| dcp2_jackhammer |
| ID: | 1502385276 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 300 (269) | ||
| Sequences: | 372 (242.5) | ||
| Seq/Len: | 1.383 | ||
| Nf(neff/√len): | 14.8 |
Jackhmmer Results: (2016_04)
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: 1.383).
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 |
| 110_Q | 181_L | 3.144 | 1.00 |
| 101_A | 144_V | 2.406 | 1.00 |
| 124_G | 127_K | 2.399 | 1.00 |
| 99_R | 136_D | 2.388 | 0.99 |
| 105_D | 109_Q | 2.369 | 0.99 |
| 101_A | 152_C | 2.277 | 0.99 |
| 48_F | 190_R | 2.083 | 0.98 |
| 163_D | 172_R | 1.984 | 0.97 |
| 115_K | 194_S | 1.876 | 0.96 |
| 155_R | 179_I | 1.869 | 0.96 |
| 32_E | 89_F | 1.845 | 0.96 |
| 13_D | 71_H | 1.805 | 0.95 |
| 103_M | 112_V | 1.793 | 0.95 |
| 136_D | 187_S | 1.690 | 0.92 |
| 26_E | 54_D | 1.635 | 0.90 |
| 56_L | 232_W | 1.626 | 0.90 |
| 105_D | 110_Q | 1.615 | 0.90 |
| 105_D | 181_L | 1.605 | 0.89 |
| 40_Q | 99_R | 1.589 | 0.89 |
| 199_H | 219_F | 1.579 | 0.88 |
| 150_F | 155_R | 1.558 | 0.87 |
| 106_M | 166_I | 1.502 | 0.85 |
| 104_L | 175_I | 1.485 | 0.84 |
| 175_I | 236_R | 1.450 | 0.82 |
| 69_F | 75_L | 1.427 | 0.80 |
| 51_A | 191_K | 1.425 | 0.80 |
| 27_E | 96_I | 1.418 | 0.80 |
| 117_W | 191_K | 1.417 | 0.80 |
| 161_F | 172_R | 1.417 | 0.80 |
| 168_G | 206_T | 1.376 | 0.77 |
| 16_S | 68_L | 1.359 | 0.76 |
| 98_V | 127_K | 1.349 | 0.75 |
| 157_N | 186_E | 1.348 | 0.75 |
| 132_K | 199_H | 1.348 | 0.75 |
| 99_R | 187_S | 1.317 | 0.72 |
| 30_S | 89_F | 1.316 | 0.72 |
| 201_L | 233_I | 1.303 | 0.71 |
| 189_T | 224_P | 1.297 | 0.71 |
| 262_S | 265_K | 1.289 | 0.70 |
| 21_L | 174_Y | 1.287 | 0.70 |
| 39_E | 44_F | 1.285 | 0.70 |
| 17_A | 40_Q | 1.285 | 0.70 |
| 91_R | 150_F | 1.281 | 0.69 |
| 39_E | 93_K | 1.228 | 0.64 |
| 127_K | 136_D | 1.225 | 0.64 |
| 99_R | 130_I | 1.224 | 0.64 |
| 17_A | 99_R | 1.222 | 0.64 |
| 113_L | 199_H | 1.204 | 0.62 |
| 18_R | 36_F | 1.201 | 0.62 |
| 161_F | 174_Y | 1.199 | 0.62 |
| 89_F | 115_K | 1.199 | 0.62 |
| 14_D | 18_R | 1.197 | 0.62 |
| 43_W | 47_D | 1.196 | 0.61 |
| 14_D | 44_F | 1.190 | 0.61 |
| 96_I | 131_D | 1.189 | 0.61 |
| 62_R | 157_N | 1.187 | 0.61 |
| 50_R | 61_L | 1.185 | 0.60 |
| 25_A | 234_K | 1.185 | 0.60 |
| 62_R | 105_D | 1.184 | 0.60 |
| 21_L | 68_L | 1.183 | 0.60 |
| 259_Q | 262_S | 1.181 | 0.60 |
| 32_E | 98_V | 1.176 | 0.60 |
| 157_N | 163_D | 1.172 | 0.59 |
| 174_Y | 217_N | 1.171 | 0.59 |
| 106_M | 178_G | 1.149 | 0.57 |
| 203_D | 220_Y | 1.147 | 0.57 |
| 160_E | 175_I | 1.145 | 0.56 |
| 263_L | 266_S | 1.142 | 0.56 |
| 26_E | 141_I | 1.141 | 0.56 |
| 102_I | 173_L | 1.133 | 0.55 |
| 268_T | 272_D | 1.132 | 0.55 |
| 15_L | 39_E | 1.126 | 0.55 |
| 79_S | 201_L | 1.119 | 0.54 |
| 93_K | 185_F | 1.116 | 0.54 |
