| T domain short module |
| ID: | 1506977639 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 254 (239) | ||
| Sequences: | 3126 (2547.9) | ||
| Seq/Len: | 13.079 | ||
| Nf(neff/√len): | 164.8 |
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: 13.079).
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 |
| 94_F | 99_A | 3.441 | 1.00 |
| 71_L | 147_R | 3.287 | 1.00 |
| 69_D | 147_R | 3.261 | 1.00 |
| 91_S | 140_A | 3.163 | 1.00 |
| 81_E | 110_R | 2.794 | 1.00 |
| 89_G | 92_Q | 2.628 | 1.00 |
| 75_L | 111_L | 2.619 | 1.00 |
| 93_S | 96_E | 2.547 | 1.00 |
| 68_L | 90_R | 2.446 | 1.00 |
| 79_W | 139_V | 2.374 | 1.00 |
| 100_D | 103_I | 2.318 | 1.00 |
| 93_S | 137_P | 2.226 | 1.00 |
| 196_M | 216_G | 2.124 | 1.00 |
| 35_P | 47_L | 2.113 | 1.00 |
| 76_A | 90_R | 2.055 | 1.00 |
| 72_E | 90_R | 2.045 | 1.00 |
| 189_F | 192_V | 2.039 | 1.00 |
| 90_R | 139_V | 2.007 | 1.00 |
| 82_A | 107_V | 1.998 | 1.00 |
| 242_A | 246_M | 1.988 | 1.00 |
| 190_H | 241_Y | 1.929 | 1.00 |
| 234_I | 238_A | 1.912 | 1.00 |
| 79_W | 99_A | 1.853 | 1.00 |
| 138_T | 141_D | 1.826 | 1.00 |
| 132_Q | 145_F | 1.822 | 1.00 |
| 191_A | 198_I | 1.809 | 1.00 |
| 76_A | 139_V | 1.779 | 1.00 |
| 74_I | 114_K | 1.754 | 1.00 |
| 129_L | 132_Q | 1.735 | 1.00 |
| 31_V | 34_L | 1.727 | 1.00 |
| 186_R | 215_V | 1.710 | 1.00 |
| 70_E | 73_S | 1.654 | 1.00 |
| 78_L | 107_V | 1.570 | 1.00 |
| 73_S | 77_K | 1.567 | 1.00 |
| 233_L | 236_T | 1.513 | 1.00 |
| 110_R | 114_K | 1.486 | 1.00 |
| 79_W | 142_L | 1.453 | 1.00 |
| 76_A | 80_A | 1.435 | 1.00 |
| 12_E | 16_K | 1.430 | 1.00 |
| 68_L | 140_A | 1.416 | 1.00 |
| 80_A | 87_S | 1.413 | 1.00 |
| 190_H | 196_M | 1.412 | 1.00 |
| 136_Y | 145_F | 1.405 | 0.99 |
| 69_D | 73_S | 1.403 | 0.99 |
| 95_Y | 134_L | 1.401 | 0.99 |
| 71_L | 74_I | 1.388 | 0.99 |
| 7_R | 10_E | 1.387 | 0.99 |
| 75_L | 139_V | 1.385 | 0.99 |
| 75_L | 143_A | 1.374 | 0.99 |
| 68_L | 72_E | 1.373 | 0.99 |
| 190_H | 199_F | 1.363 | 0.99 |
| 185_L | 213_S | 1.350 | 0.99 |
| 79_W | 94_F | 1.345 | 0.99 |
| 65_E | 90_R | 1.345 | 0.99 |
| 75_L | 142_L | 1.338 | 0.99 |
| 106_Q | 110_R | 1.338 | 0.99 |
| 77_K | 114_K | 1.311 | 0.99 |
| 220_A | 240_D | 1.307 | 0.99 |
| 108_A | 112_R | 1.293 | 0.99 |
| 19_V | 23_M | 1.293 | 0.99 |
| 188_V | 196_M | 1.292 | 0.99 |
