| McoA with sp |
| ID: | 1494584634 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 527 (459) | ||
| Sequences: | 2029 (1231.6) | ||
| Seq/Len: | 4.420 | ||
| Nf(neff/√len): | 57.5 |
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: 4.420).
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 |
| 96_F | 181_E | 4.953 | 1.00 |
| 299_E | 478_K | 4.828 | 1.00 |
| 247_I | 304_L | 4.226 | 1.00 |
| 104_S | 146_D | 3.711 | 1.00 |
| 252_I | 303_I | 3.312 | 1.00 |
| 278_G | 302_D | 3.291 | 1.00 |
| 66_T | 110_N | 3.041 | 1.00 |
| 62_R | 104_S | 3.039 | 1.00 |
| 265_L | 305_V | 2.973 | 1.00 |
| 295_V | 301_I | 2.964 | 1.00 |
| 64_S | 106_D | 2.943 | 1.00 |
| 106_D | 143_S | 2.935 | 1.00 |
| 256_S | 261_Y | 2.845 | 1.00 |
| 62_R | 106_D | 2.787 | 1.00 |
| 64_S | 108_V | 2.782 | 1.00 |
| 94_V | 177_M | 2.768 | 1.00 |
| 481_V | 489_V | 2.750 | 1.00 |
| 102_T | 146_D | 2.644 | 1.00 |
| 464_E | 490_R | 2.623 | 1.00 |
| 442_E | 490_R | 2.594 | 1.00 |
| 99_K | 182_D | 2.563 | 1.00 |
| 70_T | 84_V | 2.543 | 1.00 |
| 440_I | 492_A | 2.519 | 1.00 |
| 274_F | 303_I | 2.510 | 1.00 |
| 61_Q | 101_Q | 2.495 | 1.00 |
| 455_I | 493_V | 2.465 | 1.00 |
| 85_Y | 158_Y | 2.416 | 1.00 |
| 205_I | 263_L | 2.365 | 1.00 |
| 181_E | 200_D | 2.338 | 1.00 |
| 300_R | 479_D | 2.299 | 1.00 |
| 266_L | 319_Y | 2.293 | 1.00 |
| 440_I | 463_L | 2.234 | 1.00 |
| 69_W | 81_D | 2.172 | 1.00 |
| 211_D | 215_Q | 2.143 | 1.00 |
| 273_R | 291_N | 2.138 | 1.00 |
| 177_M | 253_L | 2.128 | 1.00 |
| 250_F | 303_I | 2.109 | 1.00 |
| 460_F | 491_I | 2.047 | 1.00 |
| 443_Y | 453_M | 2.024 | 1.00 |
| 201_I | 241_M | 1.995 | 1.00 |
| 107_F | 136_V | 1.989 | 1.00 |
| 108_V | 141_T | 1.973 | 1.00 |
| 177_M | 204_I | 1.947 | 1.00 |
| 128_S | 142_Y | 1.943 | 1.00 |
| 71_T | 81_D | 1.922 | 1.00 |
| 137_K | 140_E | 1.900 | 1.00 |
| 66_T | 108_V | 1.871 | 1.00 |
| 252_I | 263_L | 1.866 | 1.00 |
| 243_V | 307_F | 1.859 | 1.00 |
| 276_V | 290_V | 1.842 | 1.00 |
| 484_A | 487_E | 1.822 | 1.00 |
| 156_Y | 281_G | 1.822 | 1.00 |
| 72_L | 82_M | 1.792 | 1.00 |
| 175_A | 206_Q | 1.791 | 1.00 |
| 199_I | 246_K | 1.785 | 1.00 |
| 443_Y | 491_I | 1.775 | 1.00 |
| 115_S | 169_Q | 1.761 | 1.00 |
| 262_R | 292_E | 1.693 | 0.99 |
| 249_R | 302_D | 1.691 | 0.99 |
| 201_I | 250_F | 1.688 | 0.99 |
| 199_I | 248_Y | 1.626 | 0.99 |
| 96_F | 200_D | 1.626 | 0.99 |
