| mpv17 |
| ID: | 1404227586 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 176 (173) | ||
| Sequences: | 1068 (817.5) | ||
| Seq/Len: | 6.173 | ||
| Nf(neff/√len): | 62.2 |
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: 6.173).
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 |
| 31_D | 50_R | 3.007 | 1.00 |
| 141_V | 157_V | 2.278 | 1.00 |
| 19_Q | 67_G | 2.265 | 1.00 |
| 49_G | 53_T | 2.246 | 1.00 |
| 122_K | 126_D | 2.238 | 1.00 |
| 137_L | 161_V | 2.178 | 1.00 |
| 105_L | 130_A | 2.068 | 1.00 |
| 142_Q | 145_N | 2.067 | 1.00 |
| 106_P | 123_L | 2.022 | 1.00 |
| 131_L | 135_Y | 2.018 | 1.00 |
| 33_I | 163_V | 2.008 | 1.00 |
| 74_D | 154_R | 1.981 | 1.00 |
| 6_A | 10_A | 1.946 | 1.00 |
| 156_A | 159_Q | 1.921 | 1.00 |
| 74_D | 88_K | 1.883 | 1.00 |
| 102_G | 127_Y | 1.775 | 1.00 |
| 28_G | 55_V | 1.764 | 1.00 |
| 46_H | 51_T | 1.731 | 1.00 |
| 127_Y | 131_L | 1.680 | 1.00 |
| 31_D | 35_Q | 1.678 | 1.00 |
| 128_P | 132_I | 1.667 | 1.00 |
| 31_D | 51_T | 1.643 | 1.00 |
| 141_V | 161_V | 1.621 | 1.00 |
| 74_D | 151_L | 1.605 | 1.00 |
| 130_A | 172_K | 1.592 | 0.99 |
| 58_G | 63_G | 1.571 | 0.99 |
| 97_A | 134_N | 1.540 | 0.99 |
| 109_G | 119_N | 1.507 | 0.99 |
| 132_I | 136_Y | 1.501 | 0.99 |
| 20_V | 63_G | 1.479 | 0.99 |
| 94_G | 98_P | 1.434 | 0.99 |
| 11_L | 19_Q | 1.420 | 0.99 |
| 93_Q | 135_Y | 1.401 | 0.98 |
| 72_V | 76_F | 1.381 | 0.98 |
| 137_L | 164_I | 1.366 | 0.98 |
| 7_Y | 22_T | 1.352 | 0.98 |
| 120_W | 124_Q | 1.331 | 0.97 |
| 14_H | 17_K | 1.329 | 0.97 |
| 53_T | 112_N | 1.323 | 0.97 |
| 160_C | 164_I | 1.307 | 0.97 |
| 15_P | 19_Q | 1.306 | 0.97 |
| 128_P | 135_Y | 1.295 | 0.97 |
| 102_G | 123_L | 1.277 | 0.97 |
| 32_I | 46_H | 1.271 | 0.96 |
| 7_Y | 15_P | 1.265 | 0.96 |
| 115_S | 118_D | 1.263 | 0.96 |
| 33_I | 167_S | 1.247 | 0.96 |
| 7_Y | 11_L | 1.239 | 0.96 |
| 70_Y | 74_D | 1.213 | 0.95 |
| 121_A | 125_R | 1.196 | 0.95 |
| 93_Q | 139_P | 1.192 | 0.94 |
| 59_C | 63_G | 1.190 | 0.94 |
| 149_V | 157_V | 1.184 | 0.94 |
| 27_M | 166_N | 1.183 | 0.94 |
| 165_W | 168_Y | 1.160 | 0.93 |
| 30_G | 163_V | 1.158 | 0.93 |
| 27_M | 62_V | 1.138 | 0.92 |
| 110_A | 121_A | 1.123 | 0.92 |
| 62_V | 66_V | 1.119 | 0.92 |
| 53_T | 111_L | 1.119 | 0.92 |
| 142_Q | 158_V | 1.116 | 0.91 |
| 20_V | 59_C | 1.108 | 0.91 |
| 50_R | 170_S | 1.108 | 0.91 |
| 35_Q | 165_W | 1.098 | 0.90 |
| 10_A | 17_K | 1.083 | 0.90 |
| 19_Q | 22_T | 1.083 | 0.90 |
| 83_V | 87_K | 1.081 | 0.90 |
| 57_L | 107_L | 1.078 | 0.89 |
| 88_K | 134_N | 1.070 | 0.89 |
| 65_V | 96_F | 1.058 | 0.88 |
| 133_T | 136_Y | 1.053 | 0.88 |
| 136_Y | 168_Y | 1.053 | 0.88 |
| 28_G | 51_T | 1.049 | 0.88 |
| 97_A | 135_Y | 1.049 | 0.88 |
| 16_W | 19_Q | 1.049 | 0.88 |
| 155_L | 159_Q | 1.047 | 0.87 |
| 48_R | 52_L | 1.046 | 0.87 |
| 53_T | 108_V | 1.041 | 0.87 |
| 63_G | 70_Y | 1.038 | 0.87 |
| 29_L | 163_V | 1.033 | 0.87 |
| 145_N | 149_V | 1.026 | 0.86 |
| 10_A | 14_H | 1.024 | 0.86 |
| 7_Y | 18_V | 1.024 | 0.86 |
| 117_Q | 120_W | 1.022 | 0.86 |
| 119_N | 123_L | 1.021 | 0.86 |
| 133_T | 137_L | 1.006 | 0.85 |
| 36_Q | 46_H | 1.005 | 0.84 |
| 34_S | 50_R | 1.004 | 0.84 |
| 17_K | 20_V | 1.001 | 0.84 |
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 | |
| 4bduA | 4 | 0.358 | 4.2 | 0.955 | Contact Map |
| 2lonA | 1 | 0.4659 | 3.8 | 0.956 | Contact Map |
| 2lomA | 1 | 0.4375 | 3.4 | 0.957 | Contact Map |
| 2ksdA | 1 | 0.4261 | 3 | 0.958 | Contact Map |
| 4g1uA | 2 | 0.3523 | 2.6 | 0.96 | Contact Map |
| 4lz6A | 1 | 0.9602 | 2.4 | 0.96 | Contact Map |
| 2qi9A | 2 | 0.3636 | 2.3 | 0.961 | Contact Map |
| 3w4tA | 1 | 0.9148 | 2.1 | 0.961 | Contact Map |
| 1nkzA | 3 | 0.2727 | 2 | 0.962 | Contact Map |
| 3l09A | 4 | 0.2784 | 1.7 | 0.963 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)