| thrombin |
| ID: | 1445595481 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 259 (247) | ||
| Sequences: | 13845 (10168.3) | ||
| Seq/Len: | 56.053 | ||
| Nf(neff/√len): | 647.0 |
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: 56.053).
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 |
| 136_G | 211_M | 4.992 | 1.00 |
| 30_A | 38_V | 3.417 | 1.00 |
| 28_C | 44_C | 3.387 | 1.00 |
| 11_M | 162_V | 3.156 | 1.00 |
| 37_W | 102_L | 3.134 | 1.00 |
| 6_D | 161_Q | 3.057 | 1.00 |
| 82_E | 104_K | 2.980 | 1.00 |
| 15_Q | 139_T | 2.850 | 1.00 |
| 45_L | 101_A | 2.803 | 1.00 |
| 17_M | 26_L | 2.788 | 1.00 |
| 37_W | 104_K | 2.621 | 1.00 |
| 12_S | 162_V | 2.613 | 1.00 |
| 43_H | 205_S | 2.604 | 1.00 |
| 201_C | 231_C | 2.593 | 1.00 |
| 32_L | 109_V | 2.555 | 1.00 |
| 63_I | 109_V | 2.497 | 1.00 |
| 31_S | 221_Q | 2.493 | 1.00 |
| 98_R | 246_L | 2.448 | 1.00 |
| 80_M | 106_K | 2.430 | 1.00 |
| 39_L | 221_Q | 2.277 | 1.00 |
| 88_P | 253_V | 2.227 | 1.00 |
| 173_C | 187_C | 2.212 | 1.00 |
| 105_L | 109_V | 2.205 | 1.00 |
| 36_R | 104_K | 2.196 | 1.00 |
| 34_S | 37_W | 2.163 | 1.00 |
| 83_K | 104_K | 2.148 | 1.00 |
| 36_R | 108_P | 2.124 | 1.00 |
| 16_V | 30_A | 2.046 | 1.00 |
| 136_G | 167_I | 2.018 | 1.00 |
| 227_W | 239_F | 2.016 | 1.00 |
| 12_S | 139_T | 1.997 | 1.00 |
| 6_D | 159_V | 1.988 | 1.00 |
| 35_D | 108_P | 1.975 | 1.00 |
| 138_V | 200_A | 1.973 | 1.00 |
| 81_L | 103_M | 1.952 | 1.00 |
| 85_Y | 253_V | 1.952 | 1.00 |
| 100_I | 246_L | 1.913 | 1.00 |
| 97_D | 184_N | 1.911 | 1.00 |
| 79_S | 109_V | 1.910 | 1.00 |
| 62_R | 78_I | 1.852 | 1.00 |
| 184_N | 245_R | 1.851 | 1.00 |
| 16_V | 63_I | 1.840 | 1.00 |
| 111_F | 117_P | 1.813 | 1.00 |
| 139_T | 210_V | 1.777 | 1.00 |
| 199_D | 238_G | 1.752 | 1.00 |
| 19_F | 26_L | 1.719 | 1.00 |
| 82_E | 106_K | 1.714 | 1.00 |
| 1_I | 4_G | 1.705 | 1.00 |
| 163_V | 198_G | 1.653 | 1.00 |
| 247_K | 251_Q | 1.624 | 1.00 |
| 138_V | 163_V | 1.607 | 1.00 |
| 79_S | 106_K | 1.605 | 1.00 |
| 7_A | 12_S | 1.597 | 1.00 |
| 146_E | 233_R | 1.575 | 1.00 |
| 118_V | 221_Q | 1.573 | 1.00 |
| 89_R | 98_R | 1.568 | 1.00 |
| 241_T | 246_L | 1.545 | 1.00 |
| 200_A | 225_V | 1.538 | 1.00 |
| 31_S | 118_V | 1.520 | 1.00 |
| 186_F | 209_F | 1.516 | 1.00 |
| 157_P | 161_Q | 1.494 | 1.00 |
| 31_S | 224_I | 1.492 | 1.00 |
| 16_V | 38_V | 1.490 | 1.00 |
| 40_T | 45_L | 1.487 | 1.00 |
| 76_E | 79_S | 1.473 | 1.00 |
| 166_P | 189_G | 1.449 | 1.00 |
| 14_W | 119_C | 1.432 | 1.00 |
| 15_Q | 160_L | 1.429 | 1.00 |
| 225_V | 228_G | 1.400 | 0.99 |
| 62_R | 65_K | 1.386 | 0.99 |
| 118_V | 210_V | 1.376 | 0.99 |
| 7_A | 162_V | 1.369 | 0.99 |
