| T0776 |
| ID: | 1400004946 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 256 (227) | ||
| Sequences: | 2495 (2152.8) | ||
| Seq/Len: | 10.991 | ||
| Nf(neff/√len): | 142.9 |
Jackhmmer Results: (2014_04_16)
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: 10.991).
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 |
| 155_R | 206_E | 3.915 | 1.00 |
| 174_E | 211_F | 3.716 | 1.00 |
| 151_E | 202_K | 3.592 | 1.00 |
| 110_L | 130_I | 3.029 | 1.00 |
| 107_V | 153_D | 2.993 | 1.00 |
| 105_N | 113_R | 2.823 | 1.00 |
| 126_L | 161_T | 2.771 | 1.00 |
| 115_E | 160_Y | 2.463 | 1.00 |
| 159_K | 207_F | 2.388 | 1.00 |
| 48_V | 96_K | 2.372 | 1.00 |
| 51_F | 57_T | 2.350 | 1.00 |
| 155_R | 207_F | 2.325 | 1.00 |
| 243_Q | 247_N | 1.864 | 1.00 |
| 151_E | 199_S | 1.857 | 1.00 |
| 162_K | 207_F | 1.843 | 1.00 |
| 204_S | 211_F | 1.834 | 1.00 |
| 107_V | 157_L | 1.833 | 1.00 |
| 175_P | 197_R | 1.828 | 1.00 |
| 172_L | 200_A | 1.810 | 1.00 |
| 237_P | 245_M | 1.800 | 1.00 |
| 56_I | 132_V | 1.786 | 1.00 |
| 248_M | 251_E | 1.774 | 1.00 |
| 49_I | 127_S | 1.763 | 1.00 |
| 126_L | 168_T | 1.762 | 1.00 |
| 214_F | 245_M | 1.752 | 1.00 |
| 51_F | 127_S | 1.745 | 1.00 |
| 174_E | 213_P | 1.741 | 1.00 |
| 111_R | 156_A | 1.693 | 1.00 |
| 51_F | 82_T | 1.682 | 1.00 |
| 154_L | 200_A | 1.676 | 1.00 |
| 161_T | 168_T | 1.645 | 1.00 |
| 150_Y | 196_F | 1.643 | 1.00 |
| 201_R | 211_F | 1.633 | 1.00 |
| 169_Q | 210_I | 1.546 | 1.00 |
| 155_R | 159_K | 1.545 | 1.00 |
| 47_C | 124_D | 1.542 | 1.00 |
| 57_T | 101_G | 1.529 | 1.00 |
| 52_Q | 110_L | 1.519 | 1.00 |
| 146_T | 149_T | 1.509 | 1.00 |
| 172_L | 204_S | 1.429 | 1.00 |
| 107_V | 150_Y | 1.419 | 1.00 |
| 160_Y | 164_K | 1.418 | 1.00 |
| 213_P | 216_S | 1.405 | 0.99 |
| 47_C | 95_P | 1.403 | 0.99 |
| 111_R | 153_D | 1.400 | 0.99 |
| 150_Y | 200_A | 1.386 | 0.99 |
| 60_G | 103_S | 1.358 | 0.99 |
| 158_L | 172_L | 1.351 | 0.99 |
| 173_C | 249_W | 1.348 | 0.99 |
| 63_R | 239_L | 1.348 | 0.99 |
| 158_L | 203_L | 1.335 | 0.99 |
| 49_I | 97_I | 1.327 | 0.99 |
| 85_Q | 247_N | 1.324 | 0.99 |
| 102_I | 113_R | 1.312 | 0.99 |
| 240_P | 243_Q | 1.307 | 0.99 |
| 114_W | 161_T | 1.296 | 0.99 |
| 58_D | 103_S | 1.287 | 0.99 |
| 151_E | 155_R | 1.281 | 0.99 |
| 165_L | 168_T | 1.278 | 0.99 |
| 201_R | 205_E | 1.277 | 0.99 |
| 107_V | 111_R | 1.220 | 0.98 |
| 106_K | 109_Q | 1.215 | 0.98 |
| 57_T | 129_L | 1.207 | 0.98 |
| 125_V | 171_V | 1.206 | 0.98 |
| 154_L | 203_L | 1.199 | 0.98 |
| 154_L | 172_L | 1.191 | 0.98 |
| 203_L | 207_F | 1.189 | 0.98 |
| 113_R | 117_D | 1.175 | 0.98 |
| 105_N | 109_Q | 1.173 | 0.98 |
| 156_A | 160_Y | 1.171 | 0.98 |
| 114_W | 157_L | 1.168 | 0.97 |
| 114_W | 117_D | 1.162 | 0.97 |
| 54_D | 131_G | 1.151 | 0.97 |
| 36_V | 39_P | 1.144 | 0.97 |
| 59_C | 242_R | 1.106 | 0.96 |
| 158_L | 207_F | 1.101 | 0.96 |
| 229_Y | 240_P | 1.099 | 0.96 |
| 127_S | 173_C | 1.084 | 0.96 |
| 167_N | 170_I | 1.080 | 0.95 |
| 81_F | 85_Q | 1.074 | 0.95 |
| 26_A | 29_A | 1.073 | 0.95 |
| 171_V | 210_I | 1.072 | 0.95 |
| 56_I | 237_P | 1.069 | 0.95 |
| 202_K | 206_E | 1.060 | 0.95 |
| 197_R | 200_A | 1.059 | 0.95 |
| 136_W | 235_V | 1.051 | 0.94 |
| 217_G | 248_M | 1.050 | 0.94 |
| 174_E | 201_R | 1.045 | 0.94 |
| 172_L | 203_L | 1.043 | 0.94 |
| 193_F | 197_R | 1.031 | 0.94 |
| 62_D | 239_L | 1.029 | 0.94 |
| 230_W | 244_L | 1.026 | 0.94 |
| 147_V | 199_S | 1.024 | 0.93 |
| 107_V | 154_L | 1.023 | 0.93 |
| 127_S | 249_W | 1.021 | 0.93 |
| 31_K | 34_T | 1.018 | 0.93 |
| 215_Q | 219_D | 1.018 | 0.93 |
| 198_K | 202_K | 1.011 | 0.93 |
| 52_Q | 114_W | 1.007 | 0.93 |
| 158_L | 209_T | 1.004 | 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 | |
| 4jhlA | 2 | 0.8203 | 100 | 0.388 | Contact Map |
| 3rjtA | 2 | 0.8164 | 100 | 0.389 | Contact Map |
| 1vjgA | 1 | 0.7578 | 100 | 0.419 | Contact Map |
| 4jggA | 2 | 0.6992 | 100 | 0.426 | Contact Map |
| 2q0qA | 8 | 0.7539 | 100 | 0.427 | Contact Map |
| 3bzwA | 6 | 0.7891 | 100 | 0.428 | Contact Map |
| 3dciA | 3 | 0.7383 | 100 | 0.433 | Contact Map |
| 3dc7A | 3 | 0.7578 | 100 | 0.437 | Contact Map |
| 1ivnA | 1 | 0.6875 | 100 | 0.442 | Contact Map |
| 3hp4A | 1 | 0.6992 | 100 | 0.444 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)