| test |
| ID: | 1490181598 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 151 (150) | ||
| Sequences: | 1282 (1221.8) | ||
| Seq/Len: | 8.547 | ||
| Nf(neff/√len): | 99.8 |
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: 8.547).
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 |
| 65_K | 68_D | 2.565 | 1.00 |
| 142_L | 145_H | 2.316 | 1.00 |
| 64_G | 68_D | 2.269 | 1.00 |
| 139_D | 142_L | 2.231 | 1.00 |
| 27_D | 30_G | 2.170 | 1.00 |
| 53_Q | 57_E | 1.983 | 1.00 |
| 123_K | 126_T | 1.903 | 1.00 |
| 58_Q | 61_T | 1.889 | 1.00 |
| 144_T | 147_D | 1.889 | 1.00 |
| 50_I | 54_K | 1.794 | 1.00 |
| 94_L | 97_E | 1.703 | 1.00 |
| 6_S | 9_A | 1.670 | 1.00 |
| 12_W | 16_H | 1.646 | 1.00 |
| 108_E | 111_R | 1.644 | 1.00 |
| 57_E | 60_K | 1.638 | 1.00 |
| 61_T | 65_K | 1.619 | 1.00 |
| 45_C | 49_C | 1.592 | 1.00 |
| 30_G | 34_N | 1.571 | 1.00 |
| 112_I | 115_L | 1.543 | 1.00 |
| 26_R | 30_G | 1.539 | 1.00 |
| 107_N | 110_K | 1.533 | 1.00 |
| 92_K | 96_L | 1.496 | 1.00 |
| 140_K | 144_T | 1.495 | 1.00 |
| 13_M | 16_H | 1.454 | 0.99 |
| 113_E | 116_L | 1.425 | 0.99 |
| 117_E | 120_G | 1.425 | 0.99 |
| 6_S | 12_W | 1.420 | 0.99 |
| 57_E | 61_T | 1.409 | 0.99 |
| 136_K | 140_K | 1.405 | 0.99 |
| 95_L | 98_I | 1.394 | 0.99 |
| 138_A | 143_K | 1.379 | 0.99 |
| 96_L | 99_I | 1.367 | 0.99 |
| 142_L | 146_T | 1.366 | 0.99 |
| 50_I | 53_Q | 1.338 | 0.99 |
| 111_R | 114_A | 1.338 | 0.99 |
| 68_D | 72_K | 1.321 | 0.99 |
| 136_K | 139_D | 1.317 | 0.99 |
| 145_H | 148_D | 1.315 | 0.99 |
| 27_D | 31_R | 1.313 | 0.99 |
| 132_Q | 135_Q | 1.302 | 0.99 |
| 20_I | 24_K | 1.293 | 0.98 |
| 94_L | 98_I | 1.292 | 0.98 |
| 127_I | 131_L | 1.277 | 0.98 |
| 17_D | 20_I | 1.275 | 0.98 |
| 3_K | 6_S | 1.271 | 0.98 |
| 139_D | 143_K | 1.263 | 0.98 |
| 122_G | 126_T | 1.237 | 0.98 |
| 99_I | 102_T | 1.230 | 0.98 |
| 44_G | 48_K | 1.224 | 0.98 |
| 16_H | 20_I | 1.224 | 0.98 |
| 69_H | 72_K | 1.208 | 0.97 |
| 46_N | 50_I | 1.197 | 0.97 |
| 9_A | 13_M | 1.197 | 0.97 |
| 6_S | 13_M | 1.191 | 0.97 |
| 8_N | 12_W | 1.189 | 0.97 |
| 84_D | 88_T | 1.178 | 0.97 |
| 92_K | 95_L | 1.167 | 0.96 |
| 70_F | 73_Q | 1.162 | 0.96 |
| 4_I | 9_A | 1.162 | 0.96 |
| 54_K | 57_E | 1.160 | 0.96 |
| 69_H | 74_K | 1.159 | 0.96 |
| 60_K | 64_G | 1.147 | 0.96 |
| 97_E | 100_Q | 1.143 | 0.96 |
| 108_E | 112_I | 1.124 | 0.95 |
| 113_E | 117_E | 1.110 | 0.95 |
| 115_L | 118_Q | 1.106 | 0.95 |
| 103_Y | 106_A | 1.092 | 0.94 |
| 116_L | 119_A | 1.086 | 0.94 |
| 85_F | 88_T | 1.079 | 0.94 |
| 82_H | 85_F | 1.068 | 0.93 |
| 44_G | 47_K | 1.066 | 0.93 |
| 13_M | 17_D | 1.051 | 0.93 |
| 47_K | 50_I | 1.050 | 0.93 |
| 5_M | 13_M | 1.044 | 0.92 |
| 140_K | 143_K | 1.043 | 0.92 |
| 130_L | 133_H | 1.041 | 0.92 |
| 109_I | 112_I | 1.036 | 0.92 |
| 9_A | 16_H | 1.034 | 0.92 |
| 7_Y | 13_M | 1.023 | 0.91 |
| 139_D | 144_T | 1.020 | 0.91 |
| 110_K | 113_E | 1.020 | 0.91 |
| 95_L | 99_I | 1.018 | 0.91 |
| 143_K | 146_T | 1.011 | 0.91 |
| 26_R | 31_R | 1.011 | 0.91 |
| 99_I | 103_Y | 1.008 | 0.91 |
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 | |
| 3c64A | 1 | 0.8874 | 100 | 0.035 | Contact Map |
| 2yk0A | 1 | 0.9404 | 100 | 0.053 | Contact Map |
| 4v3dA | 2 | 0.9139 | 100 | 0.094 | Contact Map |
| 1zroA | 2 | 0.9338 | 98.9 | 0.715 | Contact Map |
| 4gf2A | 1 | 0.9205 | 98.8 | 0.728 | Contact Map |
| 2xu0A | 1 | 0.9272 | 98.6 | 0.743 | Contact Map |
| 3rrcA | 2 | 0.8013 | 98.6 | 0.746 | Contact Map |
| 4p1tA | 1 | 0.6225 | 98.6 | 0.747 | Contact Map |
| 3vuvA | 1 | 0.6689 | 98.4 | 0.76 | Contact Map |
| 3vuuA | 1 | 0.6821 | 98.3 | 0.767 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)