| BubR1 -force run 1-200 |
| ID: | 1408540805 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 200 (189) | ||
| Sequences: | 277 (193.4) | ||
| Seq/Len: | 1.466 | ||
| Nf(neff/√len): | 14.1 |
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: 1.466).
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 |
| 156_I | 188_R | 2.488 | 1.00 |
| 163_E | 199_R | 2.136 | 0.99 |
| 63_E | 104_R | 2.095 | 0.99 |
| 76_D | 80_R | 2.057 | 0.98 |
| 177_E | 181_Q | 2.054 | 0.98 |
| 159_A | 196_F | 2.020 | 0.98 |
| 196_F | 199_R | 1.827 | 0.96 |
| 82_I | 124_L | 1.816 | 0.96 |
| 172_D | 193_H | 1.711 | 0.93 |
| 105_A | 124_L | 1.680 | 0.93 |
| 119_P | 151_L | 1.662 | 0.92 |
| 86_E | 127_K | 1.603 | 0.90 |
| 22_W | 29_V | 1.549 | 0.88 |
| 192_Q | 195_Q | 1.543 | 0.88 |
| 63_E | 81_Y | 1.536 | 0.87 |
| 121_F | 125_W | 1.534 | 0.87 |
| 175_F | 196_F | 1.522 | 0.87 |
| 32_L | 36_R | 1.485 | 0.85 |
| 122_L | 142_L | 1.466 | 0.84 |
| 66_I | 158_W | 1.445 | 0.83 |
| 58_Q | 61_A | 1.434 | 0.82 |
| 65_E | 80_R | 1.434 | 0.82 |
| 178_G | 189_L | 1.433 | 0.82 |
| 85_T | 154_F | 1.405 | 0.80 |
| 111_G | 137_D | 1.404 | 0.80 |
| 30_Q | 95_E | 1.373 | 0.78 |
| 82_I | 105_A | 1.334 | 0.75 |
| 41_L | 72_N | 1.309 | 0.73 |
| 151_L | 178_G | 1.271 | 0.70 |
| 72_N | 75_L | 1.271 | 0.70 |
| 85_T | 101_L | 1.265 | 0.70 |
| 135_P | 163_E | 1.261 | 0.69 |
| 81_Y | 158_W | 1.259 | 0.69 |
| 29_V | 141_Y | 1.255 | 0.69 |
| 72_N | 136_L | 1.250 | 0.68 |
| 81_Y | 117_S | 1.244 | 0.68 |
| 148_G | 196_F | 1.240 | 0.67 |
| 181_Q | 192_Q | 1.237 | 0.67 |
| 29_V | 38_M | 1.236 | 0.67 |
| 54_T | 174_I | 1.233 | 0.67 |
| 61_A | 197_Q | 1.232 | 0.67 |
| 31_P | 92_G | 1.227 | 0.66 |
| 109_L | 121_F | 1.223 | 0.66 |
| 110_Q | 137_D | 1.220 | 0.65 |
| 19_G | 22_W | 1.218 | 0.65 |
| 45_L | 90_P | 1.206 | 0.64 |
| 90_P | 96_S | 1.206 | 0.64 |
| 103_E | 128_L | 1.192 | 0.63 |
| 156_I | 160_E | 1.169 | 0.61 |
| 119_P | 129_G | 1.164 | 0.60 |
| 142_L | 159_A | 1.163 | 0.60 |
| 188_R | 191_S | 1.159 | 0.60 |
| 62_F | 81_Y | 1.146 | 0.58 |
| 25_S | 89_Y | 1.141 | 0.58 |
| 29_V | 45_L | 1.140 | 0.58 |
| 109_L | 159_A | 1.132 | 0.57 |
| 102_L | 106_V | 1.118 | 0.56 |
| 162_Y | 167_N | 1.116 | 0.55 |
| 25_S | 45_L | 1.114 | 0.55 |
| 62_F | 77_V | 1.112 | 0.55 |
| 193_H | 196_F | 1.110 | 0.55 |
| 129_G | 151_L | 1.109 | 0.55 |
| 179_I | 189_L | 1.100 | 0.54 |
| 36_R | 41_L | 1.095 | 0.53 |
| 78_W | 123_N | 1.091 | 0.53 |
| 22_W | 25_S | 1.089 | 0.53 |
| 122_L | 125_W | 1.073 | 0.51 |
| 117_S | 149_V | 1.070 | 0.51 |
| 101_L | 166_E | 1.065 | 0.50 |
| 129_G | 138_M | 1.065 | 0.50 |
| 26_K | 32_L | 1.063 | 0.50 |
| 175_F | 193_H | 1.058 | 0.49 |
| 159_A | 189_L | 1.057 | 0.49 |
| 109_L | 120_R | 1.049 | 0.48 |
| 102_L | 135_P | 1.047 | 0.48 |
| 29_V | 155_Y | 1.044 | 0.48 |
| 27_E | 36_R | 1.043 | 0.48 |
| 70_T | 152_A | 1.043 | 0.48 |
| 40_T | 152_A | 1.043 | 0.48 |
| 72_N | 188_R | 1.040 | 0.48 |
| 19_G | 38_M | 1.038 | 0.47 |
| 33_R | 86_E | 1.036 | 0.47 |
| 92_G | 96_S | 1.035 | 0.47 |
| 117_S | 151_L | 1.024 | 0.46 |
| 124_L | 187_E | 1.024 | 0.46 |
| 22_W | 129_G | 1.023 | 0.46 |
| 73_D | 120_R | 1.018 | 0.45 |
| 48_E | 57_Q | 1.016 | 0.45 |
| 125_W | 156_I | 1.014 | 0.45 |
| 66_I | 117_S | 1.013 | 0.45 |
| 107_E | 138_M | 1.012 | 0.45 |
| 45_L | 96_S | 1.011 | 0.45 |
| 70_T | 128_L | 1.009 | 0.44 |
| 19_G | 37_I | 1.007 | 0.44 |
| 29_V | 42_Q | 1.002 | 0.44 |
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 | |
| 4aezC | 3 | 0.93 | 100 | 0.222 | Contact Map |
| 4a1gA | 4 | 0.735 | 100 | 0.394 | Contact Map |
| 2wviA | 1 | 0.7 | 100 | 0.531 | Contact Map |
| 3eslA | 2 | 0.765 | 100 | 0.572 | Contact Map |
| 4b94A | 4 | 0.63 | 99.9 | 0.713 | Contact Map |
| 4h7yA | 4 | 0.63 | 99.8 | 0.743 | Contact Map |
| 4ggdC | 2 | 0.04 | 98.5 | 0.865 | Contact Map |
| 2ondA | 2 | 0.61 | 96.6 | 0.908 | Contact Map |
| 2ooeA | 1 | 0.905 | 96.2 | 0.911 | Contact Map |
| 2uy1A | 1 | 0.565 | 92.1 | 0.928 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)