| PhD |
| ID: | 1516009600 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 128 (125) | ||
| Sequences: | 3108 (2416.1) | ||
| Seq/Len: | 24.864 | ||
| Nf(neff/√len): | 216.1 |
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: 24.864).
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 |
| 12_S | 120_D | 3.169 | 1.00 |
| 53_F | 99_G | 3.090 | 1.00 |
| 38_Y | 41_G | 2.615 | 1.00 |
| 23_S | 26_L | 2.109 | 1.00 |
| 20_P | 36_K | 2.097 | 1.00 |
| 71_E | 125_R | 1.972 | 1.00 |
| 22_Y | 34_R | 1.839 | 1.00 |
| 52_V | 124_L | 1.826 | 1.00 |
| 27_Q | 32_C | 1.813 | 1.00 |
| 34_R | 57_S | 1.787 | 1.00 |
| 99_G | 103_F | 1.742 | 1.00 |
| 54_L | 68_Y | 1.645 | 1.00 |
| 51_S | 103_F | 1.614 | 1.00 |
| 7_V | 121_T | 1.548 | 1.00 |
| 36_K | 55_E | 1.546 | 1.00 |
| 35_L | 126_F | 1.533 | 1.00 |
| 70_V | 100_Y | 1.520 | 1.00 |
| 25_P | 32_C | 1.516 | 1.00 |
| 109_L | 115_L | 1.495 | 1.00 |
| 6_F | 37_V | 1.448 | 1.00 |
| 34_R | 55_E | 1.444 | 1.00 |
| 23_S | 33_W | 1.421 | 1.00 |
| 109_L | 122_V | 1.377 | 0.99 |
| 9_E | 121_T | 1.373 | 0.99 |
| 97_C | 101_N | 1.365 | 0.99 |
| 10_N | 13_T | 1.343 | 0.99 |
| 104_F | 109_L | 1.296 | 0.99 |
| 42_N | 97_C | 1.287 | 0.99 |
| 74_H | 113_G | 1.277 | 0.99 |
| 55_E | 97_C | 1.270 | 0.99 |
| 31_L | 56_L | 1.222 | 0.98 |
| 37_V | 50_L | 1.199 | 0.98 |
| 4_A | 23_S | 1.197 | 0.98 |
| 8_L | 12_S | 1.195 | 0.98 |
| 43_G | 47_G | 1.182 | 0.98 |
| 68_Y | 88_F | 1.177 | 0.98 |
| 31_L | 49_Y | 1.166 | 0.97 |
| 29_S | 33_W | 1.162 | 0.97 |
| 49_Y | 105_R | 1.161 | 0.97 |
| 49_Y | 102_R | 1.160 | 0.97 |
| 5_T | 125_R | 1.150 | 0.97 |
| 5_T | 123_I | 1.147 | 0.97 |
| 106_L | 110_A | 1.138 | 0.97 |
| 6_F | 10_N | 1.136 | 0.97 |
| 6_F | 23_S | 1.130 | 0.97 |
| 97_C | 100_Y | 1.119 | 0.96 |
| 105_R | 108_L | 1.085 | 0.96 |
| 41_G | 51_S | 1.079 | 0.95 |
| 42_N | 53_F | 1.078 | 0.95 |
| 22_Y | 55_E | 1.069 | 0.95 |
| 75_Q | 116_N | 1.060 | 0.95 |
| 68_Y | 99_G | 1.057 | 0.95 |
| 90_S | 98_W | 1.056 | 0.95 |
| 35_L | 124_L | 1.056 | 0.95 |
| 113_G | 116_N | 1.054 | 0.95 |
| 51_S | 99_G | 1.049 | 0.94 |
| 41_G | 53_F | 1.034 | 0.94 |
| 52_V | 70_V | 1.031 | 0.94 |
| 30_G | 33_W | 1.031 | 0.94 |
| 37_V | 52_V | 1.027 | 0.94 |
| 4_A | 26_L | 1.025 | 0.93 |
| 75_Q | 123_I | 1.018 | 0.93 |
| 73_V | 125_R | 1.017 | 0.93 |
| 93_E | 96_E | 1.017 | 0.93 |
| 6_F | 11_F | 1.014 | 0.93 |
| 98_W | 102_R | 1.013 | 0.93 |
| 72_M | 104_F | 1.006 | 0.93 |
| 45_V | 49_Y | 1.002 | 0.92 |
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 | |
| 1flkA | 2 | 0.9688 | 99.8 | 0.088 | Contact Map |
| 4ghuA | 1 | 0.9688 | 99.8 | 0.095 | Contact Map |
| 2f1zA | 2 | 0.9453 | 99.8 | 0.1 | Contact Map |
| 3ivvA | 1 | 0.9766 | 99.8 | 0.101 | Contact Map |
| 3zjbA | 3 | 0.9844 | 99.8 | 0.105 | Contact Map |
| 1lb6A | 1 | 0.9844 | 99.8 | 0.107 | Contact Map |
| 1ca9A | 6 | 0.9609 | 99.8 | 0.109 | Contact Map |
| 1d00A | 8 | 0.9609 | 99.8 | 0.111 | Contact Map |
| 3hqiA | 2 | 0.9453 | 99.8 | 0.125 | Contact Map |
| 4gwmA | 2 | 0.9453 | 99.8 | 0.126 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)