| T0812 -force run |
| ID: | 1402423018 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 204 (201) | ||
| Sequences: | 110 (70.2) | ||
| Seq/Len: | 0.547 | ||
| Nf(neff/√len): | 5.0 |
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: 0.547).
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 |
| 179_I | 182_I | 2.245 | 0.94 |
| 199_A | 203_E | 1.889 | 0.83 |
| 80_Y | 98_Q | 1.884 | 0.83 |
| 66_F | 161_I | 1.767 | 0.77 |
| 4_K | 50_R | 1.762 | 0.77 |
| 155_L | 160_D | 1.730 | 0.75 |
| 73_A | 130_E | 1.704 | 0.73 |
| 145_V | 159_Y | 1.541 | 0.62 |
| 1_S | 50_R | 1.529 | 0.61 |
| 80_Y | 84_F | 1.520 | 0.61 |
| 38_Q | 122_G | 1.503 | 0.59 |
| 80_Y | 170_Y | 1.469 | 0.57 |
| 167_K | 181_E | 1.462 | 0.56 |
| 101_I | 129_I | 1.445 | 0.55 |
| 199_A | 202_I | 1.427 | 0.53 |
| 1_S | 4_K | 1.422 | 0.53 |
| 155_L | 176_Q | 1.422 | 0.53 |
| 45_H | 160_D | 1.410 | 0.52 |
| 62_L | 76_G | 1.409 | 0.52 |
| 69_K | 131_M | 1.401 | 0.51 |
| 4_K | 51_E | 1.400 | 0.51 |
| 62_L | 66_F | 1.399 | 0.51 |
| 37_F | 47_D | 1.386 | 0.50 |
| 31_T | 97_P | 1.359 | 0.48 |
| 113_V | 157_I | 1.349 | 0.47 |
| 33_K | 69_K | 1.346 | 0.47 |
| 44_A | 97_P | 1.328 | 0.46 |
| 46_M | 97_P | 1.309 | 0.44 |
| 62_L | 136_W | 1.308 | 0.44 |
| 127_H | 148_T | 1.302 | 0.44 |
| 70_K | 189_Q | 1.287 | 0.42 |
| 48_L | 187_A | 1.286 | 0.42 |
| 179_I | 184_M | 1.266 | 0.41 |
| 151_R | 168_A | 1.257 | 0.40 |
| 145_V | 160_D | 1.256 | 0.40 |
| 131_M | 150_T | 1.249 | 0.39 |
| 137_K | 167_K | 1.248 | 0.39 |
| 138_Y | 149_V | 1.234 | 0.38 |
| 84_F | 174_M | 1.221 | 0.37 |
| 150_T | 187_A | 1.213 | 0.37 |
| 146_H | 160_D | 1.211 | 0.37 |
| 69_K | 189_Q | 1.210 | 0.37 |
| 192_G | 196_T | 1.200 | 0.36 |
| 44_A | 82_I | 1.198 | 0.36 |
| 168_A | 187_A | 1.192 | 0.35 |
| 57_P | 80_Y | 1.190 | 0.35 |
| 154_F | 167_K | 1.170 | 0.34 |
| 151_R | 158_L | 1.158 | 0.33 |
| 101_I | 131_M | 1.149 | 0.32 |
| 1_S | 79_K | 1.140 | 0.32 |
| 84_F | 176_Q | 1.138 | 0.31 |
| 29_H | 69_K | 1.136 | 0.31 |
| 66_F | 76_G | 1.134 | 0.31 |
| 74_Y | 158_L | 1.132 | 0.31 |
| 50_R | 107_T | 1.123 | 0.30 |
| 187_A | 199_A | 1.117 | 0.30 |
| 136_W | 169_T | 1.117 | 0.30 |
| 20_L | 23_V | 1.116 | 0.30 |
| 88_E | 137_K | 1.113 | 0.30 |
| 138_Y | 153_D | 1.112 | 0.30 |
| 64_E | 183_S | 1.109 | 0.30 |
| 71_L | 184_M | 1.106 | 0.29 |
| 66_F | 136_W | 1.105 | 0.29 |
| 42_I | 159_Y | 1.099 | 0.29 |
| 96_N | 102_R | 1.093 | 0.28 |
| 6_L | 69_K | 1.092 | 0.28 |
| 30_T | 111_I | 1.084 | 0.28 |
| 60_W | 168_A | 1.084 | 0.28 |
| 6_L | 106_P | 1.081 | 0.28 |
| 43_V | 73_A | 1.080 | 0.28 |
| 35_I | 96_N | 1.077 | 0.27 |
| 59_Y | 84_F | 1.076 | 0.27 |
| 174_M | 179_I | 1.072 | 0.27 |
| 117_A | 120_L | 1.069 | 0.27 |
| 29_H | 161_I | 1.069 | 0.27 |
| 2_E | 142_D | 1.065 | 0.27 |
| 83_Y | 169_T | 1.064 | 0.27 |
| 124_L | 185_E | 1.053 | 0.26 |
| 107_T | 194_T | 1.052 | 0.26 |
| 49_M | 73_A | 1.052 | 0.26 |
| 58_F | 130_E | 1.051 | 0.26 |
| 117_A | 162_H | 1.049 | 0.26 |
| 50_R | 194_T | 1.045 | 0.25 |
| 130_E | 185_E | 1.043 | 0.25 |
| 72_M | 146_H | 1.039 | 0.25 |
| 165_L | 183_S | 1.032 | 0.25 |
| 50_R | 193_T | 1.030 | 0.25 |
| 2_E | 51_E | 1.026 | 0.24 |
| 56_E | 165_L | 1.026 | 0.24 |
| 74_Y | 133_E | 1.026 | 0.24 |
| 99_V | 152_E | 1.024 | 0.24 |
| 101_I | 202_I | 1.023 | 0.24 |
| 158_L | 168_A | 1.022 | 0.24 |
| 20_L | 154_F | 1.022 | 0.24 |
| 37_F | 184_M | 1.022 | 0.24 |
| 75_G | 154_F | 1.020 | 0.24 |
| 21_P | 37_F | 1.017 | 0.24 |
| 46_M | 155_L | 1.016 | 0.24 |
| 1_S | 51_E | 1.011 | 0.23 |
| 1_S | 107_T | 1.010 | 0.23 |
| 148_T | 186_V | 1.005 | 0.23 |
| 129_I | 158_L | 1.004 | 0.23 |
| 4_K | 106_P | 1.001 | 0.23 |
| 160_D | 164_I | 1.000 | 0.23 |
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 | |
| 4yeqU | 1 | 0 | 100 | 0.293 | Contact Map |
| 4yepA | 2 | 0 | 100 | 0.341 | Contact Map |
| 2fokA | 2 | 0.8873 | 4.8 | 0.967 | Contact Map |
| 2di9A | 1 | 0.3627 | 4 | 0.969 | Contact Map |
| 4mkqC | 2 | 0.0441 | 4 | 0.969 | Contact Map |
| 4tr8A | 2 | 0.348 | 3.4 | 0.97 | Contact Map |
| 3if8B | 1 | 0.3186 | 3.2 | 0.97 | Contact Map |
| 1vpkA | 1 | 0.299 | 2.9 | 0.971 | Contact Map |
| 3t0pA | 2 | 0.299 | 2.7 | 0.971 | Contact Map |
| 4k3lA | 2 | 0.2941 | 2.6 | 0.972 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)