| C_aln |
| ID: | 1420172700 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 218 (188) | ||
| Sequences: | 3798 (2884.8) | ||
| Seq/Len: | 20.202 | ||
| Nf(neff/√len): | 210.4 |
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: 20.202).
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_R | 12_F | 3.490 | 1.00 |
| 29_L | 97_L | 3.290 | 1.00 |
| 36_A | 87_K | 2.913 | 1.00 |
| 67_T | 92_M | 2.850 | 1.00 |
| 50_K | 56_Q | 2.798 | 1.00 |
| 106_I | 141_L | 2.793 | 1.00 |
| 32_V | 88_Y | 2.721 | 1.00 |
| 44_V | 61_K | 2.719 | 1.00 |
| 46_P | 59_I | 2.651 | 1.00 |
| 165_K | 169_N | 2.647 | 1.00 |
| 91_I | 95_T | 2.420 | 1.00 |
| 46_P | 61_K | 2.383 | 1.00 |
| 19_V | 104_F | 2.297 | 1.00 |
| 133_H | 168_S | 2.295 | 1.00 |
| 144_L | 148_N | 2.283 | 1.00 |
| 158_S | 161_A | 2.124 | 1.00 |
| 114_V | 142_T | 2.088 | 1.00 |
| 177_K | 181_S | 2.031 | 1.00 |
| 10_F | 14_F | 1.977 | 1.00 |
| 34_A | 39_G | 1.885 | 1.00 |
| 144_L | 165_K | 1.871 | 1.00 |
| 30_I | 41_P | 1.851 | 1.00 |
| 49_G | 139_P | 1.847 | 1.00 |
| 29_L | 65_F | 1.757 | 1.00 |
| 16_L | 107_L | 1.740 | 1.00 |
| 42_F | 63_V | 1.702 | 1.00 |
| 34_A | 41_P | 1.680 | 1.00 |
| 119_L | 123_Y | 1.672 | 1.00 |
| 114_V | 179_I | 1.651 | 1.00 |
| 96_S | 150_R | 1.643 | 1.00 |
| 33_G | 36_A | 1.625 | 1.00 |
| 29_L | 92_M | 1.617 | 1.00 |
| 63_V | 105_N | 1.590 | 1.00 |
| 44_V | 63_V | 1.562 | 1.00 |
| 15_S | 19_V | 1.560 | 1.00 |
| 14_F | 113_I | 1.542 | 1.00 |
| 26_L | 65_F | 1.541 | 1.00 |
| 120_L | 123_Y | 1.518 | 1.00 |
| 143_G | 146_Q | 1.509 | 1.00 |
| 137_V | 167_V | 1.484 | 1.00 |
| 33_G | 37_M | 1.468 | 1.00 |
| 48_P | 59_I | 1.460 | 1.00 |
| 11_D | 112_S | 1.448 | 1.00 |
| 145_A | 159_V | 1.442 | 1.00 |
| 40_N | 70_N | 1.429 | 1.00 |
| 28_A | 32_V | 1.423 | 1.00 |
| 7_K | 11_D | 1.402 | 0.99 |
| 59_I | 121_V | 1.386 | 0.99 |
| 181_S | 185_K | 1.349 | 0.99 |
| 18_A | 103_L | 1.340 | 0.99 |
| 96_S | 159_V | 1.326 | 0.99 |
| 103_L | 113_I | 1.324 | 0.99 |
| 88_Y | 92_M | 1.319 | 0.99 |
| 22_L | 26_L | 1.312 | 0.99 |
| 18_A | 113_I | 1.311 | 0.99 |
| 15_S | 107_L | 1.306 | 0.99 |
| 18_A | 22_L | 1.299 | 0.99 |
| 40_N | 66_R | 1.294 | 0.99 |
| 12_F | 16_L | 1.280 | 0.99 |
| 165_K | 174_G | 1.277 | 0.99 |
| 50_K | 138_R | 1.275 | 0.99 |
| 104_F | 108_K | 1.261 | 0.99 |
| 7_K | 175_D | 1.257 | 0.99 |
| 12_F | 107_L | 1.246 | 0.98 |
| 184_S | 188_K | 1.243 | 0.98 |
| 8_R | 15_S | 1.231 | 0.98 |
| 94_I | 189_R | 1.230 | 0.98 |
| 133_H | 136_D | 1.218 | 0.98 |
| 113_I | 179_I | 1.199 | 0.98 |
| 20_V | 23_S | 1.196 | 0.98 |
| 12_F | 15_S | 1.192 | 0.98 |
| 144_L | 178_I | 1.174 | 0.98 |
| 119_L | 156_W | 1.169 | 0.97 |
| 186_V | 191_D | 1.166 | 0.97 |
| 172_W | 176_L | 1.157 | 0.97 |
| 19_V | 23_S | 1.142 | 0.97 |
| 34_A | 37_M | 1.135 | 0.97 |
| 119_L | 159_V | 1.130 | 0.97 |
| 119_L | 124_L | 1.115 | 0.96 |
| 143_G | 159_V | 1.115 | 0.96 |
| 179_I | 183_I | 1.114 | 0.96 |
| 146_Q | 163_D | 1.110 | 0.96 |
| 149_G | 153_I | 1.106 | 0.96 |
| 123_Y | 127_Y | 1.105 | 0.96 |
| 16_L | 20_V | 1.065 | 0.95 |
| 134_R | 163_D | 1.061 | 0.95 |
| 14_F | 18_A | 1.059 | 0.95 |
| 45_Q | 62_L | 1.059 | 0.95 |
| 144_L | 162_Y | 1.035 | 0.94 |
| 43_F | 73_D | 1.035 | 0.94 |
| 69_D | 72_K | 1.033 | 0.94 |
| 144_L | 174_G | 1.025 | 0.93 |
| 31_I | 35_V | 1.016 | 0.93 |
| 119_L | 145_A | 1.003 | 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 | |
| 1z5zA | 2 | 0.4312 | 4.3 | 0.971 | Contact Map |
| 4d25A | 1 | 0.4037 | 3.4 | 0.973 | Contact Map |
| 2fwrA | 4 | 0.3349 | 3.3 | 0.973 | Contact Map |
| 4k84A | 2 | 0.3761 | 2.7 | 0.974 | Contact Map |
| 4ezcA | 3 | 0.2936 | 2.7 | 0.974 | Contact Map |
| 1wp9A | 6 | 0.3394 | 2.7 | 0.974 | Contact Map |
| 2k44A | 1 | 0.1239 | 2.6 | 0.974 | Contact Map |
| 1z63A | 2 | 0.4633 | 2.6 | 0.974 | Contact Map |
| 2ocaA | 1 | 0.4862 | 2.5 | 0.974 | Contact Map |
| 4k0jA | 6 | 0.1514 | 2.5 | 0.974 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)