| T0774 |
| ID: | 1399925937 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 379 (359) | ||
| Sequences: | 745 (659.4) | ||
| Seq/Len: | 2.075 | ||
| Nf(neff/√len): | 34.8 |
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: 2.075).
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 |
| 61_G | 119_Y | 4.373 | 1.00 |
| 339_F | 347_Y | 3.741 | 1.00 |
| 159_D | 186_H | 3.549 | 1.00 |
| 61_G | 118_P | 3.488 | 1.00 |
| 61_G | 116_Y | 3.214 | 1.00 |
| 340_K | 343_T | 3.021 | 1.00 |
| 163_D | 184_F | 2.984 | 1.00 |
| 116_Y | 119_Y | 2.659 | 1.00 |
| 86_N | 119_Y | 2.555 | 1.00 |
| 195_K | 348_V | 2.527 | 1.00 |
| 105_P | 111_I | 2.465 | 1.00 |
| 190_Q | 344_K | 2.448 | 1.00 |
| 61_G | 86_N | 2.344 | 1.00 |
| 163_D | 182_F | 2.296 | 1.00 |
| 191_I | 347_Y | 2.127 | 0.99 |
| 195_K | 346_T | 2.091 | 0.99 |
| 59_G | 88_H | 2.088 | 0.99 |
| 54_L | 58_A | 2.074 | 0.99 |
| 64_A | 113_F | 2.070 | 0.99 |
| 117_A | 161_V | 2.068 | 0.99 |
| 189_T | 345_H | 2.034 | 0.99 |
| 162_T | 233_D | 2.003 | 0.99 |
| 36_L | 113_F | 1.978 | 0.99 |
| 194_I | 213_L | 1.949 | 0.99 |
| 190_Q | 287_A | 1.936 | 0.99 |
| 197_K | 348_V | 1.929 | 0.99 |
| 216_D | 308_K | 1.914 | 0.99 |
| 54_L | 96_W | 1.910 | 0.99 |
| 113_F | 180_V | 1.885 | 0.98 |
| 86_N | 116_Y | 1.830 | 0.98 |
| 229_K | 232_N | 1.817 | 0.98 |
| 160_L | 228_Y | 1.792 | 0.98 |
| 104_W | 113_F | 1.777 | 0.97 |
| 19_S | 22_E | 1.726 | 0.97 |
| 34_I | 104_W | 1.684 | 0.96 |
| 96_W | 104_W | 1.652 | 0.96 |
| 34_I | 113_F | 1.651 | 0.96 |
| 162_T | 187_V | 1.544 | 0.93 |
| 36_L | 64_A | 1.520 | 0.92 |
| 60_F | 96_W | 1.492 | 0.91 |
| 89_A | 98_Y | 1.491 | 0.91 |
| 186_H | 342_G | 1.481 | 0.91 |
| 191_I | 339_F | 1.477 | 0.91 |
| 61_G | 117_A | 1.451 | 0.90 |
| 14_T | 45_R | 1.432 | 0.89 |
| 91_W | 96_W | 1.430 | 0.89 |
| 192_A | 344_K | 1.417 | 0.88 |
| 160_L | 188_L | 1.404 | 0.88 |
| 11_A | 22_E | 1.400 | 0.87 |
| 115_A | 182_F | 1.395 | 0.87 |
| 190_Q | 349_L | 1.386 | 0.87 |
| 63_F | 86_N | 1.384 | 0.87 |
| 117_A | 186_H | 1.383 | 0.87 |
| 98_Y | 102_R | 1.374 | 0.86 |
| 159_D | 188_L | 1.374 | 0.86 |
| 89_A | 96_W | 1.371 | 0.86 |
| 194_I | 307_L | 1.364 | 0.86 |
| 290_F | 339_F | 1.350 | 0.85 |
| 114_F | 162_T | 1.347 | 0.85 |
| 60_F | 104_W | 1.342 | 0.84 |
| 60_F | 89_A | 1.335 | 0.84 |
| 155_K | 158_I | 1.329 | 0.83 |
| 162_T | 230_F | 1.327 | 0.83 |
| 192_A | 346_T | 1.307 | 0.82 |
| 64_A | 111_I | 1.293 | 0.81 |
| 115_A | 184_F | 1.287 | 0.81 |
| 113_F | 184_F | 1.279 | 0.80 |
| 159_D | 184_F | 1.270 | 0.79 |
| 199_D | 350_T | 1.268 | 0.79 |
| 197_K | 350_T | 1.266 | 0.79 |
| 64_A | 84_M | 1.265 | 0.79 |
| 89_A | 104_W | 1.260 | 0.79 |
| 135_G | 138_A | 1.257 | 0.79 |
| 98_Y | 112_T | 1.254 | 0.78 |
| 63_F | 116_Y | 1.252 | 0.78 |
| 104_W | 235_W | 1.250 | 0.78 |
| 51_T | 233_D | 1.242 | 0.77 |
| 2_E | 103_F | 1.239 | 0.77 |
