | 40_G | 1.374 | 0.98 |
| 72_L | 128_T | 1.374 | 0.98 |
| 122_L | 125_M | 1.372 | 0.98 |
| 56_G | 150_D | 1.340 | 0.98 |
| 126_V | 143_A | 1.337 | 0.98 |
| 40_G | 60_F | 1.326 | 0.98 |
| 148_A | 172_S | 1.307 | 0.98 |
| 10_M | 170_W | 1.298 | 0.98 |
| 146_F | 177_E | 1.295 | 0.97 |
| 40_G | 59_A | 1.295 | 0.97 |
| 60_F | 146_F | 1.285 | 0.97 |
| 60_F | 173_Y | 1.283 | 0.97 |
| 71_L | 125_M | 1.280 | 0.97 |
| 12_V | 38_A | 1.267 | 0.97 |
| 146_F | 150_D | 1.265 | 0.97 |
| 41_D | 118_Y | 1.258 | 0.97 |
| 37_S | 177_E | 1.247 | 0.97 |
| 30_L | 180_I | 1.243 | 0.97 |
| 41_D | 173_Y | 1.241 | 0.97 |
| 64_H | 68_I | 1.225 | 0.96 |
| 6_F | 10_M | 1.225 | 0.96 |
| 44_L | 53_F | 1.224 | 0.96 |
| 60_F | 149_S | 1.215 | 0.96 |
| 60_F | 150_D | 1.202 | 0.96 |
| 118_Y | 173_Y | 1.196 | 0.95 |
| 7_K | 44_L | 1.192 | 0.95 |
| 41_D | 60_F | 1.185 | 0.95 |
| 68_I | 124_A | 1.183 | 0.95 |
| 138_W | 182_A | 1.179 | 0.95 |
| 56_G | 149_S | 1.164 | 0.95 |
| 173_Y | 177_E | 1.160 | 0.94 |
| 43_L | 55_F | 1.156 | 0.94 |
| 142_G | 179_L | 1.150 | 0.94 |
| 53_F | 157_R | 1.149 | 0.94 |
| 7_K | 14_L | 1.135 | 0.93 |
| 37_S | 64_H | 1.131 | 0.93 |
| 123_S | 126_V | 1.130 | 0.93 |
| 44_L | 118_Y | 1.126 | 0.93 |
| 26_E | 183_G | 1.122 | 0.93 |
| 11_A | 177_E | 1.115 | 0.93 |
| 60_F | 64_H | 1.106 | 0.92 |
| 56_G | 118_Y | 1.101 | 0.92 |
| 130_L | 140_A | 1.096 | 0.92 |
| 29_W | 70_A | 1.091 | 0.92 |
| 146_F | 173_Y | 1.067 | 0.90 |
| 64_H | 150_D | 1.058 | 0.90 |
| 178_I | 182_A | 1.056 | 0.90 |
| 149_S | 172_S | 1.056 | 0.90 |
| 167_V | 171_W | 1.047 | 0.89 |
| 4_P | 8_A | 1.047 | 0.89 |
| 53_F | 57_L | 1.044 | 0.89 |
| 12_V | 174_A | 1.029 | 0.88 |
| 57_L | 114_P | 1.028 | 0.88 |
| 44_L | 150_D | 1.028 | 0.88 |
| 111_L | 114_P | 1.022 | 0.88 |
| 181_T | 184_F | 1.004 | 0.86 |
| 37_S | 67_F | 1.001 | 0.86 |
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 | |
| 2n2jA | 2 | 0 | 1.8 | 0.955 | Contact Map |
| 2ksfA | 1 | 0.52 | 1.5 | 0.957 | Contact Map |
| 3wu2M | 2 | 0.13 | 0.6 | 0.967 | Contact Map |
| 2hacA | 2 | 0.165 | 0.5 | 0.968 | Contact Map |
| 3qrxB | 1 | 0.1 | 0.5 | 0.968 | Contact Map |
| 3ux4A | 3 | 0.28 | 0.5 | 0.968 | Contact Map |
| 2nq2A | 2 | 0.365 | 0.5 | 0.969 | Contact Map |
| 2m7cA | 1 | 0.035 | 0.5 | 0.97 | Contact Map |
| 2dyoB | 1 | 0.01 | 0.5 | 0.97 | Contact Map |
| 3j2wE | 4 | 0.23 | 0.4 | 0.97 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)