| O-ligase |
| ID: | 1503250563 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 419 (393) | ||
| Sequences: | 924 (730.5) | ||
| Seq/Len: | 2.351 | ||
| Nf(neff/√len): | 36.8 |
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: 2.351).
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 |
| 299_F | 345_G | 3.429 | 1.00 |
| 339_N | 342_I | 2.831 | 1.00 |
| 302_S | 307_R | 2.681 | 1.00 |
| 295_G | 337_L | 2.621 | 1.00 |
| 345_G | 353_I | 2.366 | 1.00 |
| 367_A | 375_L | 2.279 | 1.00 |
| 356_T | 360_Y | 2.051 | 0.99 |
| 363_L | 401_I | 1.948 | 0.99 |
| 344_A | 356_T | 1.901 | 0.99 |
| 298_I | 307_R | 1.880 | 0.99 |
| 295_G | 299_F | 1.875 | 0.99 |
| 287_A | 291_M | 1.873 | 0.99 |
| 209_L | 217_T | 1.861 | 0.99 |
| 215_R | 265_R | 1.851 | 0.99 |
| 297_N | 300_I | 1.848 | 0.99 |
| 215_R | 286_G | 1.809 | 0.98 |
| 336_H | 390_V | 1.798 | 0.98 |
| 305_S | 351_M | 1.796 | 0.98 |
| 161_R | 215_R | 1.770 | 0.98 |
| 341_I | 386_G | 1.760 | 0.98 |
| 276_Y | 286_G | 1.721 | 0.97 |
| 343_E | 347_L | 1.687 | 0.97 |
| 283_T | 286_G | 1.629 | 0.96 |
| 299_F | 339_N | 1.620 | 0.96 |
| 295_G | 342_I | 1.607 | 0.96 |
| 336_H | 394_A | 1.586 | 0.95 |
| 341_I | 360_Y | 1.568 | 0.95 |
| 272_D | 286_G | 1.564 | 0.95 |
| 299_F | 342_I | 1.564 | 0.95 |
| 337_L | 346_S | 1.561 | 0.95 |
| 389_D | 394_A | 1.543 | 0.94 |
| 180_G | 209_L | 1.539 | 0.94 |
| 361_F | 364_F | 1.536 | 0.94 |
| 340_E | 386_G | 1.504 | 0.93 |
| 253_S | 256_I | 1.501 | 0.93 |
| 292_Y | 338_H | 1.488 | 0.93 |
| 296_L | 300_I | 1.477 | 0.93 |
| 144_F | 148_G | 1.477 | 0.93 |
| 365_Y | 369_K | 1.454 | 0.92 |
| 295_G | 343_E | 1.445 | 0.91 |
| 299_F | 303_P | 1.438 | 0.91 |
| 348_K | 352_G | 1.438 | 0.91 |
| 336_H | 389_D | 1.410 | 0.90 |
| 269_A | 272_D | 1.404 | 0.90 |
| 161_R | 265_R | 1.401 | 0.90 |
| 144_F | 200_L | 1.390 | 0.89 |
| 168_T | 389_D | 1.369 | 0.88 |
| 147_A | 204_A | 1.356 | 0.88 |
| 170_T | 389_D | 1.355 | 0.87 |
| 203_C | 207_Y | 1.349 | 0.87 |
| 340_E | 390_V | 1.336 | 0.86 |
| 61_R | 64_Q | 1.332 | 0.86 |
| 249_A | 253_S | 1.322 | 0.86 |
| 307_R | 346_S | 1.321 | 0.86 |
| 354_F | 358_F | 1.297 | 0.84 |
| 258_F | 261_P | 1.291 | 0.84 |
| 299_F | 350_L | 1.290 | 0.84 |
| 219_L | 226_V | 1.283 | 0.83 |
| 283_T | 287_A | 1.280 | 0.83 |
