| T0777 -force run |
| ID: | 1400096900 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 366 (349) | ||
| Sequences: | 98 (79.5) | ||
| Seq/Len: | 0.281 | ||
| Nf(neff/√len): | 4.3 |
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: 0.281).
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 |
| 322_M | 328_R | 2.656 | 0.93 |
| 318_W | 328_R | 2.592 | 0.92 |
| 66_K | 101_T | 2.076 | 0.75 |
| 318_W | 322_M | 1.999 | 0.71 |
| 58_Y | 101_T | 1.819 | 0.61 |
| 58_Y | 66_K | 1.786 | 0.59 |
| 137_A | 220_S | 1.783 | 0.58 |
| 315_L | 318_W | 1.765 | 0.57 |
| 139_I | 157_I | 1.704 | 0.53 |
| 311_G | 322_M | 1.694 | 0.53 |
| 118_G | 138_A | 1.685 | 0.52 |
| 74_K | 135_N | 1.638 | 0.49 |
| 132_I | 243_D | 1.638 | 0.49 |
| 18_H | 191_F | 1.625 | 0.48 |
| 322_M | 327_S | 1.577 | 0.45 |
| 44_L | 49_T | 1.573 | 0.45 |
| 319_R | 328_R | 1.560 | 0.44 |
| 315_L | 328_R | 1.537 | 0.42 |
| 104_S | 246_Y | 1.515 | 0.41 |
| 258_F | 268_F | 1.501 | 0.40 |
| 54_N | 253_F | 1.478 | 0.39 |
| 284_P | 294_N | 1.462 | 0.38 |
| 95_L | 123_L | 1.461 | 0.37 |
| 105_A | 276_Q | 1.432 | 0.36 |
| 93_I | 139_I | 1.427 | 0.35 |
| 17_G | 299_V | 1.415 | 0.35 |
| 47_T | 154_T | 1.395 | 0.33 |
| 113_C | 122_C | 1.386 | 0.33 |
| 315_L | 322_M | 1.374 | 0.32 |
| 195_M | 335_V | 1.360 | 0.31 |
| 77_D | 80_A | 1.351 | 0.31 |
| 224_S | 232_L | 1.351 | 0.31 |
| 247_L | 251_L | 1.348 | 0.31 |
| 134_Y | 294_N | 1.333 | 0.30 |
| 234_N | 310_S | 1.324 | 0.29 |
| 232_L | 243_D | 1.321 | 0.29 |
| 65_F | 68_V | 1.319 | 0.29 |
| 4_S | 255_A | 1.315 | 0.29 |
| 138_A | 257_N | 1.312 | 0.29 |
| 175_E | 253_F | 1.312 | 0.29 |
| 19_V | 179_A | 1.307 | 0.28 |
| 16_S | 29_G | 1.306 | 0.28 |
| 149_I | 195_M | 1.304 | 0.28 |
| 145_K | 191_F | 1.301 | 0.28 |
| 90_G | 246_Y | 1.295 | 0.28 |
| 60_D | 77_D | 1.286 | 0.27 |
| 315_L | 324_S | 1.286 | 0.27 |
| 319_R | 322_M | 1.284 | 0.27 |
| 64_M | 139_I | 1.282 | 0.27 |
| 90_G | 97_W | 1.278 | 0.27 |
| 4_S | 156_T | 1.270 | 0.27 |
| 245_D | 264_E | 1.262 | 0.26 |
| 107_P | 124_A | 1.262 | 0.26 |
| 4_S | 29_G | 1.261 | 0.26 |
| 46_G | 230_P | 1.260 | 0.26 |
| 62_L | 335_V | 1.259 | 0.26 |
| 47_T | 55_G | 1.256 | 0.26 |
| 191_F | 306_V | 1.249 | 0.25 |
| 321_L | 334_M | 1.249 | 0.25 |
| 26_R | 135_N | 1.242 | 0.25 |
| 235_Y | 252_Y | 1.242 | 0.25 |
| 55_G | 94_Y | 1.241 | 0.25 |
| 236_N | 276_Q | 1.229 | 0.24 |
| 210_Q | 284_P | 1.228 | 0.24 |
| 44_L | 150_F | 1.227 | 0.24 |
| 249_S | 255_A | 1.226 | 0.24 |
| 314_S | 321_L | 1.224 | 0.24 |
| 322_M | 332_R | 1.224 | 0.24 |
| 324_S | 327_S | 1.222 | 0.24 |
| 6_C | 108_T | 1.219 | 0.24 |
| 7_V | 54_N | 1.218 | 0.24 |
| 258_F | 280_G | 1.214 | 0.24 |
| 62_L | 92_T | 1.211 | 0.24 |
| 90_G | 128_W | 1.205 | 0.23 |
| 57_N | 62_L | 1.198 | 0.23 |
| 58_Y | 304_Y | 1.194 | 0.23 |
| 79_F | 287_P | 1.193 | 0.23 |
| 42_D | 145_K | 1.189 | 0.23 |
| 16_S | 135_N | 1.187 | 0.22 |
| 232_L | 280_G | 1.180 | 0.22 |
| 7_V | 13_S | 1.170 | 0.22 |
| 93_I | 255_A | 1.170 | 0.22 |
| 313_S | 324_S | 1.168 | 0.22 |
| 311_G | 328_R | 1.164 | 0.21 |
| 90_G | 98_I | 1.164 | 0.21 |
| 97_W | 140_A | 1.162 | 0.21 |
| 17_G | 243_D | 1.158 | 0.21 |
| 4_S | 11_L | 1.158 | 0.21 |
| 3_L | 18_H | 1.153 | 0.21 |