| 156_I | 170_N | 1.114 | 0.53 |
| 61_L | 86_F | 1.111 | 0.53 |
| 115_K | 199_H | 1.109 | 0.53 |
| 59_L | 91_R | 1.104 | 0.52 |
| 264_L | 268_T | 1.104 | 0.52 |
| 21_L | 161_F | 1.102 | 0.52 |
| 150_F | 185_F | 1.099 | 0.52 |
| 15_L | 44_F | 1.099 | 0.52 |
| 33_R | 39_E | 1.096 | 0.52 |
| 169_Q | 232_W | 1.091 | 0.51 |
| 264_L | 267_S | 1.090 | 0.51 |
| 260_L | 263_L | 1.087 | 0.51 |
| 27_E | 131_D | 1.085 | 0.50 |
| 254_A | 258_S | 1.084 | 0.50 |
| 253_D | 256_A | 1.082 | 0.50 |
| 267_S | 272_D | 1.074 | 0.49 |
| 35_C | 85_A | 1.073 | 0.49 |
| 266_S | 272_D | 1.073 | 0.49 |
| 38_I | 71_H | 1.069 | 0.49 |
| 205_P | 219_F | 1.064 | 0.48 |
| 68_L | 167_R | 1.063 | 0.48 |
| 114_V | 193_I | 1.062 | 0.48 |
| 37_Q | 219_F | 1.061 | 0.48 |
| 269_A | 272_D | 1.058 | 0.48 |
| 107_S | 232_W | 1.057 | 0.48 |
| 205_P | 229_L | 1.053 | 0.47 |
| 32_E | 115_K | 1.051 | 0.47 |
| 23_L | 37_Q | 1.048 | 0.47 |
| 265_K | 272_D | 1.047 | 0.47 |
| 117_W | 194_S | 1.046 | 0.46 |
| 81_V | 84_E | 1.045 | 0.46 |
| 105_D | 135_S | 1.041 | 0.46 |
| 86_F | 117_W | 1.040 | 0.46 |
| 112_V | 202_M | 1.039 | 0.46 |
| 267_S | 271_S | 1.036 | 0.45 |
| 270_P | 273_L | 1.035 | 0.45 |
| 46_E | 115_K | 1.032 | 0.45 |
| 261_L | 269_A | 1.029 | 0.45 |
| 156_I | 176_I | 1.028 | 0.45 |
| 45_Y | 149_G | 1.028 | 0.45 |
| 267_S | 270_P | 1.026 | 0.44 |
| 258_S | 262_S | 1.025 | 0.44 |
| 46_E | 118_K | 1.024 | 0.44 |
| 135_S | 233_I | 1.023 | 0.44 |
| 37_Q | 96_I | 1.023 | 0.44 |
| 257_S | 260_L | 1.022 | 0.44 |
| 203_D | 230_K | 1.021 | 0.44 |
| 6_A | 174_Y | 1.020 | 0.44 |
| 46_E | 191_K | 1.019 | 0.44 |
| 138_D | 153_S | 1.018 | 0.44 |
| 12_L | 176_I | 1.017 | 0.44 |
| 250_V | 254_A | 1.015 | 0.43 |
| 264_L | 271_S | 1.012 | 0.43 |
| 27_E | 33_R | 1.011 | 0.43 |
| 265_K | 268_T | 1.009 | 0.43 |
| 28_Q | 40_Q | 1.008 | 0.43 |
| 102_I | 204_L | 1.007 | 0.43 |
| 22_N | 33_R | 1.006 | 0.42 |
| 163_D | 170_N | 1.005 | 0.42 |
| 137_V | 179_I | 1.005 | 0.42 |
| 95_R | 98_V | 1.005 | 0.42 |
| 260_L | 268_T | 1.003 | 0.42 |
| 247_N | 251_D | 1.002 | 0.42 |
| 21_L | 172_R | 1.001 | 0.42 |
| 263_L | 273_L | 1.000 | 0.42 |
| 86_F | 118_K | 1.000 | 0.42 |
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 | |
| 2a6tA | 2 | 0.7667 | 100 | 0.526 | Contact Map |
| 2qklB | 1 | 0.3 | 100 | 0.68 | Contact Map |
| 4kg3A | 3 | 0.4833 | 99.9 | 0.794 | Contact Map |
| 3o8sA | 1 | 0.44 | 99.8 | 0.84 | Contact Map |
| 3q1pA | 2 | 0.6467 | 99.7 | 0.848 | Contact Map |
| 4hfqA | 2 | 0.6567 | 99.7 | 0.848 | Contact Map |
| 1f3yA | 1 | 0.4767 | 99.6 | 0.855 | Contact Map |
| 4ickA | 2 | 0.45 | 99.6 | 0.856 | Contact Map |
| 3fcmA | 2 | 0.5367 | 99.6 | 0.859 | Contact Map |
| 1vk6A | 1 | 0.7033 | 99.6 | 0.86 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)