| BCL-XL_1MAZ |
| ID: | 1457531545 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 143 (142) | ||
| Sequences: | 359 (255.3) | ||
| Seq/Len: | 2.528 | ||
| Nf(neff/√len): | 21.4 |
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: 2.528).
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 |
| 75_N | 120_Y | 1.965 | 0.99 |
| 12_F | 95_G | 1.885 | 0.99 |
| 87_I | 129_I | 1.774 | 0.98 |
| 82_V | 87_I | 1.744 | 0.98 |
| 128_W | 135_W | 1.739 | 0.98 |
| 86_R | 93_F | 1.710 | 0.98 |
| 11_D | 15_Y | 1.695 | 0.98 |
| 67_Y | 119_T | 1.649 | 0.97 |
| 117_M | 121_L | 1.632 | 0.97 |
| 137_T | 141_L | 1.623 | 0.97 |
| 52_F | 89_A | 1.588 | 0.96 |
| 42_D | 78_F | 1.507 | 0.94 |
| 84_W | 134_G | 1.489 | 0.94 |
| 88_V | 97_L | 1.488 | 0.94 |
| 45_E | 95_G | 1.391 | 0.90 |
| 91_F | 95_G | 1.387 | 0.90 |
| 70_F | 116_W | 1.375 | 0.90 |
| 37_L | 134_G | 1.366 | 0.89 |
| 129_I | 133_G | 1.353 | 0.89 |
| 56_T | 100_E | 1.329 | 0.87 |
| 14_S | 20_K | 1.325 | 0.87 |
| 55_L | 80_D | 1.293 | 0.85 |
| 74_V | 90_F | 1.292 | 0.85 |
| 138_F | 142_Y | 1.288 | 0.85 |
| 67_Y | 70_F | 1.283 | 0.85 |
| 70_F | 120_Y | 1.275 | 0.84 |
| 69_S | 73_V | 1.262 | 0.84 |
| 121_L | 130_Q | 1.260 | 0.83 |
| 60_H | 79_R | 1.260 | 0.83 |
| 125_L | 129_I | 1.245 | 0.82 |
| 73_V | 80_D | 1.244 | 0.82 |
| 76_E | 95_G | 1.233 | 0.82 |
| 23_S | 27_F | 1.232 | 0.82 |
| 13_L | 113_I | 1.231 | 0.81 |
| 46_L | 79_R | 1.218 | 0.80 |
| 128_W | 133_G | 1.214 | 0.80 |
| 33_V | 37_L | 1.205 | 0.80 |
| 66_A | 70_F | 1.194 | 0.79 |
| 44_F | 101_S | 1.163 | 0.76 |
| 77_L | 89_A | 1.162 | 0.76 |
| 78_F | 87_I | 1.161 | 0.76 |
| 67_Y | 116_W | 1.154 | 0.75 |
| 90_F | 125_L | 1.147 | 0.75 |
| 37_L | 133_G | 1.144 | 0.74 |
| 13_L | 94_G | 1.141 | 0.74 |
| 95_G | 118_A | 1.136 | 0.74 |
| 44_F | 74_V | 1.123 | 0.72 |
| 118_A | 121_L | 1.106 | 0.71 |
| 128_W | 132_N | 1.099 | 0.70 |
| 46_L | 77_L | 1.097 | 0.70 |
| 99_V | 102_V | 1.091 | 0.69 |
| 45_E | 128_W | 1.081 | 0.68 |
| 75_N | 123_D | 1.076 | 0.68 |
| 7_E | 18_S | 1.072 | 0.67 |
| 23_S | 26_Q | 1.072 | 0.67 |
| 136_D | 139_V | 1.068 | 0.67 |
| 43_E | 99_V | 1.068 | 0.67 |
| 73_V | 76_E | 1.059 | 0.66 |
| 91_F | 118_A | 1.058 | 0.66 |
| 4_S | 22_Y | 1.058 | 0.66 |
| 75_N | 124_H | 1.034 | 0.63 |
| 81_G | 86_R | 1.033 | 0.63 |
| 87_I | 139_V | 1.033 | 0.63 |
| 62_T | 78_F | 1.032 | 0.63 |
| 84_W | 129_I | 1.029 | 0.63 |
| 81_G | 93_F | 1.029 | 0.63 |
| 78_F | 82_V | 1.027 | 0.62 |
| 90_F | 94_G | 1.026 | 0.62 |
| 12_F | 16_K | 1.026 | 0.62 |
| 89_A | 125_L | 1.021 | 0.62 |
| 129_I | 134_G | 1.005 | 0.60 |
| 65_T | 137_T | 1.003 | 0.60 |
| 69_S | 119_T | 1.002 | 0.60 |
| 8_L | 134_G | 1.001 | 0.60 |
| 5_N | 90_F | 1.000 | 0.59 |
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 | |
| 2xa0A | 2 | 0.9371 | 100 | 0.077 | Contact Map |
| 3ilcA | 1 | 0.986 | 100 | 0.085 | Contact Map |
| 4lxdA | 1 | 0.979 | 100 | 0.085 | Contact Map |
| 1r2dA | 1 | 0.993 | 100 | 0.09 | Contact Map |
| 3sp7A | 1 | 0.993 | 100 | 0.097 | Contact Map |
| 4cimA | 2 | 0.993 | 100 | 0.116 | Contact Map |
| 4k5aA | 1 | 1 | 100 | 0.12 | Contact Map |
| 2imsA | 1 | 0.972 | 100 | 0.156 | Contact Map |
| 2a5yA | 1 | 1 | 100 | 0.159 | Contact Map |
| 1ohuA | 2 | 1 | 100 | 0.167 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)