| T0805 |
| ID: | 1401901681 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 214 (205) | ||
| Sequences: | 6025 (4460) | ||
| Seq/Len: | 29.390 | ||
| Nf(neff/√len): | 311.5 |
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: 29.390).
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 |
| 28_P | 31_V | 4.320 | 1.00 |
| 21_L | 25_K | 3.848 | 1.00 |
| 34_E | 151_R | 3.653 | 1.00 |
| 29_R | 57_E | 3.210 | 1.00 |
| 35_C | 148_L | 2.944 | 1.00 |
| 154_G | 192_T | 2.825 | 1.00 |
| 29_R | 33_M | 2.710 | 1.00 |
| 53_W | 140_A | 2.683 | 1.00 |
| 25_K | 191_Y | 2.596 | 1.00 |
| 52_Q | 210_H | 2.559 | 1.00 |
| 145_C | 155_S | 2.553 | 1.00 |
| 153_L | 191_Y | 2.440 | 1.00 |
| 31_V | 153_L | 2.236 | 1.00 |
| 21_L | 24_D | 2.216 | 1.00 |
| 13_T | 149_R | 2.149 | 1.00 |
| 31_V | 151_R | 2.126 | 1.00 |
| 53_W | 115_L | 2.085 | 1.00 |
| 54_V | 118_C | 2.053 | 1.00 |
| 39_A | 144_F | 2.008 | 1.00 |
| 37_E | 40_L | 1.987 | 1.00 |
| 171_A | 183_Q | 1.915 | 1.00 |
| 64_A | 173_V | 1.905 | 1.00 |
| 148_L | 189_I | 1.879 | 1.00 |
| 57_E | 212_N | 1.863 | 1.00 |
| 169_K | 172_D | 1.850 | 1.00 |
| 59_A | 63_K | 1.819 | 1.00 |
| 7_V | 11_L | 1.813 | 1.00 |
| 153_L | 189_I | 1.797 | 1.00 |
| 118_C | 181_Y | 1.770 | 1.00 |
| 9_E | 13_T | 1.756 | 1.00 |
| 141_V | 185_G | 1.728 | 1.00 |
| 61_K | 212_N | 1.702 | 1.00 |
| 61_K | 64_A | 1.635 | 1.00 |
| 35_C | 144_F | 1.622 | 1.00 |
| 21_L | 193_Q | 1.594 | 1.00 |
| 115_L | 144_F | 1.581 | 1.00 |
| 38_L | 147_A | 1.570 | 1.00 |
| 65_I | 170_V | 1.566 | 1.00 |
| 7_V | 10_V | 1.542 | 1.00 |
| 31_V | 191_Y | 1.534 | 1.00 |
| 20_R | 188_P | 1.534 | 1.00 |
| 33_M | 206_E | 1.527 | 1.00 |
| 19_K | 193_Q | 1.504 | 1.00 |
| 141_V | 187_L | 1.503 | 1.00 |
| 203_L | 207_S | 1.477 | 1.00 |
| 35_C | 189_I | 1.456 | 1.00 |
| 36_L | 209_T | 1.438 | 1.00 |
| 157_W | 185_G | 1.429 | 1.00 |
| 139_P | 142_W | 1.411 | 1.00 |
| 6_S | 9_E | 1.403 | 0.99 |
| 63_K | 109_H | 1.397 | 0.99 |
| 31_V | 34_E | 1.391 | 0.99 |
| 55_F | 113_V | 1.386 | 0.99 |
| 145_C | 157_W | 1.385 | 0.99 |
| 59_A | 62_K | 1.382 | 0.99 |
| 33_M | 37_E | 1.359 | 0.99 |
| 35_C | 153_L | 1.340 | 0.99 |
| 145_C | 187_L | 1.321 | 0.99 |
| 205_A | 209_T | 1.315 | 0.99 |
| 149_R | 154_G | 1.314 | 0.99 |
| 118_C | 176_I | 1.307 | 0.99 |
| 28_P | 191_Y | 1.307 | 0.99 |
| 164_D | 169_K | 1.306 | 0.99 |
| 32_L | 113_V | 1.304 | 0.99 |
| 57_E | 211_W | 1.301 | 0.99 |
| 58_D | 61_K | 1.297 | 0.99 |
| 42_A | 143_S | 1.297 | 0.99 |
| 55_F | 211_W | 1.296 | 0.99 |
| 21_L | 191_Y | 1.291 | 0.99 |
| 135_A | 138_F | 1.290 | 0.99 |
| 27_V | 153_L | 1.289 | 0.99 |
| 52_Q | 181_Y | 1.275 | 0.99 |
| 113_V | 189_I | 1.269 | 0.99 |
| 116_I | 183_Q | 1.258 | 0.99 |
| 9_E | 12_T | 1.257 | 0.99 |
| 30_D | 33_M | 1.257 | 0.99 |
| 55_F | 209_T | 1.242 | 0.98 |
| 168_H | 172_D | 1.236 | 0.98 |
| 29_R | 211_W | 1.230 | 0.98 |
| 27_V | 31_V | 1.225 | 0.98 |
| 16_S | 156_C | 1.217 | 0.98 |
| 148_L | 155_S | 1.213 | 0.98 |
| 117_P | 141_V | 1.209 | 0.98 |
| 54_V | 212_N | 1.195 | 0.98 |
| 60_A | 64_A | 1.182 | 0.98 |
| 12_T | 37_E | 1.159 | 0.97 |
| 8_D | 34_E | 1.154 | 0.97 |
| 68_V | 173_V | 1.147 | 0.97 |
| 40_L | 208_V | 1.130 | 0.97 |
| 117_P | 144_F | 1.128 | 0.97 |
| 144_F | 187_L | 1.125 | 0.97 |
| 26_P | 57_E | 1.116 | 0.96 |
| 57_E | 113_V | 1.114 | 0.96 |
| 38_L | 151_R | 1.100 | 0.96 |
| 116_I | 174_L | 1.081 | 0.95 |
| 120_K | 180_E | 1.066 | 0.95 |
| 204_P | 207_S | 1.066 | 0.95 |
| 142_W | 146_L | 1.066 | 0.95 |
| 61_K | 173_V | 1.064 | 0.95 |
| 11_L | 146_L | 1.052 | 0.95 |
| 12_T | 41_Q | 1.045 | 0.94 |
| 60_A | 63_K | 1.045 | 0.94 |
| 27_V | 191_Y | 1.023 | 0.93 |
| 8_D | 12_T | 1.007 | 0.93 |
| 11_L | 143_S | 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 | |
| 1bkjA | 2 | 0.7991 | 100 | 0.232 | Contact Map |
| 3eofA | 2 | 0.7944 | 100 | 0.233 | Contact Map |
| 3n2sA | 4 | 0.7991 | 100 | 0.234 | Contact Map |
| 1f5vA | 2 | 0.8037 | 100 | 0.237 | Contact Map |
| 1zchA | 1 | 0.8037 | 100 | 0.244 | Contact Map |
| 3of4A | 3 | 0.785 | 100 | 0.245 | Contact Map |
| 3gr3A | 2 | 0.9206 | 100 | 0.246 | Contact Map |
| 4dn2A | 2 | 0.8692 | 100 | 0.248 | Contact Map |
| 1icrA | 2 | 0.8037 | 100 | 0.248 | Contact Map |
| 1noxA | 1 | 0.785 | 100 | 0.249 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)