| 5IRE_C_Chain -force run |
| ID: | 1476559359 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 501 (488) | ||
| Sequences: | 85 (64.1) | ||
| Seq/Len: | 0.174 | ||
| Nf(neff/√len): | 2.9 |
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: 0.174).
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 |
| 141_L | 180_L | 1.956 | 0.54 |
| 12_V | 211_W | 1.716 | 0.41 |
| 85_Q | 114_V | 1.714 | 0.40 |
| 480_K | 491_L | 1.626 | 0.36 |
| 265_V | 270_A | 1.578 | 0.33 |
| 82_L | 85_Q | 1.561 | 0.32 |
| 175_R | 189_D | 1.554 | 0.32 |
| 186_L | 488_C | 1.547 | 0.32 |
| 76_T | 441_L | 1.539 | 0.31 |
| 264_A | 268_A | 1.532 | 0.31 |
| 89_Q | 120_A | 1.506 | 0.30 |
| 34_M | 422_A | 1.479 | 0.28 |
| 195_G | 252_R | 1.464 | 0.28 |
| 15_M | 491_L | 1.460 | 0.27 |
| 139_I | 221_I | 1.439 | 0.26 |
| 125_M | 265_V | 1.430 | 0.26 |
| 80_A | 112_S | 1.415 | 0.25 |
| 194_T | 200_D | 1.389 | 0.24 |
| 490_A | 493_G | 1.387 | 0.24 |
| 133_E | 289_L | 1.379 | 0.24 |
| 99_R | 105_C | 1.365 | 0.23 |
| 99_R | 111_G | 1.365 | 0.23 |
| 100_G | 105_C | 1.365 | 0.23 |
| 100_G | 111_G | 1.365 | 0.23 |
| 101_W | 105_C | 1.365 | 0.23 |
| 101_W | 111_G | 1.365 | 0.23 |
| 105_C | 111_G | 1.365 | 0.23 |
| 318_P | 453_F | 1.361 | 0.23 |
| 135_L | 203_Y | 1.355 | 0.23 |
| 2_R | 297_K | 1.351 | 0.23 |
| 171_P | 295_M | 1.346 | 0.22 |
| 341_V | 371_N | 1.332 | 0.22 |
| 33_V | 41_V | 1.328 | 0.22 |
| 113_L | 221_I | 1.321 | 0.21 |
| 417_G | 420_R | 1.320 | 0.21 |
| 82_L | 114_V | 1.305 | 0.21 |
| 14_G | 42_D | 1.296 | 0.20 |
| 117_A | 443_K | 1.290 | 0.20 |
| 298_L | 362_N | 1.290 | 0.20 |
| 43_I | 444_G | 1.279 | 0.20 |
| 41_V | 186_L | 1.275 | 0.20 |
| 300_L | 463_F | 1.274 | 0.20 |
| 69_A | 134_N | 1.271 | 0.20 |
| 127_G | 218_F | 1.268 | 0.19 |
| 33_V | 182_G | 1.265 | 0.19 |
| 310_A | 444_G | 1.249 | 0.19 |
| 424_L | 427_T | 1.248 | 0.19 |
| 421_M | 477_L | 1.247 | 0.19 |
| 19_T | 181_G | 1.245 | 0.19 |
| 209_K | 234_P | 1.240 | 0.18 |
| 165_A | 333_A | 1.240 | 0.18 |
| 222_P | 416_R | 1.239 | 0.18 |
| 246_K | 322_L | 1.237 | 0.18 |
| 252_R | 332_Y | 1.235 | 0.18 |
| 418_A | 456_L | 1.227 | 0.18 |
| 125_M | 489_L | 1.225 | 0.18 |
| 214_H | 496_I | 1.223 | 0.18 |
| 19_T | 322_L | 1.223 | 0.18 |
| 355_V | 384_D | 1.221 | 0.18 |
| 18_G | 136_E | 1.215 | 0.18 |
| 181_G | 322_L | 1.214 | 0.18 |
| 36_Q | 139_I | 1.213 | 0.17 |
| 78_G | 98_D | 1.212 | 0.17 |