| 247_I | 306_D | 1.609 | 0.99 |
| 396_Q | 439_V | 1.606 | 0.99 |
| 102_T | 148_T | 1.598 | 0.99 |
| 71_T | 79_S | 1.594 | 0.99 |
| 160_P | 169_Q | 1.592 | 0.99 |
| 276_V | 301_I | 1.586 | 0.99 |
| 98_R | 181_E | 1.557 | 0.99 |
| 509_C | 514_H | 1.551 | 0.99 |
| 92_N | 235_L | 1.544 | 0.98 |
| 460_F | 481_V | 1.541 | 0.98 |
| 264_A | 319_Y | 1.535 | 0.98 |
| 458_F | 525_V | 1.530 | 0.98 |
| 508_H | 514_H | 1.519 | 0.98 |
| 397_R | 442_E | 1.518 | 0.98 |
| 243_V | 248_Y | 1.504 | 0.98 |
| 461_Q | 477_W | 1.502 | 0.98 |
| 457_G | 505_Y | 1.500 | 0.98 |
| 275_W | 289_E | 1.483 | 0.98 |
| 240_Y | 367_R | 1.478 | 0.98 |
| 86_E | 91_Y | 1.463 | 0.98 |
| 510_H | 514_H | 1.461 | 0.98 |
| 155_T | 177_M | 1.461 | 0.98 |
| 274_F | 293_I | 1.455 | 0.97 |
| 252_I | 293_I | 1.450 | 0.97 |
| 245_R | 307_F | 1.443 | 0.97 |
| 99_K | 183_E | 1.437 | 0.97 |
| 504_I | 524_R | 1.431 | 0.97 |
| 149_I | 178_I | 1.426 | 0.97 |
| 273_R | 289_E | 1.414 | 0.97 |
| 279_V | 301_I | 1.394 | 0.97 |
| 249_R | 277_I | 1.386 | 0.96 |
| 97_L | 103_F | 1.385 | 0.96 |
| 155_T | 251_R | 1.374 | 0.96 |
| 119_W | 147_F | 1.373 | 0.96 |
| 107_F | 117_I | 1.361 | 0.96 |
| 462_V | 481_V | 1.348 | 0.96 |
| 204_I | 255_G | 1.335 | 0.95 |
| 92_N | 158_Y | 1.334 | 0.95 |
| 68_K | 84_V | 1.317 | 0.95 |
| 263_L | 318_L | 1.311 | 0.95 |
| 161_H | 509_C | 1.308 | 0.95 |
| 161_H | 510_H | 1.300 | 0.94 |
| 158_Y | 176_G | 1.296 | 0.94 |
| 265_L | 318_L | 1.294 | 0.94 |
| 83_L | 111_S | 1.286 | 0.94 |
| 293_I | 301_I | 1.286 | 0.94 |
| 97_L | 178_I | 1.279 | 0.94 |
| 483_V | 489_V | 1.277 | 0.94 |
| 143_S | 146_D | 1.274 | 0.93 |
| 515_H | 520_M | 1.273 | 0.93 |
| 203_L | 252_I | 1.267 | 0.93 |
| 315_V | 365_E | 1.261 | 0.93 |
| 236_T | 239_P | 1.252 | 0.93 |
| 252_I | 295_V | 1.249 | 0.93 |
| 282_G | 459_Q | 1.249 | 0.93 |
| 281_G | 459_Q | 1.244 | 0.92 |
| 67_A | 107_F | 1.239 | 0.92 |
| 455_I | 491_I | 1.238 | 0.92 |
| 68_K | 110_N | 1.236 | 0.92 |
| 97_L | 180_I | 1.231 | 0.92 |
| 84_V | 90_E | 1.227 | 0.92 |
| 107_F | 115_S | 1.224 | 0.92 |
| 362_E | 366_F | 1.224 | 0.92 |
| 274_F | 305_V | 1.223 | 0.92 |
| 265_L | 274_F | 1.219 | 0.91 |
| 159_H | 509_C | 1.207 | 0.91 |
| 205_I | 261_Y | 1.193 | 0.90 |
| 106_D | 141_T | 1.192 | 0.90 |
| 159_H | 510_H | 1.189 | 0.90 |
| 250_F | 305_V | 1.187 | 0.90 |
| 151_D | 180_I | 1.185 | 0.90 |
| 464_E | 488_T | 1.184 | 0.90 |
