| RASH_HUMAN |
| ID: | 1430407712 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 161 (159) | ||
| Sequences: | 25105 (15588.8) | ||
| Seq/Len: | 157.893 | ||
| Nf(neff/√len): | 1236.3 |
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: 157.893).
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 |
| 18_Q | 145_R | 3.321 | 1.00 |
| 138_I | 154_T | 3.150 | 1.00 |
| 7_A | 88_D | 2.873 | 1.00 |
| 80_I | 111_G | 2.708 | 1.00 |
| 136_P | 154_T | 2.569 | 1.00 |
| 110_V | 151_A | 2.423 | 1.00 |
| 154_T | 157_R | 2.391 | 1.00 |
| 154_T | 158_E | 2.328 | 1.00 |
| 110_V | 140_T | 2.260 | 1.00 |
| 77_V | 112_N | 2.239 | 1.00 |
| 114_C | 139_E | 2.221 | 1.00 |
| 15_L | 77_V | 2.209 | 1.00 |
| 75_L | 110_V | 2.123 | 1.00 |
| 3_V | 71_G | 1.932 | 1.00 |
| 111_G | 139_E | 1.907 | 1.00 |
| 114_C | 146_Q | 1.821 | 1.00 |
| 14_A | 142_A | 1.817 | 1.00 |
| 123_S | 127_Q | 1.789 | 1.00 |
| 4_V | 16_T | 1.762 | 1.00 |
| 147_G | 150_D | 1.740 | 1.00 |
| 73_G | 155_L | 1.725 | 1.00 |
| 112_N | 142_A | 1.699 | 1.00 |
| 127_Q | 131_R | 1.643 | 1.00 |
| 18_Q | 148_V | 1.638 | 1.00 |
| 140_T | 151_A | 1.628 | 1.00 |
| 75_L | 155_L | 1.623 | 1.00 |
| 78_F | 137_Y | 1.617 | 1.00 |
| 78_F | 109_L | 1.583 | 1.00 |
| 108_V | 138_I | 1.575 | 1.00 |
| 108_V | 154_T | 1.572 | 1.00 |
| 15_L | 151_A | 1.542 | 1.00 |
| 80_I | 114_C | 1.517 | 1.00 |
| 41_V | 46_T | 1.486 | 1.00 |
| 82_N | 85_S | 1.427 | 1.00 |
| 93_R | 107_M | 1.419 | 1.00 |
| 4_V | 75_L | 1.417 | 1.00 |
| 136_P | 158_E | 1.403 | 0.99 |
| 15_L | 148_V | 1.398 | 0.99 |
| 79_A | 82_N | 1.391 | 0.99 |
| 83_T | 125_Q | 1.371 | 0.99 |
| 111_G | 137_Y | 1.343 | 0.99 |
| 37_R | 50_D | 1.316 | 0.99 |
| 81_N | 116_L | 1.315 | 0.99 |
| 76_C | 93_R | 1.301 | 0.99 |
| 39_Q | 48_L | 1.269 | 0.99 |
| 150_D | 154_T | 1.265 | 0.99 |
| 127_Q | 130_A | 1.264 | 0.99 |
| 126_A | 130_A | 1.253 | 0.99 |
| 2_L | 73_G | 1.251 | 0.99 |
| 78_F | 111_G | 1.250 | 0.99 |
| 17_I | 25_V | 1.248 | 0.99 |
| 150_D | 153_Y | 1.238 | 0.98 |
| 94_E | 98_R | 1.219 | 0.98 |
| 93_R | 97_K | 1.214 | 0.98 |
| 39_Q | 46_T | 1.196 | 0.98 |
| 47_C | 156_V | 1.189 | 0.98 |
| 128_D | 132_S | 1.182 | 0.98 |
| 149_E | 153_Y | 1.166 | 0.97 |
| 75_L | 108_V | 1.161 | 0.97 |
| 75_L | 151_A | 1.160 | 0.97 |
| 129_L | 133_Y | 1.157 | 0.97 |
| 126_A | 137_Y | 1.155 | 0.97 |
| 125_Q | 128_D | 1.142 | 0.97 |
| 113_K | 116_L | 1.134 | 0.97 |
| 123_S | 139_E | 1.091 | 0.96 |
| 79_A | 113_K | 1.090 | 0.96 |
| 106_P | 158_E | 1.089 | 0.96 |
| 94_E | 97_K | 1.076 | 0.95 |
| 122_E | 125_Q | 1.069 | 0.95 |
| 84_K | 87_E | 1.060 | 0.95 |
| 148_V | 152_F | 1.054 | 0.95 |
| 15_L | 19_L | 1.032 | 0.94 |
| 153_Y | 157_R | 1.029 | 0.94 |
| 126_A | 139_E | 1.026 | 0.94 |
| 1_K | 52_L | 1.017 | 0.93 |
| 41_V | 44_G | 1.017 | 0.93 |
| 76_C | 89_I | 1.014 | 0.93 |
| 68_M | 71_G | 1.001 | 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 | |
| 3conA | 1 | 0.9317 | 100 | 0.023 | Contact Map |
| 3cphA | 1 | 0.9938 | 100 | 0.041 | Contact Map |
| 3clvA | 1 | 0.9752 | 100 | 0.045 | Contact Map |
| 2wkqA | 1 | 0.9876 | 100 | 0.051 | Contact Map |
| 3cpjB | 1 | 0.9317 | 100 | 0.057 | Contact Map |
| 3cbqA | 1 | 1 | 100 | 0.066 | Contact Map |
| 3c5cA | 4 | 0.9938 | 100 | 0.074 | Contact Map |
| 2y8eA | 2 | 0.9876 | 100 | 0.085 | Contact Map |
| 2yc2C | 2 | 0.7391 | 100 | 0.089 | Contact Map |
| 3bwdD | 1 | 0.8758 | 100 | 0.1 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)