| 1gv8 |
| ID: | 1453971300 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 159 (159) | ||
| Sequences: | 748 (426.6) | ||
| Seq/Len: | 4.704 | ||
| Nf(neff/√len): | 33.8 |
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: 4.704).
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 |
| 135_E | 143_R | 3.210 | 1.00 |
| 98_Y | 103_G | 2.612 | 1.00 |
| 100_G | 103_G | 2.496 | 1.00 |
| 23_T | 83_Q | 2.415 | 1.00 |
| 27_T | 31_R | 2.246 | 1.00 |
| 2_Y | 119_K | 2.151 | 1.00 |
| 99_S | 103_G | 2.101 | 1.00 |
| 98_Y | 104_A | 1.934 | 1.00 |
| 10_K | 135_E | 1.771 | 1.00 |
| 138_C | 152_C | 1.743 | 1.00 |
| 98_Y | 105_F | 1.709 | 0.99 |
| 42_L | 46_G | 1.679 | 0.99 |
| 106_Q | 110_D | 1.656 | 0.99 |
| 68_A | 82_R | 1.643 | 0.99 |
| 100_G | 104_A | 1.595 | 0.99 |
| 102_S | 105_F | 1.586 | 0.99 |
| 101_Y | 104_A | 1.583 | 0.99 |
| 90_T | 93_L | 1.573 | 0.99 |
| 109_K | 134_Y | 1.502 | 0.98 |
| 27_T | 32_S | 1.487 | 0.98 |
| 28_G | 31_R | 1.486 | 0.98 |
| 130_E | 133_E | 1.484 | 0.98 |
| 90_T | 103_G | 1.478 | 0.98 |
| 148_S | 151_T | 1.464 | 0.98 |
| 105_F | 127_A | 1.453 | 0.98 |
| 119_K | 122_T | 1.447 | 0.98 |
| 137_L | 143_R | 1.417 | 0.97 |
| 34_G | 38_P | 1.400 | 0.97 |
| 9_K | 111_G | 1.396 | 0.97 |
| 135_E | 145_P | 1.375 | 0.97 |
| 81_C | 84_C | 1.373 | 0.97 |
| 90_T | 104_A | 1.364 | 0.96 |
| 98_Y | 101_Y | 1.355 | 0.96 |
| 70_C | 84_C | 1.342 | 0.96 |
| 71_V | 78_Q | 1.340 | 0.96 |
| 99_S | 104_A | 1.326 | 0.96 |
| 69_S | 80_L | 1.306 | 0.95 |
| 98_Y | 110_D | 1.287 | 0.95 |
| 137_L | 141_G | 1.285 | 0.94 |
| 19_L | 115_V | 1.263 | 0.94 |
| 63_A | 80_L | 1.258 | 0.94 |
| 3_Y | 120_H | 1.253 | 0.93 |
| 92_C | 99_S | 1.250 | 0.93 |
| 27_T | 34_G | 1.231 | 0.93 |
| 66_F | 70_C | 1.227 | 0.93 |
| 120_H | 149_Y | 1.191 | 0.91 |
| 107_C | 113_G | 1.187 | 0.91 |
| 90_T | 96_A | 1.185 | 0.91 |
| 32_S | 36_N | 1.179 | 0.90 |
| 98_Y | 102_S | 1.174 | 0.90 |
| 99_S | 105_F | 1.167 | 0.90 |
| 96_A | 99_S | 1.158 | 0.89 |
| 140_D | 144_Q | 1.156 | 0.89 |
| 27_T | 119_K | 1.150 | 0.89 |
| 99_S | 102_S | 1.140 | 0.88 |
| 100_G | 105_F | 1.140 | 0.88 |
| 102_S | 126_N | 1.121 | 0.87 |
| 29_L | 71_V | 1.117 | 0.87 |
| 1_S | 159_A | 1.114 | 0.87 |
| 136_L | 153_N | 1.106 | 0.86 |
| 14_F | 18_D | 1.098 | 0.86 |
| 25_C | 107_C | 1.094 | 0.85 |
| 23_T | 114_D | 1.078 | 0.84 |
| 90_T | 98_Y | 1.077 | 0.84 |
| 4_A | 34_G | 1.070 | 0.84 |
| 139_L | 142_T | 1.062 | 0.83 |
| 115_V | 125_E | 1.049 | 0.82 |
| 7_V | 118_V | 1.047 | 0.82 |
| 140_D | 148_S | 1.046 | 0.82 |
| 37_I | 155_A | 1.043 | 0.81 |
| 64_K | 79_K | 1.041 | 0.81 |
| 101_Y | 105_F | 1.039 | 0.81 |
| 131_K | 147_D | 1.029 | 0.80 |
| 120_H | 157_V | 1.026 | 0.80 |
| 22_K | 110_D | 1.026 | 0.80 |
| 32_S | 40_G | 1.021 | 0.80 |
| 93_L | 96_A | 1.019 | 0.79 |
| 62_V | 71_V | 1.008 | 0.78 |
| 23_T | 130_E | 1.008 | 0.78 |
| 9_K | 22_K | 1.007 | 0.78 |
| 27_T | 36_N | 1.004 | 0.78 |
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 | |
| 2d3iA | 1 | 1 | 100 | 0.111 | Contact Map |
| 1cb6A | 1 | 0.9811 | 100 | 0.118 | Contact Map |
| 3mc2A | 4 | 0.9245 | 100 | 0.122 | Contact Map |
| 1blfA | 1 | 0.9811 | 100 | 0.131 | Contact Map |
| 3todA | 1 | 0.9308 | 100 | 0.161 | Contact Map |
| 1h45A | 1 | 0.9811 | 100 | 0.166 | Contact Map |
| 3skpA | 1 | 0.9245 | 100 | 0.18 | Contact Map |
| 3v83A | 6 | 0.9497 | 100 | 0.194 | Contact Map |
| 1ryoA | 1 | 0.9497 | 100 | 0.211 | Contact Map |
| 1iejA | 1 | 1 | 100 | 0.221 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)