| LarB |
| ID: | 1446058234 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 246 (244) | ||
| Sequences: | 804 (619.1) | ||
| Seq/Len: | 3.295 | ||
| Nf(neff/√len): | 39.6 |
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: 3.295).
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 |
| 226_T | 239_S | 4.155 | 1.00 |
| 35_F | 64_G | 3.310 | 1.00 |
| 11_V | 21_A | 3.282 | 1.00 |
| 175_V | 187_V | 3.136 | 1.00 |
| 136_A | 148_R | 2.651 | 1.00 |
| 11_V | 18_P | 2.460 | 1.00 |
| 89_L | 105_M | 2.349 | 1.00 |
| 54_G | 78_T | 2.349 | 1.00 |
| 41_D | 44_R | 2.318 | 1.00 |
| 147_E | 166_V | 2.260 | 1.00 |
| 58_T | 61_Q | 2.124 | 1.00 |
| 59_A | 85_K | 2.087 | 1.00 |
| 62_I | 85_K | 2.083 | 1.00 |
| 144_N | 241_S | 2.068 | 1.00 |
| 99_H | 102_A | 2.058 | 1.00 |
| 29_K | 41_D | 2.006 | 1.00 |
| 10_Q | 15_Q | 1.982 | 1.00 |
| 83_A | 87_A | 1.867 | 0.99 |
| 232_N | 235_G | 1.850 | 0.99 |
| 120_A | 170_A | 1.806 | 0.99 |
| 31_A | 40_L | 1.790 | 0.99 |
| 99_H | 137_V | 1.703 | 0.99 |
| 123_T | 129_Q | 1.691 | 0.99 |
| 118_Y | 145_R | 1.688 | 0.99 |
| 119_I | 139_A | 1.687 | 0.99 |
| 136_A | 140_E | 1.685 | 0.99 |
| 77_L | 104_C | 1.676 | 0.98 |
| 99_H | 104_C | 1.673 | 0.98 |
| 7_I | 16_L | 1.670 | 0.98 |
| 120_A | 149_V | 1.665 | 0.98 |
| 30_T | 162_A | 1.656 | 0.98 |
| 176_I | 198_V | 1.655 | 0.98 |
| 54_G | 81_L | 1.652 | 0.98 |
| 121_V | 136_A | 1.651 | 0.98 |
| 144_N | 244_N | 1.625 | 0.98 |
| 133_E | 150_Y | 1.622 | 0.98 |
| 120_A | 173_V | 1.610 | 0.98 |
| 212_T | 216_T | 1.568 | 0.97 |
| 67_Q | 92_A | 1.563 | 0.97 |
| 157_I | 161_F | 1.560 | 0.97 |
| 29_K | 44_R | 1.533 | 0.97 |
| 81_L | 105_M | 1.526 | 0.97 |
| 86_F | 105_M | 1.510 | 0.97 |
| 164_L | 168_R | 1.495 | 0.96 |
| 5_A | 9_Q | 1.492 | 0.96 |
| 140_E | 148_R | 1.488 | 0.96 |
| 104_C | 137_V | 1.486 | 0.96 |
| 174_I | 237_A | 1.479 | 0.96 |
| 17_S | 20_A | 1.469 | 0.96 |
| 167_I | 191_V | 1.467 | 0.96 |
| 133_E | 148_R | 1.440 | 0.95 |
| 66_V | 78_T | 1.436 | 0.95 |
| 38_V | 69_L | 1.432 | 0.95 |
| 12_A | 18_P | 1.429 | 0.95 |
| 207_S | 213_A | 1.423 | 0.95 |
| 161_F | 164_L | 1.420 | 0.95 |
| 139_A | 237_A | 1.415 | 0.95 |
| 102_A | 137_V | 1.400 | 0.94 |
| 136_A | 146_V | 1.399 | 0.94 |
| 206_T | 215_L | 1.398 | 0.94 |
| 83_A | 100_A | 1.393 | 0.94 |
| 6_E | 10_Q | 1.388 | 0.94 |
| 239_S | 242_M | 1.387 | 0.94 |
| 208_F | 211_M | 1.369 | 0.93 |
| 79_T | 234_F | 1.368 | 0.93 |
| 207_S | 212_T | 1.362 | 0.93 |
| 196_I | 228_V | 1.360 | 0.93 |
| 54_G | 62_I | 1.354 | 0.93 |
| 78_T | 81_L | 1.352 | 0.93 |
| 122_V | 187_V | 1.335 | 0.92 |
| 77_L | 138_T | 1.318 | 0.91 |
| 139_A | 146_V | 1.318 | 0.91 |
| 163_K | 166_V | 1.317 | 0.91 |
