| 2decoli |
| ID: | 1409920941 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 544 (534) | ||
| Sequences: | 1283 (1064.1) | ||
| Seq/Len: | 2.403 | ||
| Nf(neff/√len): | 46.0 |
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: 2.403).
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 |
| 382_Q | 411_D | 3.463 | 1.00 |
| 256_F | 265_L | 3.022 | 1.00 |
| 417_I | 428_A | 2.706 | 1.00 |
| 271_V | 274_A | 2.692 | 1.00 |
| 160_D | 164_P | 2.662 | 1.00 |
| 14_V | 42_A | 2.603 | 1.00 |
| 492_S | 500_Q | 2.412 | 1.00 |
| 333_R | 357_E | 2.332 | 1.00 |
| 382_Q | 409_L | 2.238 | 1.00 |
| 235_G | 252_P | 2.229 | 1.00 |
| 274_A | 323_V | 2.206 | 1.00 |
| 268_R | 316_I | 2.188 | 1.00 |
| 159_G | 164_P | 2.184 | 1.00 |
| 58_I | 87_A | 2.134 | 1.00 |
| 494_Y | 500_Q | 2.114 | 1.00 |
| 270_D | 318_H | 2.107 | 1.00 |
| 474_S | 493_G | 2.077 | 1.00 |
| 266_D | 314_N | 2.021 | 0.99 |
| 342_Q | 347_L | 1.974 | 0.99 |
| 370_R | 388_E | 1.946 | 0.99 |
| 40_G | 60_L | 1.946 | 0.99 |
| 318_H | 337_D | 1.888 | 0.99 |
| 175_V | 189_S | 1.847 | 0.99 |
| 16_L | 19_F | 1.834 | 0.99 |
| 524_L | 538_L | 1.816 | 0.98 |
| 234_K | 253_D | 1.800 | 0.98 |
| 194_N | 203_A | 1.796 | 0.98 |
| 499_L | 518_Y | 1.774 | 0.98 |
| 199_R | 218_D | 1.752 | 0.98 |
| 128_N | 154_N | 1.744 | 0.98 |
| 172_V | 175_V | 1.726 | 0.98 |
| 215_L | 233_A | 1.698 | 0.97 |
| 343_D | 347_L | 1.662 | 0.97 |
| 340_V | 349_L | 1.653 | 0.97 |
| 521_M | 524_L | 1.640 | 0.97 |
| 499_L | 516_L | 1.636 | 0.96 |
| 495_V | 499_L | 1.610 | 0.96 |
| 49_T | 54_P | 1.610 | 0.96 |
| 148_A | 176_D | 1.605 | 0.96 |
| 376_F | 383_P | 1.592 | 0.96 |
| 349_L | 380_P | 1.568 | 0.95 |
| 273_W | 322_N | 1.559 | 0.95 |
| 365_Q | 391_R | 1.540 | 0.95 |
| 314_N | 339_N | 1.540 | 0.95 |
| 266_D | 312_N | 1.538 | 0.94 |
| 319_V | 336_G | 1.537 | 0.94 |
| 374_L | 387_I | 1.525 | 0.94 |
| 35_S | 66_Q | 1.514 | 0.94 |
| 388_E | 405_R | 1.513 | 0.94 |
| 230_R | 255_V | 1.513 | 0.94 |
| 495_V | 516_L | 1.494 | 0.93 |
| 482_G | 504_G | 1.485 | 0.93 |
| 367_L | 391_R | 1.465 | 0.92 |
| 265_L | 311_I | 1.462 | 0.92 |
| 371_K | 386_N | 1.449 | 0.92 |
| 138_N | 147_A | 1.447 | 0.92 |
| 407_T | 416_E | 1.429 | 0.91 |
| 174_G | 188_P | 1.424 | 0.91 |
| 56_G | 89_L | 1.420 | 0.91 |