| 162_I | 212_T | 1.261 | 0.82 |
| 389_D | 395_R | 1.259 | 0.82 |
| 365_Y | 371_R | 1.257 | 0.82 |
| 163_S | 169_A | 1.245 | 0.81 |
| 337_L | 342_I | 1.241 | 0.80 |
| 291_M | 334_N | 1.241 | 0.80 |
| 214_T | 217_T | 1.239 | 0.80 |
| 337_L | 389_D | 1.237 | 0.80 |
| 364_F | 383_V | 1.237 | 0.80 |
| 341_I | 383_V | 1.233 | 0.80 |
| 204_A | 252_A | 1.229 | 0.80 |
| 24_I | 30_F | 1.228 | 0.79 |
| 345_G | 350_L | 1.225 | 0.79 |
| 178_L | 404_A | 1.221 | 0.79 |
| 170_T | 214_T | 1.219 | 0.79 |
| 337_L | 343_E | 1.214 | 0.78 |
| 135_V | 258_F | 1.211 | 0.78 |
| 175_S | 385_I | 1.210 | 0.78 |
| 129_K | 134_S | 1.207 | 0.78 |
| 197_L | 405_I | 1.202 | 0.77 |
| 31_F | 35_I | 1.201 | 0.77 |
| 390_V | 394_A | 1.197 | 0.77 |
| 89_Y | 262_I | 1.194 | 0.77 |
| 46_I | 55_L | 1.194 | 0.77 |
| 340_E | 360_Y | 1.193 | 0.77 |
| 343_E | 397_I | 1.177 | 0.75 |
| 148_G | 371_R | 1.176 | 0.75 |
| 114_I | 361_F | 1.172 | 0.75 |
| 140_Y | 269_A | 1.171 | 0.75 |
| 220_L | 377_I | 1.171 | 0.75 |
| 242_S | 245_V | 1.170 | 0.75 |
| 28_L | 31_F | 1.168 | 0.75 |
| 351_M | 355_S | 1.167 | 0.74 |
| 161_R | 169_A | 1.160 | 0.74 |
| 341_I | 392_I | 1.158 | 0.74 |
| 186_A | 198_F | 1.157 | 0.74 |
| 204_A | 353_I | 1.154 | 0.73 |
| 295_G | 346_S | 1.150 | 0.73 |
| 216_A | 388_S | 1.148 | 0.73 |
| 116_G | 119_I | 1.146 | 0.73 |
| 38_V | 47_Y | 1.144 | 0.72 |
| 39_D | 42_F | 1.138 | 0.72 |
| 207_Y | 247_L | 1.138 | 0.72 |
| 23_I | 40_N | 1.138 | 0.72 |
| 312_R | 337_L | 1.128 | 0.71 |
| 161_R | 214_T | 1.117 | 0.70 |
| 147_A | 205_V | 1.113 | 0.69 |
| 217_T | 353_I | 1.110 | 0.69 |
| 36_A | 44_I | 1.110 | 0.69 |
| 252_A | 264_N | 1.108 | 0.69 |
| 151_M | 210_A | 1.108 | 0.69 |
| 215_R | 220_L | 1.105 | 0.69 |
| 51_A | 54_C | 1.105 | 0.69 |
| 200_L | 376_L | 1.100 | 0.68 |
| 150_A | 201_N | 1.093 | 0.67 |
| 209_L | 220_L | 1.092 | 0.67 |
| 181_I | 381_G | 1.090 | 0.67 |
| 63_R | 66_N | 1.089 | 0.67 |
| 153_I | 386_G | 1.086 | 0.67 |
| 223_I | 361_F | 1.086 | 0.67 |
| 26_Y | 38_V | 1.082 | 0.66 |
| 83_L | 250_I | 1.081 | 0.66 |
| 291_M | 336_H | 1.080 | 0.66 |
| 265_R | 339_N | 1.076 | 0.66 |
| 28_L | 37_F | 1.073 | 0.65 |
| 291_M | 343_E | 1.073 | 0.65 |
| 220_L | 224_I | 1.073 | 0.65 |
| 116_G | 402_I | 1.072 | 0.65 |
| 191_K | 194_H | 1.071 | 0.65 |
| 43_S | 48_N | 1.071 | 0.65 |
