| nachbac |
| ID: | 1487163167 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 284 (240) | ||
| Sequences: | 4930 (3152.2) | ||
| Seq/Len: | 20.542 | ||
| Nf(neff/√len): | 203.5 |
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: 20.542).
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 |
| 69_T | 102_H | 4.706 | 1.00 |
| 159_F | 215_I | 3.626 | 1.00 |
| 26_F | 71_E | 2.967 | 1.00 |
| 163_G | 212_Y | 2.818 | 1.00 |
| 30_I | 67_I | 2.742 | 1.00 |
| 72_I | 85_F | 2.622 | 1.00 |
| 76_F | 86_F | 2.450 | 1.00 |
| 185_L | 216_F | 2.429 | 1.00 |
| 21_V | 74_L | 2.370 | 1.00 |
| 177_N | 180_L | 2.289 | 1.00 |
| 59_A | 63_A | 2.231 | 1.00 |
| 72_I | 95_L | 2.007 | 1.00 |
| 33_L | 67_I | 1.888 | 1.00 |
| 63_A | 67_I | 1.859 | 1.00 |
| 137_A | 141_T | 1.848 | 1.00 |
| 66_W | 70_I | 1.826 | 1.00 |
| 37_N | 64_L | 1.774 | 1.00 |
| 17_A | 74_L | 1.759 | 1.00 |
| 202_I | 213_F | 1.709 | 1.00 |
| 164_T | 181_S | 1.688 | 1.00 |
| 92_W | 96_L | 1.673 | 1.00 |
| 75_R | 79_A | 1.657 | 1.00 |
| 166_L | 213_F | 1.591 | 1.00 |
| 85_F | 95_L | 1.588 | 1.00 |
| 85_F | 91_N | 1.583 | 1.00 |
| 33_L | 68_F | 1.569 | 1.00 |
| 117_R | 120_R | 1.566 | 1.00 |
| 21_V | 26_F | 1.555 | 1.00 |
| 114_R | 117_R | 1.543 | 1.00 |
| 40_I | 64_L | 1.541 | 1.00 |
| 17_A | 77_I | 1.528 | 1.00 |
| 36_I | 64_L | 1.512 | 1.00 |
| 16_L | 20_I | 1.501 | 1.00 |
| 34_I | 37_N | 1.496 | 1.00 |
| 191_L | 217_I | 1.494 | 1.00 |
| 72_I | 76_F | 1.487 | 1.00 |
| 71_E | 75_R | 1.481 | 1.00 |
| 28_P | 32_T | 1.478 | 1.00 |
| 88_S | 91_N | 1.438 | 1.00 |
| 160_A | 182_L | 1.411 | 1.00 |
| 12_P | 15_A | 1.409 | 1.00 |
| 73_T | 77_I | 1.409 | 1.00 |
| 208_W | 212_Y | 1.406 | 0.99 |
| 193_S | 197_G | 1.404 | 0.99 |
| 75_R | 91_N | 1.402 | 0.99 |
| 62_L | 66_W | 1.399 | 0.99 |
| 175_F | 213_F | 1.391 | 0.99 |
| 159_F | 163_G | 1.369 | 0.99 |
| 33_L | 64_L | 1.358 | 0.99 |
| 13_L | 77_I | 1.352 | 0.99 |
| 141_T | 235_N | 1.343 | 0.99 |
| 70_I | 74_L | 1.330 | 0.99 |
| 72_I | 98_V | 1.330 | 0.99 |
| 40_I | 60_A | 1.323 | 0.99 |
| 56_W | 60_A | 1.318 | 0.99 |
| 160_A | 178_L | 1.315 | 0.99 |
| 84_S | 87_K | 1.309 | 0.99 |
| 65_L | 101_G | 1.308 | 0.99 |
| 189_V | 220_G | 1.305 | 0.99 |
| 36_I | 60_A | 1.304 | 0.99 |
| 169_S | 176_G | 1.303 | 0.99 |
| 71_E | 94_D | 1.293 | 0.99 |
| 180_L | 210_W | 1.275 | 0.99 |
| 167_F | 209_S | 1.246 | 0.98 |
| 18_Q | 22_F | 1.236 | 0.98 |