| 153_A | 170_L | 1.417 | 0.91 |
| 473_V | 493_G | 1.415 | 0.91 |
| 284_S | 374_L | 1.403 | 0.90 |
| 171_Q | 192_A | 1.402 | 0.90 |
| 378_G | 413_P | 1.393 | 0.90 |
| 494_Y | 497_P | 1.381 | 0.89 |
| 176_D | 185_D | 1.380 | 0.89 |
| 369_V | 387_I | 1.360 | 0.88 |
| 380_P | 391_R | 1.348 | 0.88 |
| 403_G | 418_F | 1.345 | 0.87 |
| 213_I | 238_V | 1.340 | 0.87 |
| 360_F | 413_P | 1.338 | 0.87 |
| 269_V | 288_V | 1.337 | 0.87 |
| 194_N | 201_T | 1.336 | 0.87 |
| 269_V | 317_V | 1.333 | 0.87 |
| 336_G | 353_I | 1.325 | 0.86 |
| 367_L | 403_G | 1.313 | 0.86 |
| 275_R | 322_N | 1.313 | 0.86 |
| 361_H | 366_D | 1.312 | 0.86 |
| 59_T | 66_Q | 1.309 | 0.85 |
| 142_T | 209_Q | 1.294 | 0.84 |
| 474_S | 492_S | 1.277 | 0.83 |
| 503_Y | 512_A | 1.271 | 0.83 |
| 232_T | 255_V | 1.271 | 0.83 |
| 125_G | 157_L | 1.269 | 0.83 |
| 362_A | 367_L | 1.264 | 0.83 |
| 503_Y | 537_D | 1.259 | 0.82 |
| 169_Q | 194_N | 1.258 | 0.82 |
| 264_T | 312_N | 1.257 | 0.82 |
| 531_G | 539_L | 1.255 | 0.82 |
| 129_I | 154_N | 1.254 | 0.82 |
| 157_L | 406_V | 1.254 | 0.82 |
| 534_Q | 539_L | 1.248 | 0.81 |
| 329_G | 364_G | 1.243 | 0.81 |
| 535_A | 542_F | 1.243 | 0.81 |
| 157_L | 161_V | 1.242 | 0.81 |
| 334_L | 353_I | 1.242 | 0.81 |
| 427_A | 431_Y | 1.240 | 0.81 |
| 326_D | 331_K | 1.235 | 0.81 |
| 239_R | 432_L | 1.234 | 0.80 |
| 268_R | 318_H | 1.232 | 0.80 |
| 329_G | 367_L | 1.230 | 0.80 |
| 275_R | 326_D | 1.229 | 0.80 |
| 336_G | 367_L | 1.219 | 0.79 |
| 251_S | 272_P | 1.212 | 0.79 |
| 402_A | 432_L | 1.204 | 0.78 |
| 364_G | 367_L | 1.199 | 0.78 |
| 237_K | 272_P | 1.195 | 0.77 |
| 316_I | 339_N | 1.195 | 0.77 |
| 126_N | 156_R | 1.191 | 0.77 |
| 250_V | 271_V | 1.187 | 0.77 |
| 45_A | 49_T | 1.183 | 0.76 |
| 148_A | 471_F | 1.181 | 0.76 |
| 382_Q | 410_A | 1.180 | 0.76 |
| 501_V | 504_G | 1.179 | 0.76 |
| 15_N | 41_K | 1.177 | 0.76 |
| 346_G | 495_V | 1.175 | 0.76 |
| 140_I | 236_S | 1.174 | 0.76 |
| 428_A | 505_V | 1.172 | 0.75 |
| 16_L | 432_L | 1.171 | 0.75 |
| 385_L | 406_V | 1.170 | 0.75 |
| 332_A | 352_Q | 1.168 | 0.75 |
| 405_R | 416_E | 1.167 | 0.75 |
| 417_I | 505_V | 1.164 | 0.75 |
| 157_L | 166_L | 1.162 | 0.75 |
| 184_F | 367_L | 1.162 | 0.75 |
| 57_S | 86_T | 1.161 | 0.74 |
| 365_Q | 378_G | 1.160 | 0.74 |
| 279_H | 357_E | 1.160 | 0.74 |
