| thrombin |
| ID: | 1446103353 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 259 (247) | ||
| Sequences: | 11829 (8393.1) | ||
| Seq/Len: | 47.891 | ||
| Nf(neff/√len): | 534.0 |
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: 47.891).
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 | 5.177 | 1.00 |
| 30_A | 38_V | 3.545 | 1.00 |
| 11_M | 162_V | 3.278 | 1.00 |
| 17_M | 26_L | 3.262 | 1.00 |
| 6_D | 161_Q | 3.186 | 1.00 |
| 37_W | 102_L | 3.120 | 1.00 |
| 15_Q | 139_T | 3.031 | 1.00 |
| 82_E | 104_K | 2.996 | 1.00 |
| 45_L | 101_A | 2.941 | 1.00 |
| 12_S | 162_V | 2.890 | 1.00 |
| 32_L | 109_V | 2.667 | 1.00 |
| 28_C | 44_C | 2.618 | 1.00 |
| 63_I | 109_V | 2.607 | 1.00 |
| 43_H | 205_S | 2.579 | 1.00 |
| 98_R | 246_L | 2.504 | 1.00 |
| 88_P | 253_V | 2.480 | 1.00 |
| 39_L | 221_Q | 2.429 | 1.00 |
| 31_S | 221_Q | 2.353 | 1.00 |
| 80_M | 106_K | 2.286 | 1.00 |
| 105_L | 109_V | 2.213 | 1.00 |
| 36_R | 104_K | 2.206 | 1.00 |
| 37_W | 104_K | 2.198 | 1.00 |
| 97_D | 184_N | 2.092 | 1.00 |
| 138_V | 200_A | 2.067 | 1.00 |
| 83_K | 104_K | 2.052 | 1.00 |
| 227_W | 239_F | 2.033 | 1.00 |
| 36_R | 108_P | 2.008 | 1.00 |
| 199_D | 238_G | 1.979 | 1.00 |
| 81_L | 103_M | 1.975 | 1.00 |
| 85_Y | 253_V | 1.969 | 1.00 |
| 12_S | 139_T | 1.912 | 1.00 |
| 19_F | 26_L | 1.888 | 1.00 |
| 16_V | 30_A | 1.873 | 1.00 |
| 201_C | 231_C | 1.870 | 1.00 |
| 16_V | 63_I | 1.861 | 1.00 |
| 79_S | 109_V | 1.852 | 1.00 |
| 136_G | 167_I | 1.852 | 1.00 |
| 40_T | 45_L | 1.841 | 1.00 |
| 34_S | 37_W | 1.839 | 1.00 |
| 1_I | 4_G | 1.831 | 1.00 |
| 6_D | 159_V | 1.825 | 1.00 |
| 31_S | 118_V | 1.823 | 1.00 |
| 138_V | 163_V | 1.797 | 1.00 |
| 111_F | 117_P | 1.794 | 1.00 |
| 146_E | 233_R | 1.786 | 1.00 |
| 184_N | 245_R | 1.760 | 1.00 |
| 163_V | 198_G | 1.733 | 1.00 |
| 62_R | 78_I | 1.726 | 1.00 |
| 100_I | 246_L | 1.701 | 1.00 |
| 35_D | 108_P | 1.672 | 1.00 |
| 118_V | 221_Q | 1.670 | 1.00 |
| 139_T | 210_V | 1.665 | 1.00 |
| 82_E | 106_K | 1.651 | 1.00 |
| 76_E | 79_S | 1.618 | 1.00 |
| 7_A | 12_S | 1.601 | 1.00 |
| 186_F | 209_F | 1.595 | 1.00 |
| 31_S | 224_I | 1.581 | 1.00 |
| 173_C | 187_C | 1.570 | 1.00 |
| 79_S | 106_K | 1.550 | 1.00 |
| 225_V | 228_G | 1.550 | 1.00 |
| 241_T | 246_L | 1.511 | 1.00 |
| 166_P | 189_G | 1.502 | 1.00 |
| 247_K | 251_Q | 1.500 | 1.00 |
| 10_G | 66_H | 1.489 | 1.00 |
| 118_V | 210_V | 1.466 | 1.00 |
| 16_V | 38_V | 1.457 | 1.00 |
| 15_Q | 160_L | 1.454 | 1.00 |
| 200_A | 225_V | 1.452 | 1.00 |
| 169_E | 172_V | 1.452 | 1.00 |
| 89_R | 98_R | 1.437 | 1.00 |
