| fam -force run |
| ID: | 1445968995 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 254 (246) | ||
| Sequences: | 86 (61.2) | ||
| Seq/Len: | 0.350 | ||
| Nf(neff/√len): | 3.9 |
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: 0.350).
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 |
| 53_S | 56_E | 2.526 | 0.94 |
| 50_D | 57_R | 2.007 | 0.78 |
| 227_S | 230_S | 1.981 | 0.76 |
| 52_R | 57_R | 1.949 | 0.75 |
| 37_K | 40_D | 1.942 | 0.74 |
| 54_L | 58_L | 1.890 | 0.72 |
| 80_R | 211_I | 1.836 | 0.68 |
| 26_K | 228_S | 1.788 | 0.65 |
| 50_D | 54_L | 1.787 | 0.65 |
| 61_Q | 64_R | 1.785 | 0.65 |
| 18_E | 64_R | 1.703 | 0.60 |
| 50_D | 60_E | 1.671 | 0.58 |
| 26_K | 84_E | 1.642 | 0.56 |
| 52_R | 60_E | 1.571 | 0.51 |
| 60_E | 64_R | 1.527 | 0.48 |
| 52_R | 58_L | 1.519 | 0.47 |
| 22_D | 76_K | 1.515 | 0.47 |
| 54_L | 57_R | 1.487 | 0.45 |
| 52_R | 55_Y | 1.439 | 0.42 |
| 151_K | 159_H | 1.433 | 0.41 |
| 53_S | 62_K | 1.432 | 0.41 |
| 115_Y | 138_V | 1.429 | 0.41 |
| 215_L | 226_S | 1.414 | 0.40 |
| 26_K | 40_D | 1.399 | 0.39 |
| 50_D | 61_Q | 1.392 | 0.38 |
| 50_D | 58_L | 1.381 | 0.38 |
| 87_T | 150_A | 1.380 | 0.38 |
| 43_E | 101_E | 1.377 | 0.37 |
| 13_K | 146_K | 1.369 | 0.37 |
| 17_S | 237_T | 1.365 | 0.37 |
| 17_S | 131_E | 1.360 | 0.36 |
| 221_S | 224_S | 1.356 | 0.36 |
| 50_D | 55_Y | 1.351 | 0.36 |
| 28_R | 34_K | 1.350 | 0.36 |
| 50_D | 64_R | 1.339 | 0.35 |
| 42_E | 205_A | 1.335 | 0.35 |
| 72_Q | 75_F | 1.331 | 0.34 |
| 93_V | 213_P | 1.322 | 0.34 |
| 16_V | 104_R | 1.313 | 0.33 |
| 29_Q | 41_P | 1.313 | 0.33 |
| 80_R | 128_N | 1.310 | 0.33 |
| 53_S | 57_R | 1.310 | 0.33 |
| 48_V | 85_D | 1.303 | 0.33 |
| 50_D | 53_S | 1.299 | 0.32 |
| 44_C | 48_V | 1.297 | 0.32 |
| 23_E | 26_K | 1.286 | 0.32 |
| 79_V | 91_D | 1.283 | 0.31 |
| 11_I | 14_R | 1.282 | 0.31 |
| 49_Y | 52_R | 1.279 | 0.31 |
| 66_Q | 75_F | 1.271 | 0.31 |
| 101_E | 223_D | 1.268 | 0.31 |
| 41_P | 93_V | 1.266 | 0.30 |
| 34_K | 48_V | 1.264 | 0.30 |
| 18_E | 61_Q | 1.262 | 0.30 |
| 49_Y | 54_L | 1.259 | 0.30 |
| 17_S | 127_E | 1.251 | 0.30 |
| 45_P | 71_E | 1.251 | 0.30 |
| 111_E | 116_R | 1.248 | 0.29 |
| 52_R | 56_E | 1.247 | 0.29 |
| 57_R | 60_E | 1.244 | 0.29 |
| 52_R | 64_R | 1.234 | 0.29 |
| 160_K | 164_S | 1.227 | 0.28 |
| 94_S | 97_Q | 1.223 | 0.28 |
| 17_S | 95_R | 1.221 | 0.28 |
| 39_E | 74_K | 1.217 | 0.28 |
| 27_R | 141_I | 1.214 | 0.27 |
| 83_D | 86_E | 1.202 | 0.27 |
| 29_Q | 45_P | 1.197 | 0.27 |
| 103_Q | 159_H | 1.177 | 0.25 |
| 25_R | 64_R | 1.176 | 0.25 |
| 111_E | 208_C | 1.167 | 0.25 |
| 55_Y | 58_L | 1.166 | 0.25 |
| 215_L | 223_D | 1.165 | 0.25 |