| 220_S | 247_L | 1.153 | 0.21 |
| 139_I | 220_S | 1.144 | 0.21 |
| 191_F | 220_S | 1.140 | 0.20 |
| 58_Y | 74_K | 1.140 | 0.20 |
| 318_W | 327_S | 1.139 | 0.20 |
| 209_A | 279_F | 1.137 | 0.20 |
| 48_D | 191_F | 1.136 | 0.20 |
| 60_D | 289_M | 1.132 | 0.20 |
| 58_Y | 175_E | 1.130 | 0.20 |
| 98_I | 136_P | 1.126 | 0.20 |
| 90_G | 102_G | 1.125 | 0.20 |
| 328_R | 332_R | 1.124 | 0.20 |
| 106_D | 268_F | 1.124 | 0.20 |
| 137_A | 224_S | 1.122 | 0.20 |
| 293_K | 296_L | 1.121 | 0.20 |
| 206_M | 221_M | 1.120 | 0.20 |
| 279_F | 301_H | 1.119 | 0.20 |
| 43_Q | 151_G | 1.116 | 0.19 |
| 5_L | 16_S | 1.114 | 0.19 |
| 249_S | 309_L | 1.111 | 0.19 |
| 56_F | 124_A | 1.110 | 0.19 |
| 169_Y | 228_C | 1.102 | 0.19 |
| 171_S | 193_Y | 1.102 | 0.19 |
| 93_I | 156_T | 1.096 | 0.19 |
| 314_S | 322_M | 1.094 | 0.18 |
| 134_Y | 284_P | 1.093 | 0.18 |
| 14_V | 27_G | 1.093 | 0.18 |
| 163_K | 274_H | 1.091 | 0.18 |
| 288_D | 335_V | 1.089 | 0.18 |
| 101_T | 118_G | 1.088 | 0.18 |
| 6_C | 17_G | 1.081 | 0.18 |
| 32_F | 310_S | 1.078 | 0.18 |
| 210_Q | 220_S | 1.076 | 0.18 |
| 244_R | 306_V | 1.073 | 0.18 |
| 28_D | 289_M | 1.070 | 0.18 |
| 135_N | 139_I | 1.068 | 0.17 |
| 128_W | 293_K | 1.065 | 0.17 |
| 31_P | 122_C | 1.065 | 0.17 |
| 29_G | 93_I | 1.061 | 0.17 |
| 72_T | 252_Y | 1.058 | 0.17 |
| 94_Y | 139_I | 1.052 | 0.17 |
| 135_N | 206_M | 1.051 | 0.17 |
| 174_E | 219_T | 1.050 | 0.17 |
| 74_K | 191_F | 1.049 | 0.17 |
| 321_L | 327_S | 1.049 | 0.17 |
| 6_C | 232_L | 1.048 | 0.17 |
| 246_Y | 252_Y | 1.047 | 0.17 |
| 90_G | 104_S | 1.044 | 0.17 |
| 90_G | 140_A | 1.043 | 0.17 |
| 324_S | 328_R | 1.041 | 0.16 |
| 111_T | 121_M | 1.039 | 0.16 |
| 150_F | 244_R | 1.039 | 0.16 |
| 328_R | 335_V | 1.038 | 0.16 |
| 62_L | 93_I | 1.031 | 0.16 |
| 65_F | 88_Y | 1.031 | 0.16 |
| 4_S | 93_I | 1.030 | 0.16 |
| 52_I | 143_A | 1.027 | 0.16 |
| 287_P | 322_M | 1.027 | 0.16 |
| 98_I | 140_A | 1.025 | 0.16 |
| 28_D | 179_A | 1.025 | 0.16 |
| 4_S | 249_S | 1.024 | 0.16 |
| 331_A | 338_I | 1.023 | 0.16 |
| 159_L | 180_Y | 1.022 | 0.16 |
| 71_G | 74_K | 1.020 | 0.16 |
| 38_A | 63_S | 1.015 | 0.16 |
| 52_I | 151_G | 1.015 | 0.16 |
| 313_S | 321_L | 1.015 | 0.16 |
| 26_R | 139_I | 1.014 | 0.16 |
| 40_T | 252_Y | 1.014 | 0.16 |
| 49_T | 252_Y | 1.014 | 0.16 |
| 94_Y | 272_M | 1.012 | 0.15 |
| 6_C | 167_S | 1.010 | 0.15 |
| 48_D | 244_R | 1.009 | 0.15 |
| 35_D | 82_N | 1.008 | 0.15 |
| 19_V | 283_A | 1.006 | 0.15 |
| 4_S | 57_N | 1.004 | 0.15 |
| 190_Y | 210_Q | 1.002 | 0.15 |
| 232_L | 304_Y | 1.002 | 0.15 |
| 107_P | 275_R | 1.000 | 0.15 |
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 | |
| 1zxhA | 1 | 0.1066 | 26 | 0.981 | Contact Map |
| 2fj6A | 1 | 0.1694 | 13.1 | 0.983 | Contact Map |
| 2o6kA | 2 | 0.153 | 7.1 | 0.985 | Contact Map |
| 4n85A | 2 | 0.2158 | 6.9 | 0.985 | Contact Map |
| 3filA | 1 | 0.1066 | 5.4 | 0.986 | Contact Map |
| 3eslA | 2 | 0.5164 | 5.2 | 0.986 | Contact Map |
| 4nyxA | 1 | 0.1311 | 4.7 | 0.986 | Contact Map |
| 2kvsA | 1 | 0.1694 | 4.4 | 0.987 | Contact Map |
| 2dt6A | 1 | 0.1257 | 4.1 | 0.987 | Contact Map |
| 1igdA | 1 | 0.123 | 4 | 0.987 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)