| T0778 |
| ID: | 1400094484 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 127 (121) | ||
| Sequences: | 3251 (2669.3) | ||
| Seq/Len: | 26.868 | ||
| Nf(neff/√len): | 242.7 |
Jackhmmer Results: (2014_04_16)
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: 26.868).
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 |
| 97_K | 100_E | 3.726 | 1.00 |
| 63_K | 66_E | 3.555 | 1.00 |
| 29_K | 32_R | 3.396 | 1.00 |
| 88_R | 104_D | 2.560 | 1.00 |
| 54_R | 70_D | 2.459 | 1.00 |
| 21_G | 37_Y | 2.394 | 1.00 |
| 17_E | 36_C | 2.369 | 1.00 |
| 38_T | 54_R | 2.340 | 1.00 |
| 89_G | 105_F | 2.299 | 1.00 |
| 55_A | 71_C | 2.212 | 1.00 |
| 51_P | 70_D | 2.160 | 1.00 |
| 85_F | 104_D | 2.081 | 1.00 |
| 72_T | 88_R | 2.078 | 1.00 |
| 73_Q | 76_L | 1.870 | 1.00 |
| 108_V | 118_A | 1.808 | 1.00 |
| 20_R | 36_C | 1.778 | 1.00 |
| 107_T | 110_L | 1.763 | 1.00 |
| 37_Y | 53_N | 1.729 | 1.00 |
| 65_E | 95_L | 1.671 | 1.00 |
| 105_F | 121_E | 1.657 | 1.00 |
| 81_Y | 84_A | 1.547 | 1.00 |
| 71_C | 87_R | 1.541 | 1.00 |
| 75_I | 84_A | 1.531 | 1.00 |
| 31_E | 61_I | 1.454 | 1.00 |
| 92_R | 100_E | 1.447 | 1.00 |
| 34_I | 57_A | 1.442 | 1.00 |
| 88_R | 92_R | 1.367 | 0.99 |
| 14_A | 40_G | 1.360 | 0.99 |
| 44_D | 47_N | 1.338 | 0.99 |
| 102_K | 106_E | 1.335 | 0.99 |
| 109_L | 119_V | 1.323 | 0.99 |
| 34_I | 54_R | 1.318 | 0.99 |
| 24_F | 36_C | 1.294 | 0.99 |
| 115_N | 118_A | 1.287 | 0.99 |
| 75_I | 85_F | 1.285 | 0.99 |
| 24_F | 32_R | 1.281 | 0.99 |
| 109_L | 118_A | 1.260 | 0.99 |
| 68_E | 88_R | 1.258 | 0.99 |
| 40_G | 50_L | 1.257 | 0.99 |
| 34_I | 58_Y | 1.239 | 0.98 |
| 102_K | 122_L | 1.232 | 0.98 |
| 41_I | 51_P | 1.230 | 0.98 |
| 39_R | 42_A | 1.217 | 0.98 |
| 58_Y | 66_E | 1.213 | 0.98 |
| 68_E | 91_A | 1.204 | 0.98 |
| 112_E | 115_N | 1.194 | 0.98 |
| 48_A | 74_A | 1.193 | 0.98 |
| 89_G | 108_V | 1.184 | 0.98 |
| 92_R | 104_D | 1.184 | 0.98 |
| 92_R | 97_K | 1.183 | 0.98 |
| 41_I | 50_L | 1.179 | 0.98 |
| 68_E | 92_R | 1.174 | 0.98 |
| 24_F | 29_K | 1.148 | 0.97 |
| 47_N | 50_L | 1.134 | 0.97 |
| 57_A | 61_I | 1.133 | 0.97 |
| 20_R | 24_F | 1.132 | 0.97 |
| 74_A | 84_A | 1.126 | 0.97 |
| 68_E | 72_T | 1.118 | 0.96 |
| 85_F | 108_V | 1.109 | 0.96 |
| 13_Q | 16_S | 1.081 | 0.95 |
| 17_E | 39_R | 1.063 | 0.95 |
| 34_I | 38_T | 1.060 | 0.95 |
| 22_N | 37_Y | 1.034 | 0.94 |
| 18_K | 53_N | 1.031 | 0.94 |
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 | |
| 4i2zA | 1 | 0.9213 | 99.6 | 0.187 | Contact Map |
| 3iegA | 2 | 0.9134 | 99.6 | 0.189 | Contact Map |
| 1p5qA | 3 | 1 | 99.6 | 0.193 | Contact Map |
| 2vyiA | 2 | 0.9606 | 99.6 | 0.194 | Contact Map |
| 3fp2A | 1 | 1 | 99.6 | 0.195 | Contact Map |
| 1dceA | 2 | 1 | 99.6 | 0.198 | Contact Map |
| 2y4tA | 3 | 0.9213 | 99.6 | 0.201 | Contact Map |
| 2pl2A | 2 | 0.9055 | 99.6 | 0.201 | Contact Map |
| 3as5A | 2 | 1 | 99.6 | 0.204 | Contact Map |
| 4gywA | 2 | 1 | 99.6 | 0.206 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)