| 2o72 |
| ID: | 1408343592 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 213 (204) | ||
| Sequences: | 5082 (3375.5) | ||
| Seq/Len: | 24.912 | ||
| Nf(neff/√len): | 236.3 |
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: 24.912).
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 |
| 115_G | 128_M | 4.583 | 1.00 |
| 68_R | 72_A | 3.434 | 1.00 |
| 146_I | 193_A | 3.297 | 1.00 |
| 68_R | 137_D | 2.999 | 1.00 |
| 181_R | 185_P | 2.937 | 1.00 |
| 105_K | 201_L | 2.927 | 1.00 |
| 54_E | 57_T | 2.427 | 1.00 |
| 34_V | 80_A | 2.416 | 1.00 |
| 7_I | 22_V | 2.365 | 1.00 |
| 26_S | 29_D | 2.320 | 1.00 |
| 151_L | 192_Q | 2.125 | 1.00 |
| 147_A | 196_L | 2.122 | 1.00 |
| 12_N | 101_Q | 2.022 | 1.00 |
| 132_A | 148_Y | 1.978 | 1.00 |
| 142_Y | 145_A | 1.928 | 1.00 |
| 138_D | 144_A | 1.898 | 1.00 |
| 126_S | 171_V | 1.865 | 1.00 |
| 165_I | 172_I | 1.865 | 1.00 |
| 39_T | 79_H | 1.856 | 1.00 |
| 164_T | 173_S | 1.847 | 1.00 |
| 53_I | 60_L | 1.840 | 1.00 |
| 69_E | 103_D | 1.792 | 1.00 |
| 172_I | 207_A | 1.752 | 1.00 |
| 118_M | 212_T | 1.731 | 1.00 |
| 108_F | 193_A | 1.729 | 1.00 |
| 149_T | 192_Q | 1.717 | 1.00 |
| 35_F | 83_S | 1.686 | 1.00 |
| 100_D | 103_D | 1.681 | 1.00 |
| 62_V | 66_L | 1.672 | 1.00 |
| 116_S | 210_T | 1.635 | 1.00 |
| 36_Y | 80_A | 1.633 | 1.00 |
| 119_E | 182_E | 1.630 | 1.00 |
| 108_F | 113_F | 1.600 | 1.00 |
| 102_N | 195_D | 1.595 | 1.00 |
| 110_Q | 113_F | 1.549 | 1.00 |
| 119_E | 180_D | 1.529 | 1.00 |
| 121_A | 174_V | 1.527 | 1.00 |
| 166_N | 169_T | 1.524 | 1.00 |
| 67_D | 103_D | 1.522 | 1.00 |
| 184_F | 187_Y | 1.512 | 1.00 |
| 192_Q | 204_T | 1.492 | 1.00 |
| 114_K | 210_T | 1.488 | 1.00 |
| 36_Y | 58_G | 1.484 | 1.00 |
| 174_V | 179_L | 1.451 | 1.00 |
| 50_V | 74_Y | 1.447 | 1.00 |
| 104_N | 135_A | 1.436 | 1.00 |
| 66_L | 98_V | 1.435 | 1.00 |
| 181_R | 213_D | 1.431 | 1.00 |
| 84_N | 88_V | 1.429 | 1.00 |
| 182_E | 213_D | 1.424 | 1.00 |
| 54_E | 58_G | 1.424 | 1.00 |
| 10_P | 99_T | 1.420 | 1.00 |
| 60_L | 94_I | 1.406 | 0.99 |
| 71_I | 74_Y | 1.394 | 0.99 |
| 75_T | 95_L | 1.390 | 0.99 |
| 192_Q | 202_S | 1.387 | 0.99 |
| 127_V | 174_V | 1.377 | 0.99 |
| 129_E | 171_V | 1.369 | 0.99 |
| 72_A | 137_D | 1.338 | 0.99 |
| 81_V | 89_E | 1.336 | 0.99 |
