| 4hi0B |
| ID: | 1491917858 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 255 (252) | ||
| Sequences: | 1720 (1233.8) | ||
| Seq/Len: | 6.825 | ||
| Nf(neff/√len): | 77.7 |
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: 6.825).
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 |
| 96_V | 100_A | 4.163 | 1.00 |
| 125_L | 129_S | 3.515 | 1.00 |
| 64_I | 68_C | 3.162 | 1.00 |
| 123_I | 131_L | 3.052 | 1.00 |
| 66_P | 97_G | 2.927 | 1.00 |
| 122_T | 158_S | 2.845 | 1.00 |
| 9_T | 70_L | 2.730 | 1.00 |
| 64_I | 100_A | 2.722 | 1.00 |
| 98_E | 128_S | 2.704 | 1.00 |
| 96_V | 125_L | 2.700 | 1.00 |
| 141_R | 146_E | 2.676 | 1.00 |
| 99_N | 128_S | 2.561 | 1.00 |
| 63_N | 97_G | 2.531 | 1.00 |
| 124_S | 160_L | 2.507 | 1.00 |
| 165_P | 168_Y | 2.493 | 1.00 |
| 191_H | 241_L | 2.400 | 1.00 |
| 127_S | 162_D | 2.263 | 1.00 |
| 8_K | 65_G | 2.262 | 1.00 |
| 111_P | 115_A | 2.170 | 1.00 |
| 235_A | 241_L | 2.149 | 1.00 |
| 66_P | 98_E | 2.098 | 1.00 |
| 6_R | 21_D | 2.066 | 1.00 |
| 93_H | 124_S | 1.971 | 1.00 |
| 98_E | 126_R | 1.924 | 1.00 |
| 64_I | 96_V | 1.910 | 1.00 |
| 128_S | 161_Q | 1.889 | 1.00 |
| 61_Q | 93_H | 1.885 | 1.00 |
| 9_T | 43_I | 1.866 | 1.00 |
| 62_L | 94_I | 1.845 | 1.00 |
| 233_A | 241_L | 1.773 | 1.00 |
| 63_N | 95_V | 1.768 | 1.00 |
| 69_K | 101_F | 1.758 | 1.00 |
| 103_D | 253_T | 1.747 | 1.00 |
| 204_L | 208_R | 1.746 | 1.00 |
| 67_N | 99_N | 1.724 | 1.00 |
| 116_H | 152_R | 1.707 | 1.00 |
| 62_L | 72_I | 1.683 | 1.00 |
| 132_L | 195_L | 1.678 | 1.00 |
| 95_V | 124_S | 1.657 | 1.00 |
| 207_V | 248_I | 1.646 | 1.00 |
| 204_L | 220_A | 1.633 | 1.00 |
| 6_R | 61_Q | 1.608 | 1.00 |
| 160_L | 165_P | 1.595 | 1.00 |
| 197_L | 252_V | 1.585 | 1.00 |
| 108_P | 242_L | 1.583 | 1.00 |
| 91_D | 120_N | 1.566 | 1.00 |
| 54_R | 83_T | 1.556 | 0.99 |
| 68_C | 100_A | 1.547 | 0.99 |
| 64_I | 102_L | 1.524 | 0.99 |
| 52_M | 88_A | 1.515 | 0.99 |
| 31_M | 46_L | 1.506 | 0.99 |
| 96_V | 129_S | 1.480 | 0.99 |
| 10_K | 20_E | 1.471 | 0.99 |
| 231_V | 248_I | 1.447 | 0.99 |
| 93_H | 122_T | 1.446 | 0.99 |
| 132_L | 197_L | 1.440 | 0.99 |
| 65_G | 97_G | 1.413 | 0.99 |
| 198_V | 228_H | 1.377 | 0.98 |
| 223_E | 228_H | 1.374 | 0.98 |
| 159_I | 196_V | 1.367 | 0.98 |
| 9_T | 19_I | 1.361 | 0.98 |
| 9_T | 68_C | 1.356 | 0.98 |
| 124_S | 163_E | 1.351 | 0.98 |
| 154_H | 170_N | 1.351 | 0.98 |
| 122_T | 160_L | 1.333 | 0.98 |
| 101_F | 130_Q | 1.330 | 0.98 |
| 169_D | 232_K | 1.313 | 0.98 |
| 71_R | 103_D | 1.310 | 0.98 |
| 11_I | 14_D | 1.306 | 0.98 |
| 136_I | 193_L | 1.284 | 0.97 |
| 29_K | 46_L | 1.281 | 0.97 |
| 94_I | 102_L | 1.262 | 0.97 |
| 137_I | 192_Y | 1.257 | 0.97 |
| 121_T | 157_I | 1.219 | 0.96 |
| 9_T | 17_C | 1.217 | 0.96 |
| 28_F | 60_V | 1.187 | 0.95 |
| 94_I | 123_I | 1.180 | 0.95 |
| 123_I | 133_Y | 1.180 | 0.95 |
| 49_S | 75_Q | 1.178 | 0.95 |
| 50_P | 53_M | 1.177 | 0.95 |
| 237_G | 240_P | 1.173 | 0.95 |
| 52_M | 117_F | 1.161 | 0.94 |
| 52_M | 58_Q | 1.132 | 0.93 |
| 139_A | 192_Y | 1.131 | 0.93 |
| 140_G | 146_E | 1.121 | 0.93 |
| 189_Y | 236_K | 1.117 | 0.93 |
| 138_V | 238_S | 1.108 | 0.92 |
| 137_I | 153_L | 1.098 | 0.92 |
| 53_M | 88_A | 1.088 | 0.91 |
| 4_K | 25_T | 1.077 | 0.91 |
| 64_I | 70_L | 1.072 | 0.91 |
| 54_R | 84_E | 1.071 | 0.91 |
| 118_K | 154_H | 1.066 | 0.90 |
| 97_G | 126_R | 1.049 | 0.89 |
| 249_A | 253_T | 1.048 | 0.89 |
| 45_L | 60_V | 1.046 | 0.89 |
| 195_L | 231_V | 1.041 | 0.89 |
| 56_D | 141_R | 1.039 | 0.89 |
| 79_K | 141_R | 1.036 | 0.89 |
| 48_V | 76_S | 1.031 | 0.88 |
| 40_L | 71_R | 1.030 | 0.88 |
| 92_M | 121_T | 1.029 | 0.88 |
| 120_N | 158_S | 1.025 | 0.88 |
| 50_P | 81_H | 1.017 | 0.87 |
| 3_S | 50_P | 1.014 | 0.87 |
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 | |
| 4hi0B | 2 | 0.9922 | 100 | 0.065 | Contact Map |
| 2k6wA | 1 | 0.3059 | 26.5 | 0.952 | Contact Map |
| 1x9lA | 1 | 0.3216 | 10.6 | 0.96 | Contact Map |
| 3zjaA | 1 | 0.3098 | 8.7 | 0.961 | Contact Map |
| 2zbcA | 8 | 0.2549 | 7.8 | 0.962 | Contact Map |
| 2cviA | 2 | 0.2588 | 6.1 | 0.964 | Contact Map |
| 2djwA | 10 | 0.2588 | 4.3 | 0.967 | Contact Map |
| 2jsxA | 1 | 0.2549 | 4 | 0.967 | Contact Map |
| 2pkhA | 8 | 0.2392 | 3.5 | 0.968 | Contact Map |
| 2xkoC | 2 | 0.2667 | 3.4 | 0.968 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)