| 187_Q | 190_T | 1.229 | 0.98 |
| 123_R | 127_V | 1.222 | 0.98 |
| 203_F | 210_W | 1.207 | 0.98 |
| 192_E | 195_A | 1.204 | 0.98 |
| 86_F | 95_L | 1.203 | 0.98 |
| 27_T | 85_F | 1.200 | 0.98 |
| 91_N | 94_D | 1.198 | 0.98 |
| 139_L | 142_I | 1.191 | 0.98 |
| 183_L | 199_M | 1.183 | 0.98 |
| 97_I | 100_A | 1.171 | 0.98 |
| 12_P | 16_L | 1.170 | 0.97 |
| 96_L | 100_A | 1.169 | 0.97 |
| 30_I | 34_I | 1.164 | 0.97 |
| 188_V | 194_W | 1.156 | 0.97 |
| 39_I | 43_L | 1.156 | 0.97 |
| 36_I | 40_I | 1.149 | 0.97 |
| 156_F | 216_F | 1.139 | 0.97 |
| 15_A | 19_R | 1.123 | 0.97 |
| 232_I | 235_N | 1.121 | 0.97 |
| 37_N | 68_F | 1.116 | 0.96 |
| 164_T | 178_L | 1.114 | 0.96 |
| 184_T | 188_V | 1.112 | 0.96 |
| 140_M | 242_E | 1.111 | 0.96 |
| 60_A | 63_A | 1.109 | 0.96 |
| 235_N | 238_K | 1.106 | 0.96 |
| 232_I | 236_V | 1.105 | 0.96 |
| 16_L | 19_R | 1.102 | 0.96 |
| 76_F | 82_T | 1.100 | 0.96 |
| 74_L | 78_A | 1.091 | 0.96 |
| 26_F | 30_I | 1.090 | 0.96 |
| 25_A | 28_P | 1.089 | 0.96 |
| 175_F | 181_S | 1.087 | 0.96 |
| 58_Y | 62_L | 1.085 | 0.96 |
| 32_T | 36_I | 1.074 | 0.95 |
| 60_A | 64_L | 1.066 | 0.95 |
| 51_Q | 55_D | 1.062 | 0.95 |
| 163_G | 167_F | 1.062 | 0.95 |
| 55_D | 59_A | 1.061 | 0.95 |
| 56_W | 59_A | 1.060 | 0.95 |
| 20_I | 26_F | 1.059 | 0.95 |
| 66_W | 69_T | 1.057 | 0.95 |
| 161_V | 178_L | 1.052 | 0.95 |
| 188_V | 191_L | 1.051 | 0.94 |
| 148_I | 227_L | 1.037 | 0.94 |
| 120_R | 123_R | 1.031 | 0.94 |
| 29_T | 33_L | 1.031 | 0.94 |
| 77_I | 82_T | 1.019 | 0.93 |
| 206_V | 209_S | 1.017 | 0.93 |
| 75_R | 94_D | 1.015 | 0.93 |
| 89_S | 93_F | 1.012 | 0.93 |
| 231_V | 235_N | 1.008 | 0.93 |
| 193_S | 196_S | 1.007 | 0.93 |
| 219_V | 244_L | 1.002 | 0.92 |
| 140_M | 239_A | 1.001 | 0.92 |
| 171_A | 202_I | 1.000 | 0.92 |
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 | |
| 4bgnA | 2 | 0.7606 | 100 | 0.325 | Contact Map |
| 3rvyA | 2 | 0.7746 | 100 | 0.352 | Contact Map |
| 4dxwA | 4 | 0.7817 | 100 | 0.41 | Contact Map |
| 3behA | 4 | 0.7923 | 100 | 0.487 | Contact Map |
| 2r9rB | 2 | 0.838 | 100 | 0.49 | Contact Map |
| 3j9pD | 4 | 0.8345 | 100 | 0.565 | Contact Map |
| 4ltoA | 4 | 0.4577 | 99.9 | 0.587 | Contact Map |
| 4cbcA | 4 | 0.3239 | 99.9 | 0.587 | Contact Map |
| 1orqC | 1 | 0.7641 | 99.9 | 0.606 | Contact Map |
| 3j5pB | 4 | 0.919 | 99.8 | 0.679 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)