| rad_fl 360-640 |
| ID: | 1509398211 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 281 (264) | ||
| Sequences: | 780 (644.4) | ||
| Seq/Len: | 2.955 | ||
| Nf(neff/√len): | 39.7 |
HHblits Results: (2016_02)
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: 2.955).
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 |
| 244_A | 269_M | 2.795 | 1.00 |
| 226_V | 259_H | 2.574 | 1.00 |
| 219_K | 253_Q | 2.408 | 1.00 |
| 18_T | 36_V | 2.255 | 1.00 |
| 30_V | 33_E | 2.157 | 1.00 |
| 171_I | 250_I | 2.096 | 1.00 |
| 226_V | 235_F | 2.093 | 1.00 |
| 35_G | 38_S | 2.017 | 1.00 |
| 170_L | 238_G | 1.989 | 1.00 |
| 172_A | 178_I | 1.867 | 0.99 |
| 169_Y | 235_F | 1.828 | 0.99 |
| 236_W | 263_S | 1.811 | 0.99 |
| 229_Q | 235_F | 1.806 | 0.99 |
| 249_E | 253_Q | 1.781 | 0.99 |
| 226_V | 257_L | 1.665 | 0.98 |
| 175_T | 240_F | 1.654 | 0.98 |
| 181_Y | 240_F | 1.653 | 0.98 |
| 232_G | 235_F | 1.639 | 0.98 |
| 241_S | 268_D | 1.608 | 0.97 |
| 173_D | 240_F | 1.598 | 0.97 |
| 31_V | 70_I | 1.598 | 0.97 |
| 249_E | 252_R | 1.594 | 0.97 |
| 45_A | 56_L | 1.572 | 0.97 |
| 218_A | 249_E | 1.537 | 0.96 |
| 14_I | 36_V | 1.529 | 0.96 |
| 167_P | 192_M | 1.528 | 0.96 |
| 173_D | 181_Y | 1.492 | 0.95 |
| 172_A | 221_I | 1.468 | 0.95 |
| 252_R | 256_A | 1.451 | 0.94 |
| 106_H | 110_P | 1.424 | 0.94 |
| 31_V | 40_M | 1.422 | 0.94 |
| 180_T | 240_F | 1.418 | 0.93 |
| 171_I | 246_I | 1.413 | 0.93 |
| 60_F | 70_I | 1.412 | 0.93 |
| 199_S | 221_I | 1.409 | 0.93 |
| 56_L | 60_F | 1.401 | 0.93 |
| 10_L | 48_V | 1.398 | 0.93 |
| 18_T | 31_V | 1.397 | 0.93 |
| 15_V | 22_P | 1.389 | 0.92 |
| 107_V | 110_P | 1.388 | 0.92 |
| 6_F | 74_F | 1.342 | 0.91 |
| 169_Y | 229_Q | 1.340 | 0.91 |
| 27_D | 71_K | 1.335 | 0.90 |
| 13_T | 48_V | 1.322 | 0.90 |
| 271_P | 277_A | 1.320 | 0.90 |
| 218_A | 246_I | 1.317 | 0.90 |
| 104_V | 107_V | 1.313 | 0.89 |
| 59_M | 63_E | 1.312 | 0.89 |
| 105_V | 110_P | 1.294 | 0.88 |
| 172_A | 240_F | 1.288 | 0.88 |
| 235_F | 259_H | 1.264 | 0.87 |
| 168_F | 272_P | 1.258 | 0.87 |
| 171_I | 225_L | 1.257 | 0.86 |
| 14_I | 18_T | 1.257 | 0.86 |
| 167_P | 193_T | 1.253 | 0.86 |
| 99_V | 102_E | 1.252 | 0.86 |
| 224_E | 227_K | 1.250 | 0.86 |
| 69_D | 72_R | 1.240 | 0.85 |
| 57_T | 60_F | 1.236 | 0.85 |
| 31_V | 36_V | 1.233 | 0.85 |
| 257_L | 267_I | 1.223 | 0.84 |
| 111_S | 114_S | 1.222 | 0.84 |
| 102_E | 105_V | 1.214 | 0.84 |
| 214_I | 246_I | 1.213 | 0.84 |
| 208_L | 277_A | 1.212 | 0.84 |
| 21_D | 24_E | 1.204 | 0.83 |
| 132_Q | 135_R | 1.196 | 0.83 |
| 32_A | 36_V | 1.194 | 0.82 |