| 332_A | 355_I | 1.157 | 0.74 |
| 404_V | 417_I | 1.151 | 0.74 |
| 162_Q | 210_Q | 1.148 | 0.73 |
| 218_D | 230_R | 1.146 | 0.73 |
| 256_F | 271_V | 1.141 | 0.73 |
| 421_P | 435_G | 1.137 | 0.72 |
| 203_A | 214_Y | 1.133 | 0.72 |
| 517_R | 525_Y | 1.132 | 0.72 |
| 330_L | 374_L | 1.131 | 0.72 |
| 41_K | 52_G | 1.130 | 0.72 |
| 315_L | 364_G | 1.130 | 0.72 |
| 452_L | 519_R | 1.129 | 0.72 |
| 453_I | 456_G | 1.127 | 0.71 |
| 431_Y | 437_G | 1.127 | 0.71 |
| 301_P | 304_P | 1.126 | 0.71 |
| 19_F | 35_S | 1.126 | 0.71 |
| 504_G | 515_T | 1.125 | 0.71 |
| 337_D | 455_L | 1.123 | 0.71 |
| 62_G | 65_V | 1.122 | 0.71 |
| 331_K | 493_G | 1.121 | 0.71 |
| 204_G | 250_V | 1.121 | 0.71 |
| 44_V | 53_L | 1.121 | 0.71 |
| 320_G | 333_R | 1.120 | 0.71 |
| 336_G | 378_G | 1.117 | 0.70 |
| 448_M | 452_L | 1.117 | 0.70 |
| 473_V | 476_L | 1.116 | 0.70 |
| 87_A | 96_L | 1.111 | 0.70 |
| 489_V | 492_S | 1.111 | 0.70 |
| 126_N | 154_N | 1.110 | 0.70 |
| 22_A | 25_K | 1.109 | 0.70 |
| 504_G | 508_F | 1.109 | 0.70 |
| 387_I | 406_V | 1.105 | 0.69 |
| 444_D | 518_Y | 1.103 | 0.69 |
| 418_F | 428_A | 1.098 | 0.68 |
| 217_G | 231_V | 1.097 | 0.68 |
| 432_L | 501_V | 1.096 | 0.68 |
| 267_G | 383_P | 1.096 | 0.68 |
| 13_V | 41_K | 1.094 | 0.68 |
| 374_L | 420_D | 1.092 | 0.68 |
| 413_P | 433_L | 1.091 | 0.68 |
| 156_R | 516_L | 1.089 | 0.68 |
| 367_L | 517_R | 1.086 | 0.67 |
| 124_G | 157_L | 1.086 | 0.67 |
| 391_R | 403_G | 1.081 | 0.67 |
| 60_L | 231_V | 1.080 | 0.67 |
| 16_L | 40_G | 1.080 | 0.67 |
| 451_M | 455_L | 1.078 | 0.66 |
| 183_P | 243_P | 1.078 | 0.66 |
| 423_M | 431_Y | 1.073 | 0.66 |
| 173_T | 192_A | 1.071 | 0.66 |
| 387_I | 456_G | 1.070 | 0.66 |
| 252_P | 504_G | 1.069 | 0.65 |
| 200_S | 221_W | 1.068 | 0.65 |
| 20_D | 37_I | 1.067 | 0.65 |
| 193_V | 420_D | 1.067 | 0.65 |
| 367_L | 418_F | 1.066 | 0.65 |
| 519_R | 541_Q | 1.065 | 0.65 |
| 335_T | 356_P | 1.064 | 0.65 |
| 520_L | 530_S | 1.064 | 0.65 |
| 347_L | 516_L | 1.062 | 0.65 |
| 21_L | 36_G | 1.060 | 0.65 |
| 33_Q | 61_S | 1.060 | 0.65 |
| 395_A | 423_M | 1.059 | 0.64 |
| 427_A | 474_S | 1.059 | 0.64 |
| 250_V | 293_V | 1.058 | 0.64 |
| 501_V | 516_L | 1.057 | 0.64 |
| 161_V | 231_V | 1.055 | 0.64 |
| 370_R | 390_I | 1.054 | 0.64 |
| 172_V | 189_S | 1.052 | 0.64 |
