| more optimized |
| ID: | 1387788027 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 192 (192) | ||
| Sequences: | 9646 (7466.8) | ||
| Seq/Len: | 50.240 | ||
| Nf(neff/√len): | 538.9 |
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: 50.240).
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 |
| 36_K | 95_T | 3.139 | 1.00 |
| 74_K | 78_E | 2.837 | 1.00 |
| 37_D | 41_G | 2.820 | 1.00 |
| 144_R | 163_D | 2.765 | 1.00 |
| 104_H | 117_D | 2.702 | 1.00 |
| 14_T | 38_T | 2.480 | 1.00 |
| 2_V | 76_I | 2.357 | 1.00 |
| 2_V | 77_I | 2.347 | 1.00 |
| 113_R | 120_E | 2.321 | 1.00 |
| 132_I | 136_K | 2.319 | 1.00 |
| 107_I | 135_A | 2.313 | 1.00 |
| 47_L | 88_S | 2.277 | 1.00 |
| 73_C | 84_I | 2.207 | 1.00 |
| 160_R | 163_D | 2.146 | 1.00 |
| 30_E | 99_K | 2.140 | 1.00 |
| 86_V | 96_F | 2.115 | 1.00 |
| 51_F | 84_I | 2.084 | 1.00 |
| 133_Y | 147_L | 2.079 | 1.00 |
| 19_E | 38_T | 2.067 | 1.00 |
| 85_D | 97_I | 2.002 | 1.00 |
| 34_Y | 95_T | 1.979 | 1.00 |
| 106_E | 115_L | 1.963 | 1.00 |
| 77_I | 82_G | 1.881 | 1.00 |
| 49_Q | 52_D | 1.865 | 1.00 |
| 87_K | 97_I | 1.838 | 1.00 |
| 89_E | 92_K | 1.838 | 1.00 |
| 34_Y | 97_I | 1.802 | 1.00 |
| 21_A | 36_K | 1.784 | 1.00 |
| 77_I | 98_I | 1.763 | 1.00 |
| 165_H | 168_R | 1.761 | 1.00 |
| 23_T | 34_Y | 1.758 | 1.00 |
| 43_A | 46_H | 1.743 | 1.00 |
| 23_T | 36_K | 1.735 | 1.00 |
| 112_H | 129_E | 1.731 | 1.00 |
| 88_S | 94_T | 1.700 | 1.00 |
| 183_Q | 191_K | 1.697 | 1.00 |
| 18_D | 38_T | 1.692 | 1.00 |
| 108_D | 111_A | 1.679 | 1.00 |
| 137_T | 140_K | 1.675 | 1.00 |
| 32_I | 99_K | 1.658 | 1.00 |
| 87_K | 95_T | 1.636 | 1.00 |
| 27_N | 32_I | 1.632 | 1.00 |
| 126_K | 129_E | 1.631 | 1.00 |
| 14_T | 18_D | 1.626 | 1.00 |
| 42_I | 50_V | 1.600 | 1.00 |
| 138_P | 142_F | 1.593 | 1.00 |
| 76_I | 80_H | 1.579 | 1.00 |
| 21_A | 38_T | 1.557 | 1.00 |
| 25_D | 32_I | 1.552 | 1.00 |
| 8_D | 12_R | 1.540 | 1.00 |
| 46_H | 57_V | 1.529 | 1.00 |
| 47_L | 86_V | 1.529 | 1.00 |
| 25_D | 34_Y | 1.473 | 1.00 |
| 46_H | 55_Y | 1.469 | 1.00 |
| 133_Y | 150_E | 1.434 | 1.00 |
| 83_S | 99_K | 1.428 | 1.00 |
| 82_G | 100_L | 1.424 | 1.00 |
| 115_L | 120_E | 1.422 | 1.00 |
| 5_N | 73_C | 1.419 | 1.00 |