| 121_A | 125_T | 1.323 | 0.99 |
| 189_L | 207_A | 1.320 | 0.99 |
| 107_E | 135_A | 1.317 | 0.99 |
| 191_V | 207_A | 1.303 | 0.99 |
| 109_T | 131_T | 1.287 | 0.99 |
| 29_D | 32_G | 1.286 | 0.99 |
| 113_F | 205_A | 1.248 | 0.99 |
| 179_L | 211_V | 1.239 | 0.98 |
| 38_I | 41_Q | 1.239 | 0.98 |
| 126_S | 129_E | 1.228 | 0.98 |
| 116_S | 212_T | 1.211 | 0.98 |
| 25_K | 29_D | 1.199 | 0.98 |
| 78_S | 94_I | 1.194 | 0.98 |
| 62_V | 98_V | 1.191 | 0.98 |
| 27_N | 32_G | 1.191 | 0.98 |
| 132_A | 146_I | 1.183 | 0.98 |
| 194_A | 200_G | 1.167 | 0.97 |
| 166_N | 173_S | 1.166 | 0.97 |
| 119_E | 181_R | 1.163 | 0.97 |
| 186_T | 208_V | 1.162 | 0.97 |
| 166_N | 170_G | 1.154 | 0.97 |
| 73_T | 97_T | 1.150 | 0.97 |
| 27_N | 82_S | 1.144 | 0.97 |
| 108_F | 205_A | 1.136 | 0.97 |
| 164_T | 175_V | 1.136 | 0.97 |
| 41_Q | 76_L | 1.130 | 0.97 |
| 54_E | 61_K | 1.117 | 0.96 |
| 68_R | 100_D | 1.111 | 0.96 |
| 162_M | 187_Y | 1.107 | 0.96 |
| 148_Y | 193_A | 1.107 | 0.96 |
| 150_I | 153_Q | 1.106 | 0.96 |
| 20_N | 23_Q | 1.094 | 0.96 |
| 13_E | 62_V | 1.085 | 0.96 |
| 108_F | 132_A | 1.081 | 0.95 |
| 180_D | 213_D | 1.076 | 0.95 |
| 197_Q | 201_L | 1.075 | 0.95 |
| 54_E | 59_W | 1.075 | 0.95 |
| 52_I | 61_K | 1.070 | 0.95 |
| 149_T | 194_A | 1.051 | 0.94 |
| 52_I | 63_T | 1.045 | 0.94 |
| 51_F | 66_L | 1.041 | 0.94 |
| 68_R | 103_D | 1.035 | 0.94 |
| 145_A | 196_L | 1.031 | 0.94 |
| 79_H | 91_P | 1.030 | 0.94 |
| 100_D | 104_N | 1.026 | 0.94 |
| 20_N | 59_W | 1.022 | 0.93 |
| 194_A | 202_S | 1.013 | 0.93 |
| 8_S | 97_T | 1.011 | 0.93 |
| 147_A | 167_R | 1.006 | 0.93 |
| 69_E | 100_D | 1.002 | 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
- 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 | |
| 3qrbA | 2 | 1 | 100 | 0.089 | Contact Map |
| 2qviA | 1 | 0.9953 | 100 | 0.09 | Contact Map |
| 3k5rA | 2 | 0.9812 | 100 | 0.114 | Contact Map |
| 1q55A | 4 | 1 | 100 | 0.115 | Contact Map |
| 3q2wA | 1 | 0.9953 | 100 | 0.118 | Contact Map |
| 3q2vA | 2 | 1 | 100 | 0.12 | Contact Map |
| 3lndA | 4 | 0.9437 | 100 | 0.121 | Contact Map |
| 1l3wA | 1 | 1 | 100 | 0.124 | Contact Map |
| 3ppeA | 2 | 0.9202 | 100 | 0.148 | Contact Map |
| 2a4eA | 1 | 0.9531 | 100 | 0.158 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)