| 7_L | 11_A | 1.236 | 0.77 |
| 340_K | 345_H | 1.235 | 0.77 |
| 294_N | 338_T | 1.231 | 0.76 |
| 64_A | 184_F | 1.225 | 0.76 |
| 104_W | 180_V | 1.223 | 0.76 |
| 146_F | 291_I | 1.222 | 0.76 |
| 312_D | 349_L | 1.221 | 0.76 |
| 184_F | 362_D | 1.216 | 0.75 |
| 235_W | 339_F | 1.212 | 0.75 |
| 189_T | 343_T | 1.212 | 0.75 |
| 157_M | 293_V | 1.207 | 0.74 |
| 83_F | 111_I | 1.204 | 0.74 |
| 312_D | 315_T | 1.203 | 0.74 |
| 162_T | 228_Y | 1.199 | 0.74 |
| 36_L | 182_F | 1.193 | 0.73 |
| 157_M | 339_F | 1.192 | 0.73 |
| 156_D | 358_I | 1.174 | 0.72 |
| 60_F | 184_F | 1.156 | 0.70 |
| 157_M | 347_Y | 1.152 | 0.69 |
| 84_M | 87_E | 1.150 | 0.69 |
| 258_T | 261_D | 1.146 | 0.69 |
| 81_P | 85_Y | 1.145 | 0.69 |
| 88_H | 119_Y | 1.139 | 0.68 |
| 255_L | 258_T | 1.139 | 0.68 |
| 57_N | 117_A | 1.135 | 0.68 |
| 293_V | 339_F | 1.133 | 0.68 |
| 9_V | 12_T | 1.126 | 0.67 |
| 152_N | 155_K | 1.116 | 0.66 |
| 104_W | 347_Y | 1.111 | 0.65 |
| 89_A | 102_R | 1.109 | 0.65 |
| 113_F | 182_F | 1.106 | 0.65 |
| 159_D | 342_G | 1.105 | 0.65 |
| 191_I | 201_N | 1.104 | 0.65 |
| 318_T | 321_S | 1.102 | 0.64 |
| 54_L | 57_N | 1.102 | 0.64 |
| 10_M | 27_N | 1.094 | 0.64 |
| 188_L | 292_P | 1.094 | 0.64 |
| 89_A | 210_V | 1.080 | 0.62 |
| 356_I | 361_E | 1.080 | 0.62 |
| 11_A | 20_Q | 1.080 | 0.62 |
| 114_F | 182_F | 1.077 | 0.62 |
| 63_F | 119_Y | 1.070 | 0.61 |
| 256_N | 261_D | 1.062 | 0.60 |
| 228_Y | 233_D | 1.062 | 0.60 |
| 113_F | 163_D | 1.056 | 0.60 |
| 86_N | 118_P | 1.055 | 0.59 |
| 214_K | 310_N | 1.053 | 0.59 |
| 46_G | 363_N | 1.048 | 0.59 |
| 255_L | 259_T | 1.046 | 0.59 |
| 189_T | 341_K | 1.046 | 0.59 |
| 187_V | 289_Y | 1.044 | 0.58 |
| 3_V | 12_T | 1.042 | 0.58 |
| 34_I | 286_E | 1.038 | 0.58 |
| 162_T | 189_T | 1.036 | 0.57 |
| 150_T | 153_N | 1.035 | 0.57 |
| 260_T | 263_W | 1.034 | 0.57 |
| 13_L | 17_G | 1.032 | 0.57 |
| 189_T | 290_F | 1.031 | 0.57 |
| 161_V | 186_H | 1.030 | 0.57 |
| 372_D | 375_I | 1.030 | 0.57 |
| 21_N | 213_L | 1.027 | 0.56 |
| 292_P | 339_F | 1.021 | 0.56 |
| 84_M | 89_A | 1.017 | 0.55 |
| 309_I | 352_K | 1.016 | 0.55 |
| 64_A | 288_L | 1.014 | 0.55 |
| 84_M | 289_Y | 1.006 | 0.54 |
| 117_A | 190_Q | 1.006 | 0.54 |
| 190_Q | 289_Y | 1.006 | 0.54 |
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 | |
| 3t2lA | 1 | 0.6992 | 100 | 0.434 | Contact Map |
| 3sy6A | 2 | 0.6939 | 100 | 0.452 | Contact Map |
| 4k4kA | 2 | 0.6491 | 100 | 0.455 | Contact Map |
| 3ufiA | 1 | 0.6491 | 100 | 0.47 | Contact Map |
| 4epsA | 1 | 0.6834 | 99.9 | 0.568 | Contact Map |
| 4dguA | 2 | 0.5937 | 99.7 | 0.689 | Contact Map |
| 4h40A | 2 | 0.7309 | 98.3 | 0.84 | Contact Map |
| 4jg5A | 1 | 0.7678 | 98.1 | 0.848 | Contact Map |
| 4gpvA | 2 | 0.7625 | 98 | 0.852 | Contact Map |
| 3up6A | 2 | 0.7784 | 97 | 0.878 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)