| 52_I | 69_L | 1.312 | 0.91 |
| 133_E | 136_A | 1.305 | 0.91 |
| 238_Y | 242_M | 1.297 | 0.90 |
| 123_T | 132_A | 1.294 | 0.90 |
| 197_A | 225_I | 1.293 | 0.90 |
| 133_E | 140_E | 1.285 | 0.90 |
| 37_N | 163_K | 1.284 | 0.90 |
| 5_A | 19_T | 1.283 | 0.90 |
| 52_I | 66_V | 1.268 | 0.89 |
| 118_Y | 147_E | 1.262 | 0.89 |
| 56_G | 132_A | 1.261 | 0.89 |
| 191_V | 195_V | 1.260 | 0.89 |
| 36_A | 65_I | 1.247 | 0.88 |
| 82_S | 85_K | 1.241 | 0.88 |
| 89_L | 93_L | 1.241 | 0.88 |
| 173_V | 191_V | 1.222 | 0.87 |
| 171_R | 244_N | 1.219 | 0.86 |
| 63_V | 93_L | 1.212 | 0.86 |
| 54_G | 85_K | 1.212 | 0.86 |
| 62_I | 81_L | 1.206 | 0.86 |
| 174_I | 236_A | 1.206 | 0.86 |
| 212_T | 219_N | 1.200 | 0.85 |
| 129_Q | 150_Y | 1.194 | 0.85 |
| 59_A | 88_A | 1.191 | 0.85 |
| 176_I | 237_A | 1.187 | 0.84 |
| 135_A | 174_I | 1.185 | 0.84 |
| 55_A | 127_S | 1.184 | 0.84 |
| 80_R | 131_V | 1.166 | 0.83 |
| 149_V | 163_K | 1.145 | 0.81 |
| 9_Q | 13_A | 1.142 | 0.81 |
| 237_A | 244_N | 1.140 | 0.81 |
| 61_Q | 101_T | 1.138 | 0.81 |
| 81_L | 85_K | 1.135 | 0.81 |
| 208_F | 219_N | 1.133 | 0.80 |
| 55_A | 103_Q | 1.127 | 0.80 |
| 11_V | 16_L | 1.120 | 0.79 |
| 184_A | 216_T | 1.111 | 0.79 |
| 46_N | 223_S | 1.107 | 0.78 |
| 124_A | 185_S | 1.106 | 0.78 |
| 139_A | 144_N | 1.102 | 0.78 |
| 208_F | 215_L | 1.092 | 0.77 |
| 119_I | 144_N | 1.090 | 0.77 |
| 155_A | 218_L | 1.079 | 0.76 |
| 17_S | 174_I | 1.071 | 0.75 |
| 185_S | 216_T | 1.071 | 0.75 |
| 117_G | 171_R | 1.068 | 0.75 |
| 103_Q | 130_P | 1.067 | 0.74 |
| 197_A | 211_M | 1.063 | 0.74 |
| 6_E | 19_T | 1.059 | 0.74 |
| 5_A | 22_A | 1.054 | 0.73 |
| 63_V | 92_A | 1.051 | 0.73 |
| 121_V | 132_A | 1.049 | 0.73 |
| 96_A | 105_M | 1.048 | 0.73 |
| 30_T | 37_N | 1.047 | 0.73 |
| 131_V | 198_V | 1.036 | 0.71 |
| 137_V | 140_E | 1.034 | 0.71 |
| 224_G | 239_S | 1.034 | 0.71 |
| 173_V | 193_K | 1.030 | 0.71 |
| 241_S | 245_Q | 1.026 | 0.70 |
| 215_L | 219_N | 1.024 | 0.70 |
| 180_E | 216_T | 1.016 | 0.69 |
| 3_T | 6_E | 1.016 | 0.69 |
| 180_E | 207_S | 1.006 | 0.68 |
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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 2h31A | 1 | 0.8455 | 100 | 0.615 | Contact Map |
| 3lp6A | 4 | 0.5244 | 100 | 0.62 | Contact Map |
| 4ja0A | 4 | 0.8943 | 100 | 0.627 | Contact Map |
| 1o4vA | 1 | 0.4959 | 100 | 0.632 | Contact Map |
| 3orsA | 8 | 0.5 | 100 | 0.634 | Contact Map |
| 3oowA | 8 | 0.5081 | 100 | 0.634 | Contact Map |
| 3rg8A | 8 | 0.5 | 100 | 0.636 | Contact Map |
| 4grdA | 4 | 0.5244 | 100 | 0.639 | Contact Map |
| 4ay3A | 4 | 0.5041 | 100 | 0.64 | Contact Map |
| 3trhA | 16 | 0.5081 | 100 | 0.64 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)