| 1fvg |
| ID: | 1453971236 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 199 (195) | ||
| Sequences: | 3036 (1728) | ||
| Seq/Len: | 15.569 | ||
| Nf(neff/√len): | 123.7 |
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: 15.569).
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 |
| 46_A | 108_F | 3.940 | 1.00 |
| 147_V | 151_L | 3.626 | 1.00 |
| 47_V | 142_T | 3.589 | 1.00 |
| 116_W | 153_S | 3.468 | 1.00 |
| 45_M | 98_R | 3.219 | 1.00 |
| 141_P | 147_V | 2.841 | 1.00 |
| 70_Q | 179_F | 2.600 | 1.00 |
| 124_G | 170_T | 2.589 | 1.00 |
| 74_A | 96_V | 2.523 | 1.00 |
| 49_G | 96_V | 2.494 | 1.00 |
| 89_G | 134_Q | 2.464 | 1.00 |
| 44_Q | 143_S | 2.364 | 1.00 |
| 48_F | 111_L | 2.320 | 1.00 |
| 116_W | 154_K | 2.317 | 1.00 |
| 154_K | 173_I | 2.297 | 1.00 |
| 141_P | 175_E | 2.202 | 1.00 |
| 75_G | 138_A | 2.166 | 1.00 |
| 47_V | 98_R | 2.135 | 1.00 |
| 50_M | 56_A | 2.110 | 1.00 |
| 63_L | 114_V | 2.096 | 1.00 |
| 63_L | 106_I | 2.052 | 1.00 |
| 78_T | 85_E | 2.012 | 1.00 |
| 94_A | 136_R | 2.007 | 1.00 |
| 94_A | 138_A | 1.993 | 1.00 |
| 109_E | 149_A | 1.883 | 1.00 |
| 29_H | 191_S | 1.862 | 1.00 |
| 70_Q | 98_R | 1.806 | 1.00 |
| 56_A | 118_N | 1.805 | 1.00 |
| 82_T | 85_E | 1.797 | 1.00 |
| 119_H | 137_S | 1.776 | 1.00 |
| 44_Q | 146_H | 1.736 | 1.00 |
| 44_Q | 101_F | 1.735 | 1.00 |
| 74_A | 176_G | 1.711 | 1.00 |
| 123_Q | 126_R | 1.642 | 1.00 |
| 47_V | 96_V | 1.592 | 1.00 |
| 139_I | 150_A | 1.591 | 1.00 |
| 53_F | 73_F | 1.574 | 1.00 |
| 47_V | 74_A | 1.571 | 1.00 |
| 148_G | 152_K | 1.552 | 1.00 |
| 61_W | 69_T | 1.548 | 1.00 |
| 55_G | 190_L | 1.546 | 1.00 |
| 76_G | 93_H | 1.473 | 1.00 |
| 64_K | 105_H | 1.471 | 1.00 |
| 107_S | 110_E | 1.444 | 1.00 |
| 43_T | 67_Y | 1.423 | 1.00 |
| 126_R | 131_H | 1.420 | 1.00 |
| 70_Q | 181_Y | 1.412 | 1.00 |
| 50_M | 118_N | 1.396 | 0.99 |
| 48_F | 108_F | 1.394 | 0.99 |
| 152_K | 156_D | 1.391 | 0.99 |
| 70_Q | 100_V | 1.378 | 0.99 |
| 43_T | 103_P | 1.378 | 0.99 |
| 71_V | 187_Q | 1.376 | 0.99 |
| 184_D | 192_K | 1.364 | 0.99 |
| 10_S | 13_E | 1.354 | 0.99 |
| 144_A | 147_V | 1.322 | 0.99 |
| 74_A | 177_Q | 1.317 | 0.99 |
| 112_L | 149_A | 1.298 | 0.99 |
| 84_K | 185_Y | 1.296 | 0.99 |
| 142_T | 146_H | 1.293 | 0.99 |
| 137_S | 171_T | 1.278 | 0.99 |
| 86_V | 91_T | 1.251 | 0.99 |
| 48_F | 60_F | 1.246 | 0.98 |
| 102_Q | 105_H | 1.232 | 0.98 |
| 158_Q | 169_I | 1.216 | 0.98 |
| 136_R | 172_D | 1.210 | 0.98 |
| 110_E | 113_K | 1.200 | 0.98 |
| 8_I | 77_Y | 1.199 | 0.98 |
| 57_E | 61_W | 1.191 | 0.98 |
| 109_E | 152_K | 1.183 | 0.98 |
| 47_V | 176_G | 1.178 | 0.98 |
| 48_F | 112_L | 1.158 | 0.97 |
| 87_C | 134_Q | 1.147 | 0.97 |
| 140_Y | 172_D | 1.129 | 0.97 |
| 49_G | 138_A | 1.126 | 0.97 |
| 73_F | 183_E | 1.120 | 0.96 |
| 101_F | 146_H | 1.116 | 0.96 |
| 71_V | 188_Q | 1.109 | 0.96 |
| 59_K | 118_N | 1.078 | 0.95 |
| 155_E | 159_K | 1.061 | 0.95 |
| 88_S | 91_T | 1.053 | 0.95 |
| 125_M | 133_S | 1.051 | 0.94 |
| 45_M | 142_T | 1.045 | 0.94 |
| 61_W | 191_S | 1.038 | 0.94 |
| 151_L | 154_K | 1.029 | 0.94 |
| 141_P | 173_I | 1.025 | 0.93 |
| 158_Q | 162_S | 1.013 | 0.93 |
| 61_W | 188_Q | 1.012 | 0.93 |
| 108_F | 146_H | 1.011 | 0.93 |
| 94_A | 174_R | 1.006 | 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 | |
| 1fvgA | 1 | 0.9648 | 100 | 0.045 | Contact Map |
| 1ff3A | 3 | 0.9849 | 100 | 0.05 | Contact Map |
| 4d7lA | 3 | 0.9648 | 100 | 0.059 | Contact Map |
| 3bqhA | 1 | 0.7688 | 100 | 0.163 | Contact Map |
| 2j89A | 1 | 0.8392 | 100 | 0.168 | Contact Map |
| 3pimA | 3 | 0.8191 | 100 | 0.175 | Contact Map |
| 3e0mA | 4 | 0.7638 | 100 | 0.178 | Contact Map |
| 1nwaA | 1 | 0.7839 | 100 | 0.217 | Contact Map |
| 4gwbA | 1 | 0.7588 | 100 | 0.221 | Contact Map |
| 4lwlA | 1 | 0.7236 | 100 | 0.269 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)