| 424_S | 444_D | 1.051 | 0.64 |
| 476_L | 491_V | 1.051 | 0.64 |
| 170_L | 241_T | 1.050 | 0.63 |
| 40_G | 120_R | 1.050 | 0.63 |
| 344_K | 349_L | 1.049 | 0.63 |
| 404_V | 431_Y | 1.048 | 0.63 |
| 127_V | 155_L | 1.047 | 0.63 |
| 391_R | 402_A | 1.046 | 0.63 |
| 11_R | 55_Q | 1.045 | 0.63 |
| 391_R | 431_Y | 1.043 | 0.63 |
| 502_K | 505_V | 1.041 | 0.62 |
| 158_G | 167_F | 1.040 | 0.62 |
| 459_Q | 498_G | 1.039 | 0.62 |
| 13_V | 43_D | 1.038 | 0.62 |
| 445_S | 452_L | 1.036 | 0.62 |
| 313_S | 342_Q | 1.036 | 0.62 |
| 360_F | 391_R | 1.035 | 0.62 |
| 274_A | 319_V | 1.033 | 0.62 |
| 427_A | 457_V | 1.033 | 0.62 |
| 364_G | 431_Y | 1.032 | 0.61 |
| 219_A | 315_L | 1.030 | 0.61 |
| 418_F | 503_Y | 1.028 | 0.61 |
| 189_S | 206_V | 1.027 | 0.61 |
| 55_Q | 88_E | 1.027 | 0.61 |
| 11_R | 43_D | 1.025 | 0.61 |
| 489_V | 493_G | 1.023 | 0.60 |
| 453_I | 473_V | 1.020 | 0.60 |
| 419_S | 428_A | 1.016 | 0.60 |
| 58_I | 62_G | 1.016 | 0.60 |
| 422_A | 495_V | 1.015 | 0.60 |
| 250_V | 258_A | 1.015 | 0.60 |
| 529_V | 542_F | 1.014 | 0.59 |
| 399_D | 431_Y | 1.013 | 0.59 |
| 141_F | 179_G | 1.011 | 0.59 |
| 85_L | 98_W | 1.010 | 0.59 |
| 384_Y | 409_L | 1.009 | 0.59 |
| 362_A | 391_R | 1.009 | 0.59 |
| 219_A | 258_A | 1.009 | 0.59 |
| 532_V | 539_L | 1.008 | 0.59 |
| 502_K | 515_T | 1.007 | 0.59 |
| 248_M | 274_A | 1.006 | 0.59 |
| 206_V | 213_I | 1.006 | 0.59 |
| 252_P | 431_Y | 1.006 | 0.59 |
| 69_Q | 105_N | 1.005 | 0.58 |
| 155_L | 340_V | 1.002 | 0.58 |
| 365_Q | 436_Q | 1.001 | 0.58 |
| 124_G | 156_R | 1.001 | 0.58 |
| 26_P | 58_I | 1.000 | 0.58 |
| 334_L | 367_L | 1.000 | 0.58 |
| 514_L | 517_R | 1.000 | 0.58 |
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 | |
| 4c69X | 1 | 0.4228 | 12.1 | 0.974 | Contact Map |
| 3hpeA | 2 | 0.2739 | 11.1 | 0.974 | Contact Map |
| 2ymzA | 6 | 0.2206 | 8.2 | 0.976 | Contact Map |
| 3lycA | 16 | 0.4118 | 6.7 | 0.977 | Contact Map |
| 3ap9A | 1 | 0.2592 | 6.2 | 0.977 | Contact Map |
| 2d6mA | 2 | 0.2647 | 6.1 | 0.977 | Contact Map |
| 3zxfA | 2 | 0.2408 | 5.8 | 0.977 | Contact Map |
| 2zhnA | 1 | 0.2537 | 5.8 | 0.977 | Contact Map |
| 1wubA | 1 | 0.2886 | 5.2 | 0.978 | Contact Map |
| 4fuvA | 1 | 0.1066 | 4.9 | 0.978 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)