| 258_L | 271_G | 1.212 | 0.17 |
| 376_L | 396_I | 1.212 | 0.17 |
| 478_N | 494_V | 1.210 | 0.17 |
| 246_K | 274_E | 1.207 | 0.17 |
| 410_A | 495_L | 1.207 | 0.17 |
| 203_Y | 228_G | 1.207 | 0.17 |
| 69_A | 84_K | 1.203 | 0.17 |
| 376_L | 499_S | 1.201 | 0.17 |
| 426_D | 496_I | 1.200 | 0.17 |
| 430_D | 435_G | 1.198 | 0.17 |
| 20_W | 104_G | 1.198 | 0.17 |
| 4_I | 419_K | 1.194 | 0.17 |
| 175_R | 314_F | 1.192 | 0.17 |
| 82_L | 481_N | 1.191 | 0.17 |
| 414_T | 450_G | 1.190 | 0.17 |
| 135_L | 310_A | 1.188 | 0.17 |
| 192_P | 289_L | 1.188 | 0.17 |
| 169_I | 186_L | 1.185 | 0.17 |
| 60_C | 121_C | 1.184 | 0.17 |
| 115_T | 354_P | 1.183 | 0.16 |
| 264_A | 385_S | 1.179 | 0.16 |
| 389_I | 452_A | 1.179 | 0.16 |
| 286_S | 337_G | 1.178 | 0.16 |
| 37_D | 465_Q | 1.175 | 0.16 |
| 117_A | 441_L | 1.174 | 0.16 |
| 168_E | 313_T | 1.172 | 0.16 |
| 137_Y | 297_K | 1.172 | 0.16 |
| 139_I | 278_D | 1.172 | 0.16 |
| 83_D | 135_L | 1.168 | 0.16 |
| 62_E | 257_V | 1.167 | 0.16 |
| 37_D | 68_M | 1.165 | 0.16 |
| 7_S | 29_G | 1.165 | 0.16 |
| 185_S | 496_I | 1.165 | 0.16 |
| 396_I | 401_H | 1.162 | 0.16 |
| 96_L | 189_D | 1.161 | 0.16 |
| 307_L | 341_V | 1.160 | 0.16 |
| 406_T | 448_I | 1.157 | 0.16 |
| 52_N | 299_R | 1.156 | 0.16 |
| 168_E | 394_K | 1.156 | 0.16 |
| 28_G | 76_T | 1.155 | 0.16 |
| 438_L | 448_I | 1.152 | 0.16 |
| 309_T | 461_S | 1.150 | 0.15 |
| 65_I | 353_T | 1.148 | 0.15 |
| 48_T | 419_K | 1.148 | 0.15 |
| 12_V | 485_S | 1.148 | 0.15 |
| 90_Y | 445_I | 1.147 | 0.15 |
| 7_S | 451_A | 1.142 | 0.15 |
| 49_T | 482_G | 1.141 | 0.15 |
| 289_L | 389_I | 1.139 | 0.15 |
| 425_G | 433_S | 1.137 | 0.15 |
| 423_V | 456_L | 1.135 | 0.15 |
| 431_F | 446_H | 1.134 | 0.15 |
| 84_K | 134_N | 1.131 | 0.15 |
| 341_V | 463_F | 1.130 | 0.15 |
| 135_L | 198_F | 1.128 | 0.15 |
| 421_M | 444_G | 1.128 | 0.15 |
| 194_T | 389_I | 1.125 | 0.15 |
| 463_F | 468_I | 1.125 | 0.15 |
| 430_D | 433_S | 1.121 | 0.15 |
| 189_D | 487_M | 1.121 | 0.15 |
| 419_K | 487_M | 1.119 | 0.15 |
| 13_E | 297_K | 1.118 | 0.15 |
| 224_P | 236_W | 1.114 | 0.14 |
| 430_D | 436_G | 1.109 | 0.14 |
| 432_G | 435_G | 1.108 | 0.14 |
| 265_V | 320_E | 1.107 | 0.14 |
| 20_W | 356_G | 1.106 | 0.14 |
| 72_S | 378_L | 1.105 | 0.14 |
| 431_F | 435_G | 1.104 | 0.14 |
| 59_Y | 170_T | 1.104 | 0.14 |
| 174_P | 253_Q | 1.103 | 0.14 |
| 170_T | 206_M | 1.103 | 0.14 |
| 20_W | 385_S | 1.102 | 0.14 |
