| T0808 19-150 |
| ID: | 1405534291 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 132 (127) | ||
| Sequences: | 156 (148) | ||
| Seq/Len: | 1.228 | ||
| Nf(neff/√len): | 13.1 |
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: 1.228).
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 |
| 68_G | 97_V | 3.154 | 1.00 |
| 89_I | 99_I | 2.212 | 0.99 |
| 55_L | 117_L | 1.830 | 0.94 |
| 48_P | 94_A | 1.787 | 0.93 |
| 40_S | 100_D | 1.765 | 0.93 |
| 53_L | 78_S | 1.726 | 0.92 |
| 51_A | 97_V | 1.486 | 0.81 |
| 6_V | 124_G | 1.478 | 0.81 |
| 76_L | 82_T | 1.416 | 0.76 |
| 58_K | 79_N | 1.391 | 0.75 |
| 58_K | 97_V | 1.385 | 0.74 |
| 47_Q | 120_D | 1.343 | 0.71 |
| 46_H | 101_L | 1.331 | 0.70 |
| 36_K | 60_H | 1.326 | 0.70 |
| 45_L | 119_A | 1.322 | 0.69 |
| 9_V | 39_V | 1.308 | 0.68 |
| 57_A | 76_L | 1.293 | 0.67 |
| 27_R | 98_R | 1.289 | 0.66 |
| 25_T | 28_G | 1.274 | 0.65 |
| 31_H | 37_S | 1.272 | 0.65 |
| 65_V | 117_L | 1.226 | 0.61 |
| 100_D | 113_E | 1.205 | 0.59 |
| 55_L | 76_L | 1.184 | 0.57 |
| 52_D | 98_R | 1.178 | 0.56 |
| 22_A | 86_V | 1.176 | 0.56 |
| 9_V | 78_S | 1.163 | 0.55 |
| 60_H | 107_S | 1.156 | 0.54 |
| 8_G | 11_G | 1.151 | 0.53 |
| 58_K | 84_V | 1.149 | 0.53 |
| 94_A | 122_V | 1.148 | 0.53 |
| 43_F | 86_V | 1.144 | 0.53 |
| 61_S | 76_L | 1.143 | 0.53 |
| 29_V | 61_S | 1.136 | 0.52 |
| 17_R | 91_I | 1.128 | 0.51 |
| 97_V | 105_S | 1.127 | 0.51 |
| 4_Q | 9_V | 1.125 | 0.51 |
| 53_L | 70_K | 1.125 | 0.51 |
| 48_P | 85_P | 1.118 | 0.50 |
| 99_I | 122_V | 1.114 | 0.50 |
| 6_V | 15_V | 1.112 | 0.50 |
| 43_F | 99_I | 1.104 | 0.49 |
| 61_S | 112_G | 1.095 | 0.48 |
| 116_Q | 120_D | 1.094 | 0.48 |
| 34_N | 103_G | 1.093 | 0.48 |
| 72_F | 102_Q | 1.089 | 0.47 |
| 20_D | 108_G | 1.085 | 0.47 |
| 113_E | 116_Q | 1.083 | 0.47 |
| 17_R | 57_A | 1.073 | 0.46 |
| 19_Q | 23_R | 1.063 | 0.45 |
| 64_K | 119_A | 1.063 | 0.45 |
| 56_Y | 116_Q | 1.063 | 0.45 |
| 40_S | 43_F | 1.050 | 0.44 |
| 98_R | 106_K | 1.050 | 0.44 |
| 10_S | 115_K | 1.042 | 0.43 |
| 36_K | 101_L | 1.041 | 0.43 |
| 61_S | 117_L | 1.040 | 0.43 |
| 9_V | 12_N | 1.037 | 0.42 |
| 21_G | 25_T | 1.037 | 0.42 |
| 27_R | 83_K | 1.032 | 0.42 |
| 88_S | 101_L | 1.031 | 0.42 |
| 31_H | 103_G | 1.024 | 0.41 |
| 28_G | 45_L | 1.024 | 0.41 |
| 52_D | 124_G | 1.017 | 0.40 |
| 12_N | 65_V | 1.012 | 0.40 |
| 33_T | 63_I | 1.010 | 0.40 |
| 20_D | 71_G | 1.009 | 0.40 |
| 43_F | 53_L | 1.009 | 0.40 |
| 93_Q | 125_K | 1.009 | 0.40 |
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 | |
| 3zm8A | 1 | 0.947 | 99.4 | 0.449 | Contact Map |
| 2vzsA | 2 | 0 | 99.4 | 0.45 | Contact Map |
| 2wz8A | 1 | 0.8712 | 99.4 | 0.453 | Contact Map |
| 4kmqA | 1 | 0.8939 | 99.4 | 0.459 | Contact Map |
| 2cdpA | 4 | 0.8864 | 99.3 | 0.467 | Contact Map |
| 2bgoA | 1 | 0.8409 | 99.3 | 0.479 | Contact Map |
| 2y8kA | 1 | 0.8864 | 99.3 | 0.479 | Contact Map |
| 3wnoA | 2 | 0.9848 | 99.3 | 0.486 | Contact Map |
| 2w87A | 2 | 0.9242 | 99.3 | 0.491 | Contact Map |
| 2w47A | 1 | 0.9167 | 99.2 | 0.498 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)