| T0762 |
| ID: | 1399049700 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 280 (271) | ||
| Sequences: | 7022 (4741.6) | ||
| Seq/Len: | 25.911 | ||
| Nf(neff/√len): | 288.0 |
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: 25.911).
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 |
| 35_G | 81_I | 4.241 | 1.00 |
| 140_A | 200_V | 4.169 | 1.00 |
| 31_T | 62_K | 3.970 | 1.00 |
| 138_Q | 184_D | 3.734 | 1.00 |
| 33_T | 62_K | 3.602 | 1.00 |
| 31_T | 60_K | 3.546 | 1.00 |
| 266_K | 270_K | 3.270 | 1.00 |
| 33_T | 64_K | 3.138 | 1.00 |
| 138_Q | 186_K | 2.968 | 1.00 |
| 128_S | 132_E | 2.899 | 1.00 |
| 137_G | 201_D | 2.836 | 1.00 |
| 162_K | 178_S | 2.833 | 1.00 |
| 94_N | 98_E | 2.829 | 1.00 |
| 102_D | 241_K | 2.737 | 1.00 |
| 240_Q | 243_W | 2.635 | 1.00 |
| 246_S | 251_A | 2.615 | 1.00 |
| 129_S | 132_E | 2.505 | 1.00 |
| 56_K | 258_A | 2.492 | 1.00 |
| 243_W | 246_S | 2.468 | 1.00 |
| 57_E | 257_K | 2.395 | 1.00 |
| 253_K | 257_K | 2.256 | 1.00 |
| 53_L | 263_A | 2.190 | 1.00 |
| 267_V | 271_T | 2.061 | 1.00 |
| 52_E | 56_K | 2.050 | 1.00 |
| 90_N | 236_I | 2.019 | 1.00 |
| 119_G | 124_K | 2.018 | 1.00 |
| 52_E | 55_K | 2.015 | 1.00 |
| 75_A | 81_I | 1.969 | 1.00 |
| 79_G | 240_Q | 1.969 | 1.00 |
| 188_V | 196_N | 1.965 | 1.00 |
| 264_V | 267_V | 1.939 | 1.00 |
| 139_I | 202_A | 1.921 | 1.00 |
| 104_V | 241_K | 1.901 | 1.00 |
| 262_D | 266_K | 1.802 | 1.00 |
| 133_I | 202_A | 1.794 | 1.00 |
| 20_L | 23_C | 1.758 | 1.00 |
| 239_A | 252_I | 1.736 | 1.00 |
| 266_K | 269_K | 1.732 | 1.00 |
| 66_F | 75_A | 1.725 | 1.00 |
| 164_N | 167_G | 1.693 | 1.00 |
| 89_Y | 93_N | 1.689 | 1.00 |
| 83_I | 239_A | 1.675 | 1.00 |
| 116_L | 202_A | 1.646 | 1.00 |
| 54_L | 61_L | 1.594 | 1.00 |
| 134_P | 182_N | 1.568 | 1.00 |
| 148_E | 152_L | 1.566 | 1.00 |
| 153_Y | 156_Q | 1.550 | 1.00 |
| 257_K | 261_T | 1.548 | 1.00 |
| 34_V | 61_L | 1.539 | 1.00 |
| 207_N | 211_V | 1.527 | 1.00 |
| 57_E | 254_K | 1.494 | 1.00 |
| 83_I | 255_L | 1.484 | 1.00 |
| 56_K | 263_A | 1.483 | 1.00 |
| 118_S | 125_A | 1.481 | 1.00 |
| 135_N | 182_N | 1.461 | 1.00 |
| 197_L | 200_V | 1.458 | 1.00 |
| 96_N | 101_G | 1.447 | 1.00 |
| 56_K | 262_D | 1.443 | 1.00 |
| 251_A | 254_K | 1.437 | 1.00 |
| 189_D | 192_Q | 1.424 | 1.00 |
| 48_D | 51_E | 1.417 | 1.00 |
| 107_A | 257_K | 1.378 | 0.99 |
| 66_F | 81_I | 1.373 | 0.99 |
| 131_K | 158_A | 1.361 | 0.99 |
| 248_K | 254_K | 1.353 | 0.99 |
| 107_A | 256_I | 1.353 | 0.99 |
| 30_N | 59_I | 1.345 | 0.99 |
| 205_V | 210_A | 1.313 | 0.99 |
| 116_L | 204_V | 1.307 | 0.99 |
| 57_E | 263_A | 1.306 | 0.99 |