| 161_H | 456_H | 1.180 | 0.89 |
| 506_L | 520_M | 1.176 | 0.89 |
| 225_G | 449_M | 1.175 | 0.89 |
| 276_V | 303_I | 1.174 | 0.89 |
| 251_R | 302_D | 1.173 | 0.89 |
| 240_Y | 365_E | 1.171 | 0.89 |
| 107_F | 178_I | 1.171 | 0.89 |
| 231_I | 261_Y | 1.170 | 0.89 |
| 463_L | 492_A | 1.153 | 0.88 |
| 170_V | 512_L | 1.149 | 0.88 |
| 171_Y | 257_N | 1.141 | 0.87 |
| 496_S | 502_H | 1.136 | 0.87 |
| 65_I | 103_F | 1.129 | 0.87 |
| 161_H | 514_H | 1.126 | 0.86 |
| 157_F | 298_G | 1.117 | 0.86 |
| 442_E | 488_T | 1.111 | 0.85 |
| 496_S | 505_Y | 1.107 | 0.85 |
| 118_H | 456_H | 1.105 | 0.85 |
| 119_W | 122_F | 1.105 | 0.85 |
| 110_N | 139_G | 1.102 | 0.85 |
| 455_I | 507_L | 1.102 | 0.85 |
| 493_V | 523_Y | 1.098 | 0.84 |
| 125_P | 128_S | 1.098 | 0.84 |
| 67_A | 136_V | 1.086 | 0.83 |
| 242_D | 367_R | 1.080 | 0.83 |
| 465_R | 487_E | 1.074 | 0.83 |
| 206_Q | 255_G | 1.071 | 0.82 |
| 452_P | 511_I | 1.069 | 0.82 |
| 307_F | 366_F | 1.069 | 0.82 |
| 118_H | 510_H | 1.069 | 0.82 |
| 293_I | 303_I | 1.068 | 0.82 |
| 205_I | 231_I | 1.063 | 0.82 |
| 284_L | 476_G | 1.046 | 0.80 |
| 512_L | 515_H | 1.045 | 0.80 |
| 460_F | 493_V | 1.043 | 0.80 |
| 438_V | 492_A | 1.043 | 0.80 |
| 456_H | 510_H | 1.041 | 0.80 |
| 276_V | 293_I | 1.039 | 0.80 |
| 512_L | 519_M | 1.038 | 0.80 |
| 200_D | 302_D | 1.034 | 0.79 |
| 62_R | 146_D | 1.033 | 0.79 |
| 98_R | 103_F | 1.031 | 0.79 |
| 161_H | 508_H | 1.029 | 0.79 |
| 58_P | 291_N | 1.028 | 0.79 |
| 262_R | 321_F | 1.022 | 0.78 |
| 451_H | 456_H | 1.022 | 0.78 |
| 507_L | 523_Y | 1.018 | 0.78 |
| 451_H | 509_C | 1.018 | 0.78 |
| 451_H | 510_H | 1.015 | 0.77 |
| 103_F | 147_F | 1.014 | 0.77 |
| 493_V | 507_L | 1.005 | 0.76 |
| 60_G | 104_S | 1.005 | 0.76 |
| 456_H | 508_H | 1.001 | 0.76 |
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 | |
| 3abgA | 2 | 0.8558 | 100 | 0.3 | Contact Map |
| 2uxtA | 2 | 0.7875 | 100 | 0.304 | Contact Map |
| 1zpuA | 6 | 0.814 | 100 | 0.317 | Contact Map |
| 4e9sA | 1 | 0.8159 | 100 | 0.317 | Contact Map |
| 2wsdA | 1 | 0.8254 | 100 | 0.317 | Contact Map |
| 2xu9A | 1 | 0.8216 | 100 | 0.32 | Contact Map |
| 3gyrA | 12 | 0.8406 | 100 | 0.321 | Contact Map |
| 3zx1A | 1 | 0.8406 | 100 | 0.322 | Contact Map |
| 3sqrA | 1 | 0.8558 | 100 | 0.324 | Contact Map |
| 3aw5A | 1 | 0.7932 | 100 | 0.328 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)