| 294_I | 319_L | 1.067 | 0.65 |
| 79_F | 114_I | 1.066 | 0.64 |
| 42_F | 45_K | 1.066 | 0.64 |
| 144_F | 199_L | 1.062 | 0.64 |
| 320_V | 330_L | 1.061 | 0.64 |
| 343_E | 389_D | 1.061 | 0.64 |
| 174_Y | 385_I | 1.049 | 0.63 |
| 49_I | 54_C | 1.049 | 0.63 |
| 167_G | 395_R | 1.047 | 0.62 |
| 41_T | 45_K | 1.045 | 0.62 |
| 187_I | 256_I | 1.043 | 0.62 |
| 339_N | 387_L | 1.042 | 0.62 |
| 48_N | 53_V | 1.041 | 0.62 |
| 44_I | 52_I | 1.039 | 0.62 |
| 31_F | 56_L | 1.038 | 0.61 |
| 31_F | 41_T | 1.036 | 0.61 |
| 284_S | 289_L | 1.036 | 0.61 |
| 53_V | 57_S | 1.035 | 0.61 |
| 173_A | 263_Q | 1.034 | 0.61 |
| 288_R | 338_H | 1.033 | 0.61 |
| 170_T | 174_Y | 1.032 | 0.61 |
| 78_I | 179_I | 1.032 | 0.61 |
| 219_L | 230_I | 1.031 | 0.61 |
| 307_R | 347_L | 1.030 | 0.61 |
| 290_A | 293_E | 1.029 | 0.60 |
| 33_M | 36_A | 1.028 | 0.60 |
| 197_L | 339_N | 1.027 | 0.60 |
| 307_R | 389_D | 1.026 | 0.60 |
| 295_G | 335_V | 1.024 | 0.60 |
| 336_H | 343_E | 1.022 | 0.60 |
| 216_A | 389_D | 1.022 | 0.60 |
| 27_I | 45_K | 1.022 | 0.60 |
| 28_L | 34_I | 1.020 | 0.59 |
| 23_I | 26_Y | 1.017 | 0.59 |
| 360_Y | 383_V | 1.014 | 0.59 |
| 76_L | 236_S | 1.014 | 0.59 |
| 171_G | 389_D | 1.014 | 0.59 |
| 49_I | 66_N | 1.010 | 0.58 |
| 142_L | 179_I | 1.010 | 0.58 |
| 27_I | 30_F | 1.009 | 0.58 |
| 161_R | 213_Q | 1.007 | 0.58 |
| 37_F | 40_N | 1.007 | 0.58 |
| 411_I | 415_N | 1.007 | 0.58 |
| 334_N | 389_D | 1.006 | 0.58 |
| 298_I | 386_G | 1.004 | 0.58 |
| 34_I | 37_F | 1.004 | 0.58 |
| 194_H | 358_F | 1.002 | 0.57 |
| 23_I | 62_G | 1.001 | 0.57 |
| 23_I | 29_C | 1.000 | 0.57 |
| 55_L | 359_L | 1.000 | 0.57 |
| 88_W | 218_L | 1.000 | 0.57 |
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 | |
| 3wxwA | 1 | 0.2721 | 9.1 | 0.964 | Contact Map |
| 1iijA | 1 | 0.0835 | 3.6 | 0.97 | Contact Map |
| 1vf6A | 2 | 0.1408 | 1.8 | 0.974 | Contact Map |
| 1pzqA | 2 | 0.1408 | 1.7 | 0.974 | Contact Map |
| 2jwaA | 2 | 0.105 | 1.3 | 0.976 | Contact Map |
| 3hxiC | 1 | 0.0334 | 1.3 | 0.976 | Contact Map |
| 2pbdV | 1 | 0.0263 | 1.3 | 0.976 | Contact Map |
| 2k1aA | 1 | 0.0979 | 1.2 | 0.977 | Contact Map |
| 3l1lA | 1 | 0.1695 | 1.2 | 0.977 | Contact Map |
| 3b5dA | 2 | 0.0143 | 1.1 | 0.977 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)