| 307_L | 313_T | 1.101 | 0.14 |
| 200_D | 398_H | 1.100 | 0.14 |
| 224_P | 287_G | 1.099 | 0.14 |
| 40_T | 289_L | 1.096 | 0.14 |
| 203_Y | 466_I | 1.096 | 0.14 |
| 186_L | 444_G | 1.096 | 0.14 |
| 192_P | 345_M | 1.092 | 0.14 |
| 316_K | 330_V | 1.092 | 0.14 |
| 255_V | 411_F | 1.091 | 0.14 |
| 123_K | 393_E | 1.091 | 0.14 |
| 11_F | 469_G | 1.089 | 0.14 |
| 104_G | 356_G | 1.087 | 0.14 |
| 422_A | 490_A | 1.086 | 0.14 |
| 365_I | 456_L | 1.085 | 0.14 |
| 431_F | 436_G | 1.085 | 0.14 |
| 59_Y | 127_G | 1.085 | 0.14 |
| 271_G | 320_E | 1.082 | 0.13 |
| 423_V | 466_I | 1.082 | 0.13 |
| 46_V | 70_S | 1.082 | 0.13 |
| 169_I | 365_I | 1.080 | 0.13 |
| 253_Q | 289_L | 1.080 | 0.13 |
| 368_S | 398_H | 1.080 | 0.13 |
| 251_K | 304_S | 1.079 | 0.13 |
| 248_A | 293_L | 1.078 | 0.13 |
| 71_D | 204_L | 1.078 | 0.13 |
| 433_S | 436_G | 1.078 | 0.13 |
| 22_D | 133_E | 1.076 | 0.13 |
| 2_R | 351_T | 1.074 | 0.13 |
| 80_A | 362_N | 1.071 | 0.13 |
| 12_V | 64_S | 1.070 | 0.13 |
| 137_Y | 288_H | 1.069 | 0.13 |
| 136_E | 419_K | 1.069 | 0.13 |
| 316_K | 389_I | 1.068 | 0.13 |
| 316_K | 409_K | 1.067 | 0.13 |
| 224_P | 363_P | 1.066 | 0.13 |
| 54_A | 428_A | 1.065 | 0.13 |
| 465_Q | 484_I | 1.065 | 0.13 |
| 84_K | 410_A | 1.063 | 0.13 |
| 420_R | 430_D | 1.063 | 0.13 |
| 104_G | 385_S | 1.062 | 0.13 |
| 418_A | 422_A | 1.062 | 0.13 |
| 417_G | 446_H | 1.060 | 0.13 |
| 270_A | 320_E | 1.060 | 0.13 |
| 432_G | 436_G | 1.059 | 0.13 |
| 166_K | 219_H | 1.059 | 0.13 |
| 217_W | 236_W | 1.058 | 0.13 |
| 86_S | 326_V | 1.058 | 0.13 |
| 425_G | 435_G | 1.058 | 0.13 |
| 95_T | 194_T | 1.056 | 0.13 |
| 173_S | 330_V | 1.056 | 0.13 |
| 358_L | 456_L | 1.055 | 0.13 |
| 131_Q | 134_N | 1.054 | 0.13 |
| 16_S | 34_M | 1.054 | 0.13 |
| 84_K | 460_M | 1.054 | 0.13 |
| 214_H | 219_H | 1.053 | 0.13 |
| 177_E | 340_K | 1.050 | 0.13 |
| 428_A | 436_G | 1.050 | 0.13 |
| 321_T | 324_G | 1.049 | 0.13 |
| 147_Q | 275_A | 1.049 | 0.13 |
| 417_G | 433_S | 1.047 | 0.13 |
| 66_S | 95_T | 1.047 | 0.13 |
| 474_W | 492_G | 1.047 | 0.13 |
| 224_P | 308_C | 1.047 | 0.13 |
| 293_L | 296_D | 1.046 | 0.13 |
| 168_E | 350_Q | 1.043 | 0.12 |
| 32_T | 492_G | 1.043 | 0.12 |
| 293_L | 311_A | 1.043 | 0.12 |
| 119_F | 435_G | 1.041 | 0.12 |
| 99_R | 190_C | 1.041 | 0.12 |
| 100_G | 190_C | 1.041 | 0.12 |
| 101_W | 190_C | 1.041 | 0.12 |
| 105_C | 190_C | 1.041 | 0.12 |
| 111_G | 190_C | 1.041 | 0.12 |
