| T0836 -force run |
| ID: | 1404161030 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 204 (201) | ||
| Sequences: | 70 (54.6) | ||
| Seq/Len: | 0.348 | ||
| Nf(neff/√len): | 3.9 |
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: 0.348).
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 |
| 60_F | 87_A | 2.635 | 0.95 |
| 99_W | 143_T | 2.026 | 0.79 |
| 176_K | 180_L | 1.909 | 0.73 |
| 112_L | 117_T | 1.716 | 0.61 |
| 87_A | 156_N | 1.707 | 0.60 |
| 5_L | 11_T | 1.706 | 0.60 |
| 106_A | 139_M | 1.701 | 0.60 |
| 65_I | 160_A | 1.657 | 0.57 |
| 142_A | 169_D | 1.640 | 0.55 |
| 167_D | 170_A | 1.637 | 0.55 |
| 60_F | 156_N | 1.630 | 0.55 |
| 22_I | 195_T | 1.605 | 0.53 |
| 158_K | 164_V | 1.588 | 0.52 |
| 136_G | 140_W | 1.574 | 0.51 |
| 146_F | 151_V | 1.526 | 0.47 |
| 59_Y | 64_Q | 1.521 | 0.47 |
| 24_I | 31_H | 1.493 | 0.45 |
| 7_N | 11_T | 1.472 | 0.44 |
| 58_Y | 172_A | 1.461 | 0.43 |
| 45_L | 101_M | 1.421 | 0.40 |
| 87_A | 177_T | 1.396 | 0.39 |
| 4_L | 11_T | 1.395 | 0.38 |
| 16_F | 190_I | 1.381 | 0.38 |
| 60_F | 88_L | 1.367 | 0.37 |
| 147_F | 152_F | 1.335 | 0.35 |
| 14_V | 18_L | 1.324 | 0.34 |
| 104_L | 108_N | 1.312 | 0.33 |
| 152_F | 181_V | 1.309 | 0.33 |
| 65_I | 77_P | 1.305 | 0.33 |
| 24_I | 142_A | 1.299 | 0.32 |
| 99_W | 146_F | 1.296 | 0.32 |
| 71_I | 78_A | 1.294 | 0.32 |
| 84_A | 161_L | 1.292 | 0.32 |
| 65_I | 181_V | 1.289 | 0.32 |
| 57_L | 192_M | 1.274 | 0.31 |
| 18_L | 21_V | 1.267 | 0.30 |
| 89_F | 99_W | 1.266 | 0.30 |
| 99_W | 103_V | 1.264 | 0.30 |
| 178_A | 192_M | 1.240 | 0.29 |
| 160_A | 181_V | 1.234 | 0.29 |
| 57_L | 153_I | 1.232 | 0.28 |
| 173_K | 177_T | 1.227 | 0.28 |
| 159_I | 174_A | 1.211 | 0.27 |
| 153_I | 178_A | 1.205 | 0.27 |
| 160_A | 179_M | 1.204 | 0.27 |
| 65_I | 179_M | 1.193 | 0.26 |
| 137_T | 195_T | 1.189 | 0.26 |
| 49_F | 101_M | 1.179 | 0.25 |
| 60_F | 177_T | 1.179 | 0.25 |
| 93_W | 96_L | 1.175 | 0.25 |
| 49_F | 58_Y | 1.173 | 0.25 |
| 103_V | 146_F | 1.148 | 0.24 |
| 153_I | 192_M | 1.147 | 0.24 |
| 159_I | 170_A | 1.142 | 0.24 |
| 60_F | 178_A | 1.141 | 0.24 |
| 50_G | 98_T | 1.136 | 0.23 |
| 96_L | 146_F | 1.136 | 0.23 |
| 77_P | 181_V | 1.135 | 0.23 |
| 88_L | 153_I | 1.135 | 0.23 |
| 89_F | 94_A | 1.133 | 0.23 |
| 98_T | 149_V | 1.132 | 0.23 |
| 16_F | 90_W | 1.129 | 0.23 |
| 18_L | 90_W | 1.125 | 0.23 |
| 147_F | 151_V | 1.122 | 0.23 |
| 159_I | 166_A | 1.121 | 0.23 |
| 3_G | 10_N | 1.106 | 0.22 |
| 149_V | 153_I | 1.101 | 0.22 |
| 112_L | 115_A | 1.089 | 0.21 |
| 13_I | 165_E | 1.086 | 0.21 |
| 57_L | 87_A | 1.085 | 0.21 |
| 144_V | 178_A | 1.083 | 0.21 |
| 21_V | 167_D | 1.082 | 0.21 |
| 85_P | 153_I | 1.078 | 0.20 |
| 71_I | 74_E | 1.077 | 0.20 |
| 77_P | 160_A | 1.076 | 0.20 |
| 57_L | 178_A | 1.074 | 0.20 |
| 3_G | 12_I | 1.074 | 0.20 |
| 67_V | 194_A | 1.072 | 0.20 |
| 17_V | 20_L | 1.070 | 0.20 |
| 150_W | 161_L | 1.066 | 0.20 |
| 25_G | 28_H | 1.065 | 0.20 |
| 100_V | 169_D | 1.065 | 0.20 |
| 75_L | 78_A | 1.064 | 0.20 |
| 21_V | 170_A | 1.055 | 0.19 |
| 29_S | 32_G | 1.049 | 0.19 |
| 9_R | 105_L | 1.048 | 0.19 |
| 115_A | 136_G | 1.040 | 0.19 |
| 13_I | 21_V | 1.039 | 0.19 |
| 95_A | 98_T | 1.035 | 0.19 |
| 85_P | 149_V | 1.033 | 0.19 |
| 60_F | 81_K | 1.024 | 0.18 |
| 71_I | 77_P | 1.022 | 0.18 |
| 57_L | 61_N | 1.018 | 0.18 |
| 17_V | 26_Y | 1.012 | 0.18 |
| 182_S | 191_P | 1.011 | 0.18 |
| 4_L | 19_A | 1.011 | 0.18 |
| 94_A | 103_V | 1.011 | 0.18 |
| 74_E | 79_V | 1.009 | 0.18 |
| 156_N | 177_T | 1.006 | 0.17 |
| 61_N | 192_M | 1.006 | 0.17 |
| 14_V | 186_T | 1.005 | 0.17 |
| 26_Y | 31_H | 1.003 | 0.17 |
| 139_M | 143_T | 1.001 | 0.17 |
| 23_V | 33_H | 1.000 | 0.17 |
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 | |
| 1fftC | 2 | 0.4902 | 2.9 | 0.977 | Contact Map |
| 3hd7A | 2 | 0.152 | 2.5 | 0.978 | Contact Map |
| 1zxgA | 1 | 0.152 | 2.4 | 0.978 | Contact Map |
| 3qe7A | 1 | 0.2696 | 2.1 | 0.978 | Contact Map |
| 1m56C | 2 | 0.4902 | 2 | 0.979 | Contact Map |
| 1qleC | 1 | 0.4902 | 1.6 | 0.98 | Contact Map |
| 1v54C | 2 | 0.4902 | 1.6 | 0.98 | Contact Map |
| 3rkoM | 2 | 0.6176 | 1.4 | 0.98 | Contact Map |
| 4rp9A | 1 | 0.3725 | 1.4 | 0.981 | Contact Map |
| 1n7lA | 1 | 0.1225 | 1.3 | 0.981 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)