| 127_Y | 134_P | 1.305 | 0.99 |
| 53_L | 258_A | 1.300 | 0.99 |
| 254_K | 258_A | 1.300 | 0.99 |
| 247_K | 253_K | 1.298 | 0.99 |
| 23_C | 26_K | 1.297 | 0.99 |
| 95_W | 101_G | 1.272 | 0.99 |
| 76_L | 81_I | 1.264 | 0.99 |
| 35_G | 66_F | 1.257 | 0.99 |
| 141_I | 148_E | 1.227 | 0.98 |
| 76_L | 84_N | 1.223 | 0.98 |
| 196_N | 199_S | 1.199 | 0.98 |
| 241_K | 244_K | 1.196 | 0.98 |
| 53_L | 56_K | 1.193 | 0.98 |
| 38_T | 65_E | 1.192 | 0.98 |
| 84_N | 88_H | 1.179 | 0.98 |
| 33_T | 82_D | 1.174 | 0.98 |
| 59_I | 251_A | 1.169 | 0.97 |
| 55_K | 60_K | 1.153 | 0.97 |
| 34_V | 83_I | 1.146 | 0.97 |
| 148_E | 187_E | 1.146 | 0.97 |
| 139_I | 183_L | 1.139 | 0.97 |
| 43_D | 110_Y | 1.139 | 0.97 |
| 102_D | 242_N | 1.135 | 0.97 |
| 134_P | 137_G | 1.124 | 0.97 |
| 74_K | 78_N | 1.124 | 0.97 |
| 173_V | 187_E | 1.120 | 0.96 |
| 79_G | 242_N | 1.118 | 0.96 |
| 35_G | 72_P | 1.114 | 0.96 |
| 127_Y | 137_G | 1.111 | 0.96 |
| 101_G | 238_A | 1.110 | 0.96 |
| 168_D | 171_A | 1.110 | 0.96 |
| 32_L | 59_I | 1.107 | 0.96 |
| 193_T | 203_A | 1.104 | 0.96 |
| 103_L | 238_A | 1.099 | 0.96 |
| 51_E | 63_F | 1.095 | 0.96 |
| 254_K | 257_K | 1.091 | 0.96 |
| 119_G | 198_A | 1.088 | 0.96 |
| 106_V | 252_I | 1.087 | 0.96 |
| 131_K | 134_P | 1.081 | 0.95 |
| 69_Y | 72_P | 1.078 | 0.95 |
| 16_A | 19_V | 1.077 | 0.95 |
| 140_A | 196_N | 1.075 | 0.95 |
| 59_I | 254_K | 1.068 | 0.95 |
| 54_L | 59_I | 1.067 | 0.95 |
| 267_V | 270_K | 1.062 | 0.95 |
| 85_S | 237_I | 1.061 | 0.95 |
| 123_G | 219_T | 1.047 | 0.94 |
| 138_Q | 201_D | 1.041 | 0.94 |
| 23_C | 27_N | 1.035 | 0.94 |
| 57_E | 258_A | 1.034 | 0.94 |
| 53_L | 57_E | 1.034 | 0.94 |
| 164_N | 181_K | 1.032 | 0.94 |
| 72_P | 84_N | 1.030 | 0.94 |
| 77_K | 102_D | 1.026 | 0.94 |
| 49_K | 53_L | 1.015 | 0.93 |
| 52_E | 259_Y | 1.015 | 0.93 |
| 162_K | 177_K | 1.014 | 0.93 |
| 107_A | 253_K | 1.009 | 0.93 |
| 49_K | 52_E | 1.008 | 0.93 |
| 76_L | 240_Q | 1.006 | 0.93 |
| 265_K | 269_K | 1.005 | 0.93 |
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 | |
| 4oteA | 2 | 0.8536 | 100 | 0.424 | Contact Map |
| 4k3fA | 1 | 0.8536 | 100 | 0.428 | Contact Map |
| 1xs5A | 1 | 0.85 | 100 | 0.428 | Contact Map |
| 4ib2A | 2 | 0.875 | 100 | 0.429 | Contact Map |
| 4gotA | 1 | 0.8571 | 100 | 0.432 | Contact Map |
| 1p99A | 1 | 0.85 | 100 | 0.433 | Contact Map |
| 4ntlA | 1 | 0.8571 | 100 | 0.435 | Contact Map |
| 3ir1A | 6 | 0.8429 | 100 | 0.435 | Contact Map |
| 3up9A | 1 | 0.8429 | 100 | 0.44 | Contact Map |
| 3gxaA | 6 | 0.8429 | 100 | 0.443 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)