| 170_R | 242_H | 1.420 | 1.00 |
| 65_K | 75_I | 1.407 | 0.99 |
| 14_W | 119_C | 1.402 | 0.99 |
| 157_P | 161_Q | 1.396 | 0.99 |
| 62_R | 65_K | 1.390 | 0.99 |
| 14_W | 210_V | 1.375 | 0.99 |
| 136_G | 222_M | 1.369 | 0.99 |
| 7_A | 162_V | 1.362 | 0.99 |
| 242_H | 245_R | 1.344 | 0.99 |
| 185_M | 227_W | 1.338 | 0.99 |
| 138_V | 165_L | 1.337 | 0.99 |
| 132_A | 169_E | 1.321 | 0.99 |
| 98_R | 184_N | 1.321 | 0.99 |
| 67_S | 158_S | 1.307 | 0.99 |
| 87_H | 98_R | 1.285 | 0.99 |
| 6_D | 66_H | 1.276 | 0.99 |
| 91_N | 95_N | 1.273 | 0.99 |
| 37_W | 253_V | 1.272 | 0.99 |
| 211_M | 222_M | 1.268 | 0.99 |
| 121_P | 247_K | 1.261 | 0.99 |
| 97_D | 182_T | 1.253 | 0.99 |
| 144_L | 161_Q | 1.235 | 0.98 |
| 45_L | 86_I | 1.209 | 0.98 |
| 137_R | 164_N | 1.207 | 0.98 |
| 79_S | 107_K | 1.206 | 0.98 |
| 45_L | 84_I | 1.203 | 0.98 |
| 168_V | 237_Y | 1.202 | 0.98 |
| 184_N | 246_L | 1.201 | 0.98 |
| 135_K | 166_P | 1.193 | 0.98 |
| 138_V | 225_V | 1.192 | 0.98 |
| 14_W | 219_W | 1.184 | 0.98 |
| 135_K | 164_N | 1.184 | 0.98 |
| 32_L | 63_I | 1.180 | 0.98 |
| 9_I | 66_H | 1.171 | 0.98 |
| 67_S | 159_V | 1.151 | 0.97 |
| 63_I | 115_I | 1.126 | 0.97 |
| 112_S | 115_I | 1.122 | 0.97 |
| 86_I | 101_A | 1.095 | 0.96 |
| 199_D | 240_Y | 1.094 | 0.96 |
| 100_I | 241_T | 1.086 | 0.96 |
| 32_L | 111_F | 1.081 | 0.95 |
| 139_T | 162_V | 1.081 | 0.95 |
| 163_V | 196_K | 1.079 | 0.95 |
| 38_V | 61_V | 1.072 | 0.95 |
| 5_S | 162_V | 1.070 | 0.95 |
| 12_S | 137_R | 1.060 | 0.95 |
| 69_T | 158_S | 1.059 | 0.95 |
| 209_F | 240_Y | 1.057 | 0.95 |
| 18_L | 61_V | 1.056 | 0.95 |
| 136_G | 209_F | 1.055 | 0.95 |
| 166_P | 190_Y | 1.050 | 0.94 |
| 32_L | 38_V | 1.048 | 0.94 |
| 45_L | 103_M | 1.045 | 0.94 |
| 120_L | 247_K | 1.039 | 0.94 |
| 79_S | 105_L | 1.035 | 0.94 |
| 10_G | 114_Y | 1.034 | 0.94 |
| 43_H | 99_D | 1.032 | 0.94 |
| 40_T | 101_A | 1.022 | 0.93 |
| 31_S | 39_L | 1.017 | 0.93 |
| 8_E | 11_M | 1.011 | 0.93 |
| 15_Q | 29_G | 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 | |
| 4nzqA | 1 | 0.9961 | 100 | -0.029 | Contact Map |
| 3nxpA | 1 | 0.9807 | 100 | -0.019 | Contact Map |
| 2f83A | 1 | 0.8224 | 100 | 0.006 | Contact Map |
| 2bdyA | 1 | 0.9614 | 100 | 0.011 | Contact Map |
| 2xxlA | 2 | 0.9266 | 100 | 0.017 | Contact Map |
| 4kkdA | 2 | 0.9305 | 100 | 0.019 | Contact Map |
| 2b9lA | 1 | 0.9305 | 100 | 0.026 | Contact Map |
| 4igdA | 1 | 0.9189 | 100 | 0.027 | Contact Map |
| 1z8gA | 1 | 0.9189 | 100 | 0.03 | Contact Map |
| 1zjkA | 1 | 0.9035 | 100 | 0.03 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)