| OsmY |
| ID: | 1417800103 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 201 (188) | ||
| Sequences: | 707 (527.1) | ||
| Seq/Len: | 3.761 | ||
| Nf(neff/√len): | 38.4 |
Jackhmmer Results: (2014_04_16)
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: 3.761).
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 |
| 139_T | 161_T | 4.671 | 1.00 |
| 63_V | 106_A | 3.541 | 1.00 |
| 81_K | 90_S | 2.941 | 1.00 |
| 93_V | 119_L | 2.432 | 1.00 |
| 60_T | 82_T | 2.335 | 1.00 |
| 182_E | 186_K | 2.106 | 1.00 |
| 138_T | 161_T | 2.098 | 1.00 |
| 172_V | 198_L | 2.059 | 1.00 |
| 51_G | 55_D | 1.975 | 1.00 |
| 157_V | 172_V | 1.939 | 1.00 |
| 120_H | 167_Q | 1.902 | 1.00 |
| 147_L | 154_S | 1.824 | 0.99 |
| 106_A | 109_V | 1.823 | 0.99 |
| 137_A | 141_E | 1.822 | 0.99 |
| 120_H | 165_V | 1.745 | 0.99 |
| 178_S | 182_E | 1.739 | 0.99 |
| 182_E | 196_N | 1.734 | 0.99 |
| 145_K | 188_V | 1.712 | 0.99 |
| 175_Q | 179_D | 1.693 | 0.99 |
| 77_D | 132_Y | 1.691 | 0.99 |
| 77_D | 127_G | 1.671 | 0.99 |
| 59_I | 87_V | 1.652 | 0.99 |
| 59_I | 82_T | 1.579 | 0.98 |
| 87_V | 112_V | 1.566 | 0.98 |
| 81_K | 158_K | 1.566 | 0.98 |
| 178_S | 198_L | 1.499 | 0.97 |
| 59_I | 112_V | 1.496 | 0.97 |
| 101_E | 104_K | 1.484 | 0.97 |
| 46_S | 53_F | 1.473 | 0.97 |
| 57_S | 60_T | 1.468 | 0.97 |
| 157_V | 181_A | 1.450 | 0.96 |
| 137_A | 140_S | 1.437 | 0.96 |
| 142_I | 185_A | 1.432 | 0.96 |
| 103_V | 117_D | 1.419 | 0.96 |
| 83_D | 169_S | 1.386 | 0.95 |
| 57_S | 82_T | 1.372 | 0.95 |
| 152_V | 180_R | 1.371 | 0.95 |
| 167_Q | 195_K | 1.363 | 0.94 |
| 24_G | 27_Y | 1.345 | 0.94 |
| 77_D | 92_F | 1.333 | 0.94 |
| 70_H | 101_E | 1.329 | 0.93 |
| 185_A | 194_V | 1.327 | 0.93 |
| 149_D | 184_I | 1.326 | 0.93 |
| 88_T | 169_S | 1.323 | 0.93 |
| 85_K | 111_G | 1.320 | 0.93 |
| 78_I | 102_A | 1.305 | 0.93 |
| 18_T | 21_V | 1.288 | 0.92 |
| 63_V | 109_V | 1.279 | 0.92 |
| 67_L | 102_A | 1.263 | 0.91 |
| 165_V | 195_K | 1.246 | 0.90 |
| 103_V | 107_K | 1.234 | 0.90 |
| 30_N | 37_E | 1.223 | 0.89 |
| 149_D | 180_R | 1.222 | 0.89 |
| 134_G | 141_E | 1.221 | 0.89 |
| 92_F | 163_D | 1.221 | 0.89 |
| 99_A | 119_L | 1.217 | 0.89 |
| 55_D | 111_G | 1.208 | 0.88 |
| 89_L | 102_A | 1.179 | 0.87 |
| 17_L | 20_A | 1.178 | 0.86 |
| 183_S | 186_K | 1.177 | 0.86 |
| 127_G | 132_Y | 1.177 | 0.86 |
| 172_V | 178_S | 1.174 | 0.86 |
| 22_A | 25_S | 1.169 | 0.86 |
| 178_S | 196_N | 1.166 | 0.86 |
| 88_T | 167_Q | 1.158 | 0.85 |
| 96_Q | 99_A | 1.153 | 0.85 |
| 92_F | 127_G | 1.152 | 0.85 |
| 121_V | 124_A | 1.148 | 0.84 |
| 142_I | 166_V | 1.138 | 0.84 |
| 86_V | 114_S | 1.137 | 0.84 |
| 152_V | 157_V | 1.126 | 0.83 |
| 41_Q | 44_D | 1.125 | 0.83 |
| 86_V | 116_S | 1.119 | 0.82 |
| 13_L | 16_M | 1.118 | 0.82 |
| 77_D | 162_T | 1.116 | 0.82 |
| 26_A | 29_E | 1.113 | 0.82 |
| 16_M | 20_A | 1.110 | 0.82 |
| 141_E | 189_D | 1.099 | 0.81 |
| 78_I | 94_E | 1.096 | 0.81 |
| 19_S | 121_V | 1.090 | 0.80 |
| 66_A | 69_D | 1.082 | 0.79 |
| 143_K | 159_V | 1.078 | 0.79 |
| 48_N | 83_D | 1.071 | 0.78 |
| 35_T | 39_A | 1.071 | 0.78 |
| 78_I | 89_L | 1.068 | 0.78 |
| 159_V | 168_L | 1.066 | 0.78 |
| 49_K | 55_D | 1.059 | 0.77 |
| 96_Q | 100_E | 1.050 | 0.76 |
| 38_S | 44_D | 1.046 | 0.76 |
| 30_N | 38_S | 1.045 | 0.76 |
| 178_S | 200_T | 1.036 | 0.75 |
| 43_V | 50_V | 1.033 | 0.75 |
| 167_Q | 197_D | 1.032 | 0.75 |
| 90_S | 177_Q | 1.018 | 0.73 |
| 179_D | 196_N | 1.005 | 0.72 |
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 | |
| 2kgsA | 1 | 0.602 | 99.9 | 0.595 | Contact Map |
| 4alzA | 1 | 0.6219 | 99.9 | 0.608 | Contact Map |
| 2l26A | 1 | 0.597 | 99.1 | 0.778 | Contact Map |
| 2z51A | 1 | 0.6915 | 23.2 | 0.946 | Contact Map |
| 3lnoA | 6 | 0.4478 | 22.6 | 0.946 | Contact Map |
| 4fybB | 2 | 0.6617 | 22 | 0.947 | Contact Map |
| 3zbiC | 14 | 0.1393 | 11.7 | 0.953 | Contact Map |
| 3tlkA | 3 | 0.7264 | 11 | 0.953 | Contact Map |
| 4kysA | 2 | 0.6318 | 10.7 | 0.953 | Contact Map |
| 4k3bA | 1 | 0.8109 | 10.6 | 0.954 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)