| Student |
| ID: | 1510276322 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 174 (165) | ||
| Sequences: | 1522 (945.9) | ||
| Seq/Len: | 9.224 | ||
| Nf(neff/√len): | 73.6 |
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: 9.224).
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 |
| 25_E | 29_E | 3.324 | 1.00 |
| 58_K | 62_Q | 2.730 | 1.00 |
| 156_L | 159_D | 2.707 | 1.00 |
| 42_K | 48_L | 2.211 | 1.00 |
| 124_E | 128_E | 2.181 | 1.00 |
| 31_K | 35_R | 2.124 | 1.00 |
| 31_K | 54_R | 2.124 | 1.00 |
| 91_K | 108_E | 1.919 | 1.00 |
| 89_A | 93_G | 1.897 | 1.00 |
| 119_Q | 122_K | 1.872 | 1.00 |
| 14_E | 70_M | 1.866 | 1.00 |
| 88_G | 91_K | 1.855 | 1.00 |
| 21_Q | 64_D | 1.828 | 1.00 |
| 145_L | 149_L | 1.771 | 1.00 |
| 169_V | 172_E | 1.769 | 1.00 |
| 147_A | 151_A | 1.759 | 1.00 |
| 41_P | 46_R | 1.718 | 1.00 |
| 84_N | 88_G | 1.695 | 1.00 |
| 98_K | 115_E | 1.646 | 1.00 |
| 28_I | 60_L | 1.607 | 1.00 |
| 33_Q | 37_Y | 1.570 | 1.00 |
| 124_E | 127_Q | 1.562 | 1.00 |
| 105_D | 108_E | 1.542 | 1.00 |
| 32_Q | 36_K | 1.524 | 1.00 |
| 165_T | 168_E | 1.472 | 1.00 |
| 77_I | 96_A | 1.449 | 1.00 |
| 14_E | 67_L | 1.446 | 1.00 |
| 114_D | 117_E | 1.444 | 1.00 |
| 29_E | 32_Q | 1.394 | 0.99 |
| 37_Y | 50_A | 1.393 | 0.99 |
| 18_E | 67_L | 1.385 | 0.99 |
| 59_Q | 62_Q | 1.369 | 0.99 |
| 33_Q | 36_K | 1.365 | 0.99 |
| 23_K | 27_Q | 1.335 | 0.99 |
| 86_V | 89_A | 1.331 | 0.99 |
| 20_K | 63_L | 1.331 | 0.99 |
| 147_A | 150_D | 1.329 | 0.99 |
| 167_P | 170_P | 1.329 | 0.99 |
| 26_K | 29_E | 1.301 | 0.99 |
| 61_D | 65_G | 1.291 | 0.99 |
| 94_A | 98_K | 1.258 | 0.98 |
| 25_E | 60_L | 1.210 | 0.98 |
| 31_K | 38_G | 1.197 | 0.98 |
| 112_L | 115_E | 1.196 | 0.97 |
| 27_Q | 56_M | 1.193 | 0.97 |
| 85_E | 88_G | 1.191 | 0.97 |
| 48_L | 55_K | 1.188 | 0.97 |
| 165_T | 172_E | 1.184 | 0.97 |
| 28_I | 57_E | 1.178 | 0.97 |
| 164_A | 168_E | 1.166 | 0.97 |
| 34_A | 50_A | 1.158 | 0.97 |
| 14_E | 71_E | 1.143 | 0.96 |
| 91_K | 95_K | 1.131 | 0.96 |
| 160_E | 164_A | 1.125 | 0.96 |
| 34_A | 47_A | 1.125 | 0.96 |
| 149_L | 153_E | 1.123 | 0.96 |
| 33_Q | 50_A | 1.121 | 0.96 |
| 116_I | 119_Q | 1.120 | 0.96 |
| 165_T | 171_S | 1.110 | 0.96 |
| 17_L | 94_A | 1.106 | 0.96 |
| 34_A | 40_G | 1.104 | 0.95 |
| 168_E | 171_S | 1.104 | 0.95 |
| 90_M | 101_H | 1.100 | 0.95 |
| 74_R | 93_G | 1.096 | 0.95 |
| 161_D | 171_S | 1.092 | 0.95 |
| 26_K | 30_E | 1.084 | 0.95 |
| 94_A | 116_I | 1.066 | 0.94 |
| 49_Q | 53_K | 1.063 | 0.94 |
| 35_R | 38_G | 1.061 | 0.94 |
| 166_L | 171_S | 1.061 | 0.94 |
| 163_A | 168_E | 1.054 | 0.94 |
| 160_E | 163_A | 1.050 | 0.94 |
| 37_Y | 46_R | 1.048 | 0.94 |
| 95_K | 98_K | 1.044 | 0.93 |
| 67_L | 86_V | 1.043 | 0.93 |
| 110_D | 114_D | 1.041 | 0.93 |
| 36_K | 40_G | 1.032 | 0.93 |
| 59_Q | 63_L | 1.029 | 0.93 |
| 153_E | 156_L | 1.014 | 0.92 |
| 36_K | 39_R | 1.005 | 0.92 |
| 37_Y | 41_P | 1.001 | 0.91 |
| 76_A | 123_A | 1.000 | 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 | |
| 2gd5A | 4 | 0.8506 | 99.7 | 0.529 | Contact Map |
| 3frtA | 2 | 0.7701 | 99.7 | 0.551 | Contact Map |
| 3um3B | 1 | 0 | 99.3 | 0.639 | Contact Map |
| 4abmA | 4 | 0.4368 | 98.9 | 0.7 | Contact Map |
| 2luhB | 1 | 0.3276 | 98.6 | 0.72 | Contact Map |
| 4txrC | 1 | 0.2011 | 97.9 | 0.775 | Contact Map |
| 3ulyB | 1 | 0 | 91.9 | 0.858 | Contact Map |
| 3htuB | 4 | 0.1839 | 78.7 | 0.883 | Contact Map |
| 2dfsA | 2 | 0.6494 | 30.7 | 0.915 | Contact Map |
| 2lp4A | 1 | 0.7299 | 23.3 | 0.919 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)