| 107_I | 128_Y | 1.388 | 0.99 |
| 32_I | 97_I | 1.382 | 0.99 |
| 185_V | 191_K | 1.368 | 0.99 |
| 3_L | 33_L | 1.367 | 0.99 |
| 44_P | 47_L | 1.355 | 0.99 |
| 176_S | 179_A | 1.348 | 0.99 |
| 127_E | 172_K | 1.347 | 0.99 |
| 109_N | 132_I | 1.331 | 0.99 |
| 58_D | 61_R | 1.304 | 0.99 |
| 50_V | 86_V | 1.264 | 0.99 |
| 112_H | 188_V | 1.256 | 0.99 |
| 107_I | 114_V | 1.235 | 0.98 |
| 133_Y | 142_F | 1.219 | 0.98 |
| 140_K | 146_Q | 1.214 | 0.98 |
| 42_I | 94_T | 1.192 | 0.98 |
| 124_T | 172_K | 1.187 | 0.98 |
| 2_V | 98_I | 1.176 | 0.98 |
| 85_D | 99_K | 1.167 | 0.97 |
| 114_V | 121_V | 1.165 | 0.97 |
| 37_D | 93_G | 1.163 | 0.97 |
| 46_H | 49_Q | 1.161 | 0.97 |
| 13_Y | 56_K | 1.148 | 0.97 |
| 107_I | 132_I | 1.144 | 0.97 |
| 115_L | 118_N | 1.142 | 0.97 |
| 110_D | 140_K | 1.141 | 0.97 |
| 78_E | 83_S | 1.138 | 0.97 |
| 133_Y | 137_T | 1.136 | 0.97 |
| 102_F | 192_F | 1.136 | 0.97 |
| 88_S | 92_K | 1.134 | 0.97 |
| 2_V | 73_C | 1.134 | 0.97 |
| 177_E | 180_H | 1.123 | 0.97 |
| 33_L | 98_I | 1.122 | 0.97 |
| 86_V | 94_T | 1.113 | 0.96 |
| 30_E | 83_S | 1.109 | 0.96 |
| 56_K | 65_G | 1.103 | 0.96 |
| 102_F | 135_A | 1.088 | 0.96 |
| 105_L | 114_V | 1.087 | 0.96 |
| 49_Q | 55_Y | 1.075 | 0.95 |
| 142_F | 146_Q | 1.066 | 0.95 |
| 143_D | 146_Q | 1.056 | 0.95 |
| 167_K | 171_E | 1.054 | 0.95 |
| 37_D | 94_T | 1.049 | 0.94 |
| 77_I | 84_I | 1.048 | 0.94 |
| 161_T | 165_H | 1.040 | 0.94 |
| 104_H | 116_A | 1.034 | 0.94 |
| 126_K | 152_W | 1.029 | 0.94 |
| 4_T | 8_D | 1.022 | 0.93 |
| 82_G | 98_I | 1.015 | 0.93 |
| 112_H | 128_Y | 1.008 | 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 | |
| 4i5sA | 2 | 0.5156 | 100 | 0.557 | Contact Map |
| 2e0aA | 2 | 0.625 | 100 | 0.564 | Contact Map |
| 2c2aA | 1 | 0.5052 | 99.9 | 0.573 | Contact Map |
| 4e01A | 1 | 0.5156 | 99.9 | 0.573 | Contact Map |
| 1y8oA | 1 | 0.7031 | 99.9 | 0.578 | Contact Map |
| 4mpcA | 1 | 0.6458 | 99.9 | 0.583 | Contact Map |
| 2q8gA | 1 | 0.6771 | 99.9 | 0.586 | Contact Map |
| 1ysrA | 3 | 0.474 | 99.9 | 0.587 | Contact Map |
| 4gczA | 2 | 0.5573 | 99.9 | 0.588 | Contact Map |
| 3d36A | 2 | 0.526 | 99.9 | 0.595 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)