| traf2 c domain |
| ID: | 1509941579 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 171 (157) | ||
| Sequences: | 1910 (1384) | ||
| Seq/Len: | 12.166 | ||
| Nf(neff/√len): | 110.5 |
HHblits Results: (2016_02)
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: 12.166).
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 |
| 80_F | 138_G | 3.285 | 1.00 |
| 65_Y | 68_G | 2.555 | 1.00 |
| 32_A | 158_D | 2.386 | 1.00 |
| 62_L | 164_A | 2.274 | 1.00 |
| 81_F | 100_V | 2.048 | 1.00 |
| 52_Y | 59_K | 1.878 | 1.00 |
| 82_V | 136_A | 1.678 | 1.00 |
| 79_L | 162_I | 1.667 | 1.00 |
| 103_M | 163_K | 1.642 | 1.00 |
| 79_L | 102_L | 1.638 | 1.00 |
| 31_F | 149_E | 1.632 | 1.00 |
| 68_G | 78_S | 1.604 | 1.00 |
| 27_K | 159_A | 1.595 | 1.00 |
| 69_D | 136_A | 1.590 | 1.00 |
| 28_I | 46_I | 1.557 | 1.00 |
| 138_G | 142_F | 1.535 | 1.00 |
| 107_Q | 156_R | 1.524 | 1.00 |
| 58_Y | 89_D | 1.494 | 1.00 |
| 14_E | 17_A | 1.459 | 1.00 |
| 26_W | 49_P | 1.449 | 1.00 |
| 105_L | 163_K | 1.434 | 1.00 |
| 35_R | 149_E | 1.393 | 0.99 |
| 102_L | 164_A | 1.389 | 0.99 |
| 61_C | 84_M | 1.383 | 0.99 |
| 63_R | 82_V | 1.369 | 0.99 |
| 61_C | 82_V | 1.355 | 0.99 |
| 107_Q | 161_F | 1.347 | 0.99 |
| 22_G | 53_T | 1.347 | 0.99 |
| 39_V | 67_N | 1.317 | 0.99 |
| 45_A | 63_R | 1.309 | 0.99 |
| 101_T | 165_I | 1.274 | 0.99 |
| 76_H | 141_L | 1.271 | 0.99 |
| 26_W | 48_S | 1.270 | 0.99 |
| 48_S | 51_F | 1.264 | 0.99 |
| 56_Y | 168_L | 1.258 | 0.99 |
| 64_I | 77_L | 1.256 | 0.99 |
| 47_F | 61_C | 1.245 | 0.98 |
| 92_L | 95_P | 1.233 | 0.98 |
| 68_G | 76_H | 1.229 | 0.98 |
| 27_K | 105_L | 1.223 | 0.98 |
| 102_L | 139_C | 1.217 | 0.98 |
| 47_F | 63_R | 1.212 | 0.98 |
| 144_P | 147_K | 1.211 | 0.98 |
| 30_D | 33_R | 1.202 | 0.98 |
| 106_D | 112_H | 1.200 | 0.98 |
| 66_L | 98_Q | 1.197 | 0.98 |
| 23_V | 165_I | 1.188 | 0.98 |
| 78_S | 138_G | 1.176 | 0.98 |
| 50_A | 59_K | 1.170 | 0.97 |
| 113_V | 143_C | 1.157 | 0.97 |
| 58_Y | 95_P | 1.155 | 0.97 |
| 155_V | 158_D | 1.143 | 0.97 |
| 64_I | 79_L | 1.129 | 0.97 |
| 148_M | 155_V | 1.126 | 0.97 |
| 67_N | 145_V | 1.123 | 0.97 |
| 83_V | 94_W | 1.118 | 0.96 |
| 86_G | 95_P | 1.114 | 0.96 |
| 42_R | 131_N | 1.114 | 0.96 |
| 58_Y | 96_F | 1.109 | 0.96 |
| 59_K | 84_M | 1.103 | 0.96 |
| 15_M | 130_V | 1.101 | 0.96 |
| 27_K | 161_F | 1.100 | 0.96 |
| 128_R | 131_N | 1.088 | 0.96 |
| 63_R | 134_N | 1.083 | 0.96 |
| 101_T | 116_A | 1.082 | 0.96 |
| 123_S | 137_S | 1.074 | 0.95 |
| 60_M | 81_F | 1.064 | 0.95 |
| 98_Q | 126_F | 1.063 | 0.95 |
| 30_D | 34_K | 1.052 | 0.95 |
| 24_F | 51_F | 1.038 | 0.94 |
| 78_S | 141_L | 1.031 | 0.94 |
| 112_H | 115_D | 1.025 | 0.93 |
| 72_G | 76_H | 1.023 | 0.93 |
| 42_R | 55_R | 1.022 | 0.93 |
| 56_Y | 106_D | 1.021 | 0.93 |
| 56_Y | 66_L | 1.015 | 0.93 |
| 126_F | 137_S | 1.007 | 0.93 |
| 113_V | 116_A | 1.006 | 0.93 |
| 136_A | 140_P | 1.005 | 0.93 |
| 112_H | 116_A | 1.001 | 0.92 |
| 28_I | 32_A | 1.000 | 0.92 |
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 | |
| 1ca9A | 6 | 0.9883 | 100 | 0.093 | Contact Map |
| 4ghuA | 1 | 0.9942 | 100 | 0.1 | Contact Map |
| 1d00A | 8 | 0.9708 | 100 | 0.101 | Contact Map |
| 1flkA | 2 | 0.9825 | 100 | 0.102 | Contact Map |
| 3zjbA | 3 | 0.9766 | 100 | 0.133 | Contact Map |
| 1lb6A | 1 | 0.8655 | 100 | 0.167 | Contact Map |
| 4gjhA | 3 | 0.9825 | 100 | 0.171 | Contact Map |
| 4gwmA | 2 | 0.8947 | 99.9 | 0.231 | Contact Map |
| 3ivvA | 1 | 0.7953 | 99.9 | 0.268 | Contact Map |
| 2f1zA | 2 | 0.7895 | 99.9 | 0.281 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)