| 87_H | 98_R | 1.361 | 0.99 |
| 242_H | 245_R | 1.360 | 0.99 |
| 10_G | 66_H | 1.360 | 0.99 |
| 209_F | 240_Y | 1.357 | 0.99 |
| 185_M | 227_W | 1.349 | 0.99 |
| 136_G | 222_M | 1.337 | 0.99 |
| 65_K | 75_I | 1.331 | 0.99 |
| 169_E | 172_V | 1.323 | 0.99 |
| 135_K | 164_N | 1.314 | 0.99 |
| 137_R | 164_N | 1.313 | 0.99 |
| 170_R | 242_H | 1.309 | 0.99 |
| 14_W | 210_V | 1.300 | 0.99 |
| 45_L | 86_I | 1.290 | 0.99 |
| 132_A | 169_E | 1.272 | 0.99 |
| 98_R | 184_N | 1.262 | 0.99 |
| 37_W | 253_V | 1.259 | 0.99 |
| 67_S | 158_S | 1.257 | 0.99 |
| 138_V | 165_L | 1.253 | 0.99 |
| 79_S | 107_K | 1.237 | 0.98 |
| 168_V | 237_Y | 1.217 | 0.98 |
| 211_M | 222_M | 1.215 | 0.98 |
| 9_I | 66_H | 1.200 | 0.98 |
| 41_A | 224_I | 1.197 | 0.98 |
| 144_L | 161_Q | 1.191 | 0.98 |
| 14_W | 219_W | 1.178 | 0.98 |
| 163_V | 196_K | 1.175 | 0.98 |
| 91_N | 95_N | 1.173 | 0.98 |
| 38_V | 61_V | 1.171 | 0.98 |
| 8_E | 11_M | 1.167 | 0.97 |
| 121_P | 247_K | 1.161 | 0.97 |
| 6_D | 66_H | 1.160 | 0.97 |
| 135_K | 166_P | 1.150 | 0.97 |
| 37_W | 254_I | 1.150 | 0.97 |
| 67_S | 159_V | 1.149 | 0.97 |
| 86_I | 101_A | 1.145 | 0.97 |
| 12_S | 137_R | 1.138 | 0.97 |
| 15_Q | 29_G | 1.134 | 0.97 |
| 32_L | 111_F | 1.130 | 0.97 |
| 69_T | 158_S | 1.126 | 0.97 |
| 85_Y | 104_K | 1.119 | 0.96 |
| 10_G | 114_Y | 1.114 | 0.96 |
| 45_L | 84_I | 1.108 | 0.96 |
| 112_S | 115_I | 1.106 | 0.96 |
| 43_H | 99_D | 1.104 | 0.96 |
| 97_D | 182_T | 1.095 | 0.96 |
| 136_G | 209_F | 1.092 | 0.96 |
| 32_L | 63_I | 1.088 | 0.96 |
| 184_N | 246_L | 1.080 | 0.95 |
| 100_I | 241_T | 1.077 | 0.95 |
| 63_I | 115_I | 1.075 | 0.95 |
| 138_V | 225_V | 1.074 | 0.95 |
| 5_S | 162_V | 1.068 | 0.95 |
| 18_L | 61_V | 1.042 | 0.94 |
| 120_L | 247_K | 1.042 | 0.94 |
| 79_S | 105_L | 1.039 | 0.94 |
| 249_W | 253_V | 1.039 | 0.94 |
| 15_Q | 208_P | 1.031 | 0.94 |
| 45_L | 103_M | 1.026 | 0.94 |
| 139_T | 162_V | 1.018 | 0.93 |
| 142_G | 204_D | 1.012 | 0.93 |
| 31_S | 39_L | 1.009 | 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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 4nzqA | 1 | 0.9961 | 100 | -0.014 | Contact Map |
| 3nxpA | 1 | 0.9807 | 100 | -0.006 | Contact Map |
| 2bdyA | 1 | 0.9614 | 100 | 0.014 | Contact Map |
| 2f83A | 1 | 0.8224 | 100 | 0.029 | Contact Map |
| 2xxlA | 2 | 0.9266 | 100 | 0.037 | Contact Map |
| 3rm2H | 1 | 0.9691 | 100 | 0.038 | Contact Map |
| 4kkdA | 2 | 0.9305 | 100 | 0.049 | Contact Map |
| 4igdA | 1 | 0.9189 | 100 | 0.049 | Contact Map |
| 1zjkA | 1 | 0.9035 | 100 | 0.054 | Contact Map |
| 2b9lA | 1 | 0.9305 | 100 | 0.059 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)