| 191_A | 241_Y | 1.289 | 0.99 |
| 189_F | 203_L | 1.274 | 0.99 |
| 69_D | 90_R | 1.262 | 0.99 |
| 88_I | 97_H | 1.258 | 0.99 |
| 232_E | 236_T | 1.255 | 0.99 |
| 90_R | 140_A | 1.253 | 0.99 |
| 14_F | 18_H | 1.248 | 0.99 |
| 82_A | 103_I | 1.233 | 0.98 |
| 240_D | 244_C | 1.232 | 0.98 |
| 24_L | 28_L | 1.227 | 0.98 |
| 64_S | 87_S | 1.219 | 0.98 |
| 12_E | 28_L | 1.218 | 0.98 |
| 79_W | 107_V | 1.216 | 0.98 |
| 69_D | 72_E | 1.212 | 0.98 |
| 72_E | 143_A | 1.211 | 0.98 |
| 231_A | 240_D | 1.209 | 0.98 |
| 191_A | 199_F | 1.190 | 0.98 |
| 163_I | 167_N | 1.184 | 0.98 |
| 71_L | 115_L | 1.182 | 0.98 |
| 92_Q | 97_H | 1.181 | 0.98 |
| 65_E | 91_S | 1.159 | 0.97 |
| 80_A | 86_V | 1.153 | 0.97 |
| 163_I | 166_Q | 1.152 | 0.97 |
| 20_P | 23_M | 1.152 | 0.97 |
| 191_A | 197_D | 1.145 | 0.97 |
| 72_E | 140_A | 1.143 | 0.97 |
| 203_L | 214_I | 1.140 | 0.97 |
| 244_C | 247_A | 1.137 | 0.97 |
| 233_L | 237_V | 1.134 | 0.97 |
| 190_H | 194_G | 1.129 | 0.97 |
| 243_E | 247_A | 1.126 | 0.97 |
| 29_Q | 48_A | 1.125 | 0.97 |
| 75_L | 78_L | 1.122 | 0.97 |
| 243_E | 246_M | 1.121 | 0.97 |
| 187_V | 245_L | 1.111 | 0.96 |
| 136_Y | 141_D | 1.102 | 0.96 |
| 10_E | 14_F | 1.098 | 0.96 |
| 184_L | 212_G | 1.093 | 0.96 |
| 43_D | 46_T | 1.085 | 0.96 |
| 31_V | 47_L | 1.074 | 0.95 |
| 37_T | 43_D | 1.072 | 0.95 |
| 25_P | 41_K | 1.070 | 0.95 |
| 108_A | 133_M | 1.062 | 0.95 |
| 231_A | 237_V | 1.051 | 0.94 |
| 237_V | 240_D | 1.051 | 0.94 |
| 76_A | 88_I | 1.050 | 0.94 |
| 71_L | 146_I | 1.047 | 0.94 |
| 188_V | 214_I | 1.040 | 0.94 |
| 99_A | 103_I | 1.025 | 0.93 |
| 112_R | 127_D | 1.024 | 0.93 |
| 95_Y | 137_P | 1.012 | 0.93 |
| 88_I | 92_Q | 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 | |
| 2vsqA | 1 | 0.815 | 100 | 0.308 | Contact Map |
| 4r0mB | 2 | 0.5315 | 100 | 0.462 | Contact Map |
| 4dg8A | 1 | 0.2008 | 100 | 0.462 | Contact Map |
| 4iz6A | 2 | 0.5315 | 100 | 0.468 | Contact Map |
| 4f6lB | 2 | 0.3661 | 99.9 | 0.535 | Contact Map |
| 4oqjA | 1 | 0.1299 | 99.9 | 0.54 | Contact Map |
| 3tejA | 2 | 0.6457 | 99.9 | 0.554 | Contact Map |
| 2vz8A | 2 | 0.1772 | 99.8 | 0.622 | Contact Map |
| 2jgpA | 1 | 0.622 | 99.7 | 0.644 | Contact Map |
| 2cq8A | 1 | 0.4252 | 99.7 | 0.646 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)