| tcr |
| ID: | 1418860761 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 236 (208) | ||
| Sequences: | 1876 (1284) | ||
| Seq/Len: | 9.019 | ||
| Nf(neff/√len): | 89.0 |
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: 9.019).
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 |
| 13_A | 81_A | 4.798 | 1.00 |
| 63_G | 85_Q | 3.638 | 1.00 |
| 140_C | 201_C | 2.451 | 1.00 |
| 19_V | 107_L | 2.395 | 1.00 |
| 140_C | 154_W | 2.140 | 1.00 |
| 145_F | 150_V | 2.043 | 1.00 |
| 13_A | 19_V | 2.027 | 1.00 |
| 151_E | 204_Q | 1.988 | 1.00 |
| 155_W | 202_Q | 1.926 | 1.00 |
| 120_V | 138_L | 1.797 | 1.00 |
| 21_L | 34_W | 1.725 | 1.00 |
| 102_G | 105_T | 1.712 | 1.00 |
| 23_C | 91_C | 1.709 | 1.00 |
| 14_V | 17_G | 1.645 | 1.00 |
| 60_I | 64_Y | 1.579 | 1.00 |
| 36_R | 87_S | 1.548 | 1.00 |
| 154_W | 183_S | 1.529 | 1.00 |
| 145_F | 205_F | 1.499 | 1.00 |
| 152_L | 183_S | 1.495 | 1.00 |
| 88_V | 106_R | 1.472 | 1.00 |
| 18_K | 77_I | 1.440 | 0.99 |
| 58_G | 61_P | 1.425 | 0.99 |
| 16_G | 85_Q | 1.417 | 0.99 |
| 164_G | 167_T | 1.405 | 0.99 |
| 38_D | 42_G | 1.397 | 0.99 |
| 142_A | 145_F | 1.381 | 0.99 |
| 110_E | 205_F | 1.378 | 0.99 |
| 23_C | 34_W | 1.368 | 0.99 |
| 13_A | 17_G | 1.355 | 0.99 |
| 64_Y | 76_L | 1.352 | 0.99 |
| 21_L | 205_F | 1.341 | 0.99 |
| 147_P | 154_W | 1.329 | 0.99 |
| 101_F | 104_G | 1.327 | 0.99 |
| 153_S | 160_E | 1.316 | 0.99 |
| 156_V | 197_N | 1.312 | 0.99 |
| 142_A | 206_H | 1.312 | 0.99 |
| 140_C | 147_P | 1.299 | 0.99 |
| 48_Y | 52_A | 1.276 | 0.98 |
| 142_A | 152_L | 1.275 | 0.98 |
| 34_W | 76_L | 1.231 | 0.98 |
| 27_N | 74_F | 1.222 | 0.98 |
| 150_V | 205_F | 1.215 | 0.98 |
| 43_L | 46_I | 1.208 | 0.98 |
| 85_Q | 89_Y | 1.205 | 0.98 |
| 117_P | 120_V | 1.203 | 0.97 |
| 152_L | 203_V | 1.196 | 0.97 |
| 4_V | 7_S | 1.191 | 0.97 |
| 118_P | 121_S | 1.189 | 0.97 |
| 76_L | 89_Y | 1.185 | 0.97 |
| 147_P | 150_V | 1.168 | 0.97 |
| 45_L | 53_G | 1.162 | 0.97 |
| 65_K | 77_I | 1.157 | 0.97 |
| 116_T | 136_A | 1.151 | 0.96 |
| 107_L | 126_S | 1.147 | 0.96 |
| 18_K | 80_L | 1.138 | 0.96 |
| 203_V | 208_L | 1.136 | 0.96 |
| 25_Q | 32_M | 1.135 | 0.96 |
| 63_G | 78_L | 1.122 | 0.96 |
| 67_S | 73_N | 1.120 | 0.96 |
| 25_Q | 36_R | 1.111 | 0.95 |
| 15_T | 32_M | 1.106 | 0.95 |
| 5_T | 9_R | 1.105 | 0.95 |
| 30_N | 72_E | 1.093 | 0.95 |
| 129_E | 192_W | 1.090 | 0.95 |
| 143_R | 175_S | 1.081 | 0.95 |
| 160_E | 190_T | 1.076 | 0.94 |
| 46_I | 52_A | 1.075 | 0.94 |
| 15_T | 83_P | 1.074 | 0.94 |
| 33_Y | 92_A | 1.073 | 0.94 |
| 35_Y | 92_A | 1.071 | 0.94 |
| 117_P | 124_E | 1.068 | 0.94 |
| 60_I | 66_A | 1.067 | 0.94 |
| 31_N | 96_G | 1.066 | 0.94 |
| 135_K | 189_A | 1.064 | 0.94 |
| 20_T | 77_I | 1.064 | 0.94 |
| 185_L | 201_C | 1.058 | 0.94 |
| 18_K | 81_A | 1.058 | 0.94 |
| 60_I | 87_S | 1.057 | 0.94 |
| 73_N | 97_G | 1.053 | 0.93 |
| 81_A | 85_Q | 1.052 | 0.93 |
| 49_S | 52_A | 1.047 | 0.93 |
| 120_V | 140_C | 1.045 | 0.93 |
| 59_D | 84_S | 1.042 | 0.93 |
| 156_V | 161_V | 1.040 | 0.93 |
| 16_G | 30_N | 1.039 | 0.93 |
| 160_E | 163_S | 1.035 | 0.93 |
| 89_Y | 138_L | 1.031 | 0.93 |
| 12_V | 82_T | 1.031 | 0.93 |
| 44_R | 49_S | 1.028 | 0.92 |
| 178_S | 207_G | 1.027 | 0.92 |
| 51_G | 57_K | 1.026 | 0.92 |
| 152_L | 199_F | 1.021 | 0.92 |
| 120_V | 208_L | 1.013 | 0.92 |
| 149_H | 155_W | 1.013 | 0.92 |
| 115_V | 156_V | 1.011 | 0.92 |
| 69_P | 72_E | 1.008 | 0.91 |
| 149_H | 154_W | 1.008 | 0.91 |
| 42_G | 47_H | 1.007 | 0.91 |
| 86_T | 146_F | 1.006 | 0.91 |
| 198_H | 210_E | 1.002 | 0.91 |
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 | |
| 1ogaE | 1 | 0.9831 | 100 | 0.311 | Contact Map |
| 1becA | 1 | 0.9873 | 100 | 0.321 | Contact Map |
| 3q5yA | 4 | 1 | 100 | 0.322 | Contact Map |
| 3to4D | 1 | 0.9703 | 100 | 0.333 | Contact Map |
| 3pl6D | 1 | 0.9873 | 100 | 0.334 | Contact Map |
| 4ei6B | 2 | 0.9873 | 100 | 0.336 | Contact Map |
| 4dzbB | 1 | 0.9831 | 100 | 0.341 | Contact Map |
| 4jfhE | 1 | 0.9873 | 100 | 0.341 | Contact Map |
| 4mayD | 1 | 0.9873 | 100 | 0.341 | Contact Map |
| 4ndmA | 1 | 0.9619 | 100 | 0.342 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)