| Tcb1 |
| ID: | 1441328363 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 207 (180) | ||
| Sequences: | 700 (530.3) | ||
| Seq/Len: | 3.889 | ||
| Nf(neff/√len): | 39.5 |
HHblits Results: (2015_06)
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: 3.889).
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 |
| 32_N | 41_E | 3.357 | 1.00 |
| 73_D | 78_G | 3.186 | 1.00 |
| 178_N | 185_E | 2.939 | 1.00 |
| 34_N | 41_E | 2.735 | 1.00 |
| 77_N | 84_E | 2.701 | 1.00 |
| 134_D | 143_E | 2.405 | 1.00 |
| 73_D | 77_N | 2.303 | 1.00 |
| 174_D | 179_G | 2.173 | 1.00 |
| 174_D | 185_E | 2.082 | 1.00 |
| 41_E | 84_E | 2.044 | 1.00 |
| 136_S | 143_E | 1.891 | 1.00 |
| 73_D | 84_E | 1.866 | 1.00 |
| 132_D | 137_G | 1.751 | 0.99 |
| 143_E | 178_N | 1.656 | 0.99 |
| 143_E | 176_D | 1.654 | 0.99 |
| 143_E | 185_E | 1.650 | 0.99 |
| 45_L | 147_V | 1.639 | 0.99 |
| 42_V | 82_Y | 1.620 | 0.99 |
| 139_L | 144_V | 1.579 | 0.98 |
| 181_V | 188_D | 1.568 | 0.98 |
| 174_D | 178_N | 1.521 | 0.98 |
| 60_V | 80_V | 1.520 | 0.98 |
| 66_K | 141_E | 1.519 | 0.98 |
| 72_V | 173_T | 1.508 | 0.98 |
| 124_A | 186_Y | 1.501 | 0.97 |
| 69_M | 170_M | 1.491 | 0.97 |
| 77_N | 178_N | 1.488 | 0.97 |
| 26_F | 85_Y | 1.445 | 0.97 |
| 41_E | 143_E | 1.409 | 0.96 |
| 143_E | 174_D | 1.402 | 0.96 |
| 144_V | 169_W | 1.391 | 0.95 |
| 36_T | 79_L | 1.365 | 0.95 |
| 156_G | 190_V | 1.363 | 0.95 |
| 34_N | 136_S | 1.351 | 0.94 |
| 46_I | 148_I | 1.336 | 0.94 |
| 138_Q | 180_T | 1.324 | 0.94 |
| 176_D | 185_E | 1.286 | 0.92 |
| 176_D | 182_S | 1.281 | 0.92 |
| 23_R | 172_M | 1.276 | 0.92 |
| 128_F | 186_Y | 1.275 | 0.92 |
| 30_D | 35_G | 1.266 | 0.92 |
| 15_T | 18_K | 1.242 | 0.90 |
| 140_E | 180_T | 1.233 | 0.90 |
| 25_L | 127_L | 1.205 | 0.89 |
| 143_E | 179_G | 1.185 | 0.88 |
| 43_A | 181_V | 1.179 | 0.87 |
| 37_L | 96_A | 1.172 | 0.87 |
| 61_T | 65_V | 1.166 | 0.86 |
| 155_M | 169_W | 1.150 | 0.85 |
| 151_T | 154_Q | 1.149 | 0.85 |
| 144_V | 173_T | 1.133 | 0.84 |
| 145_Y | 163_E | 1.132 | 0.84 |
| 32_N | 140_E | 1.129 | 0.84 |
| 30_D | 37_L | 1.128 | 0.84 |
| 26_F | 37_L | 1.127 | 0.84 |
| 124_A | 147_V | 1.114 | 0.83 |
| 176_D | 179_G | 1.098 | 0.82 |
| 141_E | 167_K | 1.087 | 0.81 |
| 131_Y | 139_L | 1.076 | 0.80 |
| 29_F | 50_F | 1.071 | 0.79 |
| 128_F | 137_G | 1.062 | 0.78 |
| 15_T | 19_L | 1.061 | 0.78 |
| 148_I | 166_V | 1.053 | 0.78 |
| 36_T | 77_N | 1.045 | 0.77 |
| 33_K | 41_E | 1.028 | 0.75 |
| 19_L | 80_V | 1.027 | 0.75 |
| 42_V | 60_V | 1.024 | 0.75 |
| 119_M | 144_V | 1.020 | 0.74 |
| 144_V | 170_M | 1.015 | 0.74 |
| 26_F | 30_D | 1.014 | 0.74 |
| 131_Y | 150_E | 1.012 | 0.74 |
| 98_F | 118_E | 1.011 | 0.73 |
| 66_K | 70_K | 1.008 | 0.73 |
| 58_Y | 83_S | 1.008 | 0.73 |
| 60_V | 63_D | 1.002 | 0.73 |
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 | |
| 3u0kA | 1 | 0.7198 | 99.9 | 0.408 | Contact Map |
| 3mwuA | 1 | 0.6908 | 99.9 | 0.41 | Contact Map |
| 4mvfA | 1 | 0.744 | 99.9 | 0.413 | Contact Map |
| 3q5iA | 1 | 0.7826 | 99.9 | 0.417 | Contact Map |
| 4i2yA | 2 | 0.7488 | 99.9 | 0.417 | Contact Map |
| 4c0kA | 1 | 0.8792 | 99.9 | 0.421 | Contact Map |
| 3lijA | 1 | 0.7826 | 99.9 | 0.421 | Contact Map |
| 3ox6A | 6 | 0.7391 | 99.9 | 0.426 | Contact Map |
| 4n5xA | 1 | 0.7101 | 99.9 | 0.427 | Contact Map |
| 2lhiA | 1 | 0.7778 | 99.9 | 0.428 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)