| 295_M | 483_S | 1.041 | 0.12 |
| 220_D | 224_P | 1.039 | 0.12 |
| 254_T | 401_H | 1.039 | 0.12 |
| 289_L | 357_R | 1.039 | 0.12 |
| 58_S | 216_E | 1.038 | 0.12 |
| 183_F | 265_V | 1.037 | 0.12 |
| 257_V | 273_L | 1.036 | 0.12 |
| 248_A | 284_L | 1.035 | 0.12 |
| 414_T | 417_G | 1.034 | 0.12 |
| 479_T | 495_L | 1.034 | 0.12 |
| 432_G | 455_S | 1.032 | 0.12 |
| 67_D | 84_K | 1.032 | 0.12 |
| 95_T | 485_S | 1.032 | 0.12 |
| 238_N | 343_A | 1.031 | 0.12 |
| 337_G | 361_A | 1.031 | 0.12 |
| 35_A | 245_F | 1.030 | 0.12 |
| 134_N | 253_Q | 1.030 | 0.12 |
| 424_L | 439_N | 1.029 | 0.12 |
| 223_L | 301_K | 1.029 | 0.12 |
| 53_M | 282_G | 1.027 | 0.12 |
| 189_D | 255_V | 1.026 | 0.12 |
| 175_R | 402_R | 1.025 | 0.12 |
| 420_R | 425_G | 1.025 | 0.12 |
| 183_F | 223_L | 1.023 | 0.12 |
| 464_S | 499_S | 1.023 | 0.12 |
| 192_P | 253_Q | 1.021 | 0.12 |
| 367_E | 491_L | 1.020 | 0.12 |
| 78_G | 110_K | 1.019 | 0.12 |
| 115_T | 169_I | 1.018 | 0.12 |
| 184_G | 339_C | 1.017 | 0.12 |
| 183_F | 301_K | 1.017 | 0.12 |
| 113_L | 475_L | 1.017 | 0.12 |
| 322_L | 421_M | 1.016 | 0.12 |
| 399_H | 483_S | 1.014 | 0.12 |
| 158_H | 169_I | 1.014 | 0.12 |
| 19_T | 173_S | 1.012 | 0.12 |
| 139_I | 315_T | 1.012 | 0.12 |
| 466_I | 484_I | 1.010 | 0.12 |
| 131_Q | 345_M | 1.010 | 0.12 |
| 48_T | 289_L | 1.009 | 0.12 |
| 65_I | 90_Y | 1.008 | 0.12 |
| 88_T | 486_L | 1.008 | 0.12 |
| 306_S | 412_E | 1.006 | 0.12 |
| 185_S | 468_I | 1.006 | 0.12 |
| 448_I | 486_L | 1.006 | 0.12 |
| 19_T | 29_G | 1.004 | 0.12 |
| 162_E | 299_R | 1.003 | 0.11 |
| 72_S | 472_L | 1.003 | 0.11 |
| 203_Y | 423_V | 1.003 | 0.11 |
| 286_S | 357_R | 1.001 | 0.11 |
| 236_W | 377_E | 1.001 | 0.11 |
| 424_L | 428_A | 1.001 | 0.11 |
| 33_V | 215_K | 1.000 | 0.11 |
| 302_G | 363_P | 1.000 | 0.11 |
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 | |
| 4cctA | 3 | 0.982 | 100 | 0 | Contact Map |
| 3j27A | 3 | 0.982 | 100 | 0.003 | Contact Map |
| 4cbfA | 3 | 0.982 | 100 | 0.007 | Contact Map |
| 4gsxA | 2 | 0.7824 | 100 | 0.186 | Contact Map |
| 3p54A | 1 | 0.8024 | 100 | 0.189 | Contact Map |
| 4fg0A | 1 | 0.7705 | 100 | 0.19 | Contact Map |
| 3uajB | 2 | 0.7505 | 100 | 0.206 | Contact Map |
| 1ok8A | 1 | 0.7585 | 100 | 0.221 | Contact Map |
| 1svbA | 1 | 0.7705 | 100 | 0.23 | Contact Map |
| 3uc0A | 2 | 0.2315 | 100 | 0.76 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)