| 172_A | 196_G | 1.193 | 0.82 |
| 252_R | 272_P | 1.182 | 0.82 |
| 110_P | 114_S | 1.167 | 0.80 |
| 231_Q | 259_H | 1.167 | 0.80 |
| 245_M | 275_I | 1.159 | 0.80 |
| 112_S | 115_L | 1.156 | 0.80 |
| 172_A | 242_G | 1.155 | 0.79 |
| 218_A | 250_I | 1.152 | 0.79 |
| 16_S | 47_K | 1.150 | 0.79 |
| 169_Y | 225_L | 1.148 | 0.79 |
| 222_V | 250_I | 1.145 | 0.79 |
| 23_S | 67_I | 1.144 | 0.79 |
| 167_P | 195_Y | 1.137 | 0.78 |
| 117_A | 120_T | 1.136 | 0.78 |
| 39_I | 42_I | 1.135 | 0.78 |
| 253_Q | 256_A | 1.127 | 0.77 |
| 32_A | 62_H | 1.126 | 0.77 |
| 201_Y | 277_A | 1.126 | 0.77 |
| 215_P | 253_Q | 1.125 | 0.77 |
| 213_G | 216_G | 1.122 | 0.77 |
| 176_G | 249_E | 1.119 | 0.76 |
| 236_W | 262_D | 1.117 | 0.76 |
| 274_Q | 277_A | 1.116 | 0.76 |
| 149_L | 152_G | 1.114 | 0.76 |
| 215_P | 256_A | 1.113 | 0.76 |
| 111_S | 115_L | 1.112 | 0.76 |
| 107_V | 111_S | 1.109 | 0.75 |
| 229_Q | 232_G | 1.108 | 0.75 |
| 175_T | 181_Y | 1.107 | 0.75 |
| 39_I | 48_V | 1.101 | 0.75 |
| 92_Y | 95_L | 1.100 | 0.75 |
| 229_Q | 259_H | 1.097 | 0.74 |
| 167_P | 232_G | 1.095 | 0.74 |
| 172_A | 200_P | 1.093 | 0.74 |
| 117_A | 122_S | 1.089 | 0.74 |
| 26_T | 29_T | 1.078 | 0.73 |
| 109_S | 114_S | 1.078 | 0.73 |
| 175_T | 270_C | 1.076 | 0.72 |
| 107_V | 112_S | 1.074 | 0.72 |
| 64_Y | 73_A | 1.073 | 0.72 |
| 27_D | 67_I | 1.072 | 0.72 |
| 106_H | 111_S | 1.071 | 0.72 |
| 43_E | 46_N | 1.069 | 0.72 |
| 31_V | 37_D | 1.062 | 0.71 |
| 31_V | 62_H | 1.055 | 0.70 |
| 101_E | 105_V | 1.051 | 0.70 |
| 30_V | 36_V | 1.051 | 0.70 |
| 230_P | 235_F | 1.033 | 0.68 |
| 33_E | 78_T | 1.025 | 0.67 |
| 243_G | 254_L | 1.022 | 0.67 |
| 122_S | 125_T | 1.021 | 0.67 |
| 113_T | 117_A | 1.021 | 0.67 |
| 66_T | 225_L | 1.019 | 0.66 |
| 239_G | 243_G | 1.016 | 0.66 |
| 240_F | 244_A | 1.014 | 0.66 |
| 112_S | 117_A | 1.012 | 0.66 |
| 195_Y | 199_S | 1.007 | 0.65 |
| 117_A | 121_G | 1.007 | 0.65 |
| 251_A | 264_L | 1.002 | 0.64 |
| 99_V | 107_V | 1.001 | 0.64 |
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 | |
| 2vz8A | 2 | 0 | 100 | 0.355 | Contact Map |
| 3tejA | 2 | 0.7295 | 100 | 0.445 | Contact Map |
| 2vsqA | 1 | 0.669 | 100 | 0.48 | Contact Map |
| 2px6A | 2 | 0.427 | 99.8 | 0.656 | Contact Map |
| 2cb9A | 1 | 0.4128 | 99.8 | 0.677 | Contact Map |
| 1jmkC | 2 | 0.4235 | 99.8 | 0.677 | Contact Map |
| 1kezA | 3 | 0.5907 | 99.7 | 0.685 | Contact Map |
| 3ilsA | 1 | 0.4733 | 99.7 | 0.7 | Contact Map |
| 2k2qB | 1 | 0.4413 | 99.7 | 0.704 | Contact Map |
| 4r0mB | 2 | 0.2598 | 99.6 | 0.72 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)