| test1 |
| ID: | 1420170672 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 199 (186) | ||
| Sequences: | 3818 (2867.9) | ||
| Seq/Len: | 20.527 | ||
| Nf(neff/√len): | 210.3 |
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: 20.527).
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 |
| 8_P | 12_V | 3.559 | 1.00 |
| 29_V | 92_L | 3.289 | 1.00 |
| 36_V | 82_K | 3.002 | 1.00 |
| 62_T | 87_V | 2.859 | 1.00 |
| 101_V | 136_I | 2.791 | 1.00 |
| 159_W | 163_N | 2.751 | 1.00 |
| 46_M | 54_I | 2.744 | 1.00 |
| 32_L | 83_I | 2.700 | 1.00 |
| 44_T | 56_K | 2.694 | 1.00 |
| 46_M | 56_K | 2.445 | 1.00 |
| 86_I | 90_T | 2.401 | 1.00 |
| 139_W | 143_N | 2.345 | 1.00 |
| 19_F | 99_F | 2.235 | 1.00 |
| 128_K | 162_S | 2.115 | 1.00 |
| 109_V | 137_T | 2.084 | 1.00 |
| 152_K | 155_D | 2.051 | 1.00 |
| 10_A | 14_T | 2.001 | 1.00 |
| 171_K | 175_M | 1.989 | 1.00 |
| 49_G | 134_P | 1.977 | 1.00 |
| 34_I | 39_G | 1.811 | 1.00 |
| 139_W | 159_W | 1.809 | 1.00 |
| 30_C | 41_P | 1.777 | 1.00 |
| 16_S | 102_I | 1.732 | 1.00 |
| 29_V | 87_V | 1.709 | 1.00 |
| 140_A | 153_K | 1.689 | 1.00 |
| 91_S | 145_R | 1.682 | 1.00 |
| 29_V | 60_F | 1.673 | 1.00 |
| 109_V | 173_L | 1.650 | 1.00 |
| 34_I | 41_P | 1.632 | 1.00 |
| 42_F | 58_F | 1.611 | 1.00 |
| 15_A | 19_F | 1.593 | 1.00 |
| 58_F | 100_N | 1.592 | 1.00 |
| 132_V | 161_V | 1.587 | 1.00 |
| 44_T | 58_F | 1.584 | 1.00 |
| 33_L | 36_V | 1.581 | 1.00 |
| 138_G | 141_Q | 1.544 | 1.00 |
| 11_D | 107_S | 1.542 | 1.00 |
| 14_T | 108_F | 1.491 | 1.00 |
| 33_L | 37_N | 1.484 | 1.00 |
| 40_N | 65_D | 1.479 | 1.00 |
| 26_F | 60_F | 1.478 | 1.00 |
| 114_L | 118_Y | 1.465 | 1.00 |
| 48_P | 54_I | 1.453 | 1.00 |
| 175_M | 179_K | 1.432 | 1.00 |
| 91_S | 153_K | 1.422 | 1.00 |
| 144_G | 148_I | 1.408 | 1.00 |
| 18_V | 98_L | 1.368 | 0.99 |
| 83_I | 87_V | 1.365 | 0.99 |
| 28_I | 32_L | 1.357 | 0.99 |
| 18_V | 22_F | 1.345 | 0.99 |
| 7_K | 169_D | 1.344 | 0.99 |
| 22_F | 26_F | 1.333 | 0.99 |
| 98_L | 108_F | 1.330 | 0.99 |
| 178_M | 182_K | 1.305 | 0.99 |
| 99_F | 103_K | 1.299 | 0.99 |
| 54_I | 116_V | 1.292 | 0.99 |
| 8_P | 15_A | 1.285 | 0.99 |
| 15_A | 102_I | 1.282 | 0.99 |
| 7_K | 11_D | 1.281 | 0.99 |
| 115_L | 118_Y | 1.271 | 0.99 |
| 18_V | 108_F | 1.262 | 0.99 |
| 159_W | 168_L | 1.257 | 0.99 |
| 12_V | 16_S | 1.249 | 0.99 |
| 50_K | 133_K | 1.245 | 0.98 |
| 108_F | 173_L | 1.239 | 0.98 |
| 138_G | 153_K | 1.232 | 0.98 |
| 115_L | 122_Y | 1.204 | 0.98 |
| 114_L | 150_W | 1.199 | 0.98 |
| 139_W | 172_I | 1.196 | 0.98 |
| 12_V | 15_A | 1.179 | 0.98 |
| 160_Y | 169_D | 1.177 | 0.98 |
| 118_Y | 122_Y | 1.173 | 0.98 |
| 89_K | 183_S | 1.162 | 0.97 |
| 180_V | 185_G | 1.159 | 0.97 |
| 166_M | 170_I | 1.158 | 0.97 |
| 20_I | 23_L | 1.143 | 0.97 |
| 114_L | 119_L | 1.136 | 0.97 |
| 19_F | 23_L | 1.135 | 0.97 |
| 45_Q | 57_I | 1.132 | 0.97 |
| 129_R | 157_D | 1.126 | 0.97 |
| 149_S | 152_K | 1.112 | 0.96 |
| 128_K | 131_K | 1.112 | 0.96 |
| 40_N | 61_K | 1.112 | 0.96 |
| 12_V | 102_I | 1.110 | 0.96 |
| 145_R | 148_I | 1.108 | 0.96 |
| 173_L | 177_V | 1.090 | 0.96 |
| 34_I | 37_N | 1.086 | 0.96 |
| 14_T | 18_V | 1.079 | 0.95 |
| 141_Q | 157_D | 1.074 | 0.95 |
| 119_L | 122_Y | 1.071 | 0.95 |
| 114_L | 153_K | 1.071 | 0.95 |
| 16_S | 20_I | 1.069 | 0.95 |
| 114_L | 140_A | 1.069 | 0.95 |
| 41_P | 60_F | 1.041 | 0.94 |
| 31_I | 35_V | 1.040 | 0.94 |
| 95_L | 98_L | 1.029 | 0.94 |
| 139_W | 168_L | 1.028 | 0.94 |
| 58_F | 103_K | 1.018 | 0.93 |
| 52_G | 130_L | 1.010 | 0.93 |
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 | |
| 3wguG | 2 | 0.1759 | 3.3 | 0.971 | Contact Map |
| 3hinA | 2 | 0.3869 | 3.2 | 0.971 | Contact Map |
| 2clyA | 2 | 0.0653 | 2.9 | 0.972 | Contact Map |
| 3j7aN | 1 | 0.191 | 2.5 | 0.973 | Contact Map |
| 4k84A | 2 | 0.4271 | 2.5 | 0.973 | Contact Map |
| 1vx5U | 1 | 0.191 | 2.4 | 0.973 | Contact Map |
| 4kt0F | 1 | 0.6784 | 2.2 | 0.974 | Contact Map |
| 2k44A | 1 | 0.1357 | 2.1 | 0.974 | Contact Map |
| 4k0jA | 6 | 0.1658 | 2.1 | 0.974 | Contact Map |
| 1jb0F | 1 | 0.6784 | 1.8 | 0.975 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)