| 49_Y | 58_L | 1.164 | 0.25 |
| 18_E | 60_E | 1.156 | 0.24 |
| 242_S | 247_T | 1.145 | 0.24 |
| 18_E | 50_D | 1.144 | 0.24 |
| 41_P | 213_P | 1.144 | 0.24 |
| 21_L | 247_T | 1.136 | 0.23 |
| 35_V | 41_P | 1.135 | 0.23 |
| 152_L | 208_C | 1.128 | 0.23 |
| 17_S | 137_T | 1.127 | 0.23 |
| 100_I | 139_K | 1.115 | 0.22 |
| 60_E | 82_L | 1.114 | 0.22 |
| 97_Q | 206_A | 1.112 | 0.22 |
| 49_Y | 57_R | 1.109 | 0.22 |
| 35_V | 213_P | 1.104 | 0.22 |
| 52_R | 61_Q | 1.100 | 0.22 |
| 82_L | 101_E | 1.100 | 0.22 |
| 209_I | 229_D | 1.092 | 0.21 |
| 20_E | 83_D | 1.089 | 0.21 |
| 29_Q | 36_R | 1.086 | 0.21 |
| 43_E | 47_E | 1.084 | 0.21 |
| 46_E | 107_E | 1.083 | 0.21 |
| 223_D | 226_S | 1.083 | 0.21 |
| 243_S | 247_T | 1.083 | 0.21 |
| 53_S | 58_L | 1.082 | 0.21 |
| 160_K | 242_S | 1.082 | 0.21 |
| 64_R | 69_Y | 1.079 | 0.21 |
| 158_K | 162_S | 1.078 | 0.21 |
| 38_P | 51_P | 1.070 | 0.20 |
| 43_E | 148_S | 1.070 | 0.20 |
| 138_V | 209_I | 1.070 | 0.20 |
| 107_E | 114_E | 1.069 | 0.20 |
| 75_F | 94_S | 1.068 | 0.20 |
| 235_N | 239_K | 1.064 | 0.20 |
| 12_K | 133_E | 1.060 | 0.20 |
| 137_T | 152_L | 1.059 | 0.20 |
| 149_Q | 152_L | 1.052 | 0.19 |
| 161_S | 227_S | 1.050 | 0.19 |
| 52_R | 82_L | 1.044 | 0.19 |
| 25_R | 148_S | 1.039 | 0.19 |
| 80_R | 148_S | 1.037 | 0.19 |
| 132_V | 163_E | 1.037 | 0.19 |
| 71_E | 74_K | 1.035 | 0.19 |
| 210_G | 229_D | 1.035 | 0.19 |
| 200_I | 204_S | 1.034 | 0.19 |
| 209_I | 226_S | 1.032 | 0.19 |
| 61_Q | 111_E | 1.030 | 0.18 |
| 42_E | 91_D | 1.030 | 0.18 |
| 77_N | 81_G | 1.029 | 0.18 |
| 18_E | 47_E | 1.021 | 0.18 |
| 19_A | 59_Q | 1.019 | 0.18 |
| 76_K | 79_V | 1.019 | 0.18 |
| 59_Q | 122_V | 1.016 | 0.18 |
| 234_I | 242_S | 1.016 | 0.18 |
| 77_N | 83_D | 1.016 | 0.18 |
| 126_Q | 241_V | 1.011 | 0.18 |
| 55_Y | 227_S | 1.011 | 0.18 |
| 122_V | 128_N | 1.009 | 0.18 |
| 129_K | 224_S | 1.009 | 0.18 |
| 31_E | 213_P | 1.009 | 0.18 |
| 240_I | 243_S | 1.005 | 0.17 |
| 139_K | 230_S | 1.002 | 0.17 |
| 52_R | 157_V | 1.001 | 0.17 |
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 | |
| 2wujA | 2 | 0.1929 | 14 | 0.97 | Contact Map |
| 1qs0A | 1 | 0.2559 | 11.7 | 0.971 | Contact Map |
| 1umdA | 2 | 0.2638 | 6.1 | 0.974 | Contact Map |
| 1e52A | 2 | 0.2205 | 4.1 | 0.976 | Contact Map |
| 4uerb | 1 | 0.0276 | 3.7 | 0.977 | Contact Map |
| 2gp4A | 2 | 0.2559 | 3.4 | 0.977 | Contact Map |
| 2bfdA | 1 | 0.2992 | 3.4 | 0.977 | Contact Map |
| 1w85A | 4 | 0.2717 | 3.3 | 0.978 | Contact Map |
| 4noxA | 1 | 0.0354 | 3.1 | 0.978 | Contact Map |
| 4hfxA | 4 | 0.2598 | 3 | 0.978 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)