| seta -force run |
| ID: | 1504609794 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 283 (264) | ||
| Sequences: | 183 (150.8) | ||
| Seq/Len: | 0.693 | ||
| Nf(neff/√len): | 9.3 |
Jackhmmer Results: (2016_04)
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: 0.693).
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 |
| 108_L | 154_I | 2.852 | 0.99 |
| 16_H | 47_W | 2.809 | 0.99 |
| 115_Y | 119_D | 1.920 | 0.89 |
| 46_I | 153_I | 1.808 | 0.85 |
| 103_L | 107_I | 1.685 | 0.79 |
| 25_P | 28_N | 1.670 | 0.78 |
| 267_R | 270_I | 1.647 | 0.76 |
| 85_I | 88_E | 1.634 | 0.75 |
| 21_G | 35_W | 1.629 | 0.75 |
| 104_R | 206_P | 1.547 | 0.70 |
| 99_V | 200_T | 1.545 | 0.70 |
| 14_K | 43_E | 1.513 | 0.67 |
| 16_H | 115_Y | 1.509 | 0.67 |
| 50_K | 130_I | 1.481 | 0.65 |
| 12_D | 112_G | 1.450 | 0.62 |
| 119_D | 205_G | 1.446 | 0.62 |
| 268_P | 271_E | 1.444 | 0.62 |
| 31_V | 35_W | 1.442 | 0.62 |
| 107_I | 162_I | 1.442 | 0.62 |
| 104_R | 115_Y | 1.424 | 0.60 |
| 18_I | 115_Y | 1.421 | 0.60 |
| 110_A | 159_G | 1.417 | 0.60 |
| 234_D | 237_Y | 1.415 | 0.60 |
| 17_F | 49_D | 1.401 | 0.58 |
| 63_L | 67_S | 1.379 | 0.57 |
| 86_R | 89_L | 1.362 | 0.55 |
| 163_I | 167_A | 1.339 | 0.53 |
| 49_D | 151_N | 1.323 | 0.52 |
| 115_Y | 206_P | 1.312 | 0.51 |
| 31_V | 121_L | 1.308 | 0.51 |
| 12_D | 158_K | 1.308 | 0.51 |
| 250_Y | 253_Q | 1.308 | 0.51 |
| 72_V | 210_F | 1.307 | 0.51 |
| 149_L | 152_D | 1.305 | 0.50 |
| 130_I | 252_P | 1.303 | 0.50 |
| 49_D | 122_C | 1.299 | 0.50 |
| 46_I | 53_A | 1.283 | 0.49 |
| 19_W | 35_W | 1.281 | 0.48 |
| 101_D | 119_D | 1.280 | 0.48 |
| 85_I | 89_L | 1.279 | 0.48 |
| 155_L | 209_L | 1.276 | 0.48 |
| 250_Y | 254_N | 1.258 | 0.46 |
| 176_A | 179_S | 1.237 | 0.45 |
| 62_I | 72_V | 1.235 | 0.45 |
| 11_I | 155_L | 1.231 | 0.44 |
| 104_R | 205_G | 1.219 | 0.43 |
| 32_V | 36_A | 1.217 | 0.43 |
| 109_A | 164_Q | 1.215 | 0.43 |
| 47_W | 260_S | 1.214 | 0.43 |
| 45_I | 158_K | 1.214 | 0.43 |
| 124_A | 206_P | 1.210 | 0.42 |
| 75_I | 120_I | 1.206 | 0.42 |
| 101_D | 206_P | 1.198 | 0.42 |
| 21_G | 97_G | 1.197 | 0.41 |
| 61_F | 90_D | 1.196 | 0.41 |
| 234_D | 238_L | 1.194 | 0.41 |
| 267_R | 271_E | 1.192 | 0.41 |
| 17_F | 21_G | 1.185 | 0.40 |
| 125_P | 177_R | 1.180 | 0.40 |
| 20_V | 167_A | 1.177 | 0.40 |
| 48_V | 52_I | 1.173 | 0.39 |
| 60_L | 87_H | 1.172 | 0.39 |
| 57_E | 61_F | 1.172 | 0.39 |
| 157_S | 220_N | 1.171 | 0.39 |
| 57_E | 249_F | 1.161 | 0.39 |
| 19_W | 111_E | 1.160 | 0.38 |
| 65_M | 69_G | 1.157 | 0.38 |
| 245_E | 248_Y | 1.156 | 0.38 |
| 66_K | 70_I | 1.154 | 0.38 |
| 18_I | 103_L | 1.146 | 0.37 |
| 60_L | 72_V | 1.143 | 0.37 |
| 97_G | 260_S | 1.134 | 0.36 |
| 66_K | 73_K | 1.132 | 0.36 |
| 240_D | 246_P | 1.129 | 0.36 |
| 186_Y | 190_K | 1.125 | 0.36 |
| 108_L | 127_P | 1.124 | 0.36 |
| 39_N | 101_D | 1.117 | 0.35 |
| 35_W | 49_D | 1.113 | 0.35 |
| 151_N | 205_G | 1.110 | 0.35 |
| 42_Y | 101_D | 1.110 | 0.35 |
| 239_I | 244_K | 1.110 | 0.35 |
| 238_L | 242_S | 1.108 | 0.34 |
| 47_W | 98_M | 1.105 | 0.34 |
| 236_R | 260_S | 1.098 | 0.34 |
| 61_F | 65_M | 1.098 | 0.34 |
| 42_Y | 45_I | 1.097 | 0.34 |
| 46_I | 107_I | 1.094 | 0.33 |
| 48_V | 200_T | 1.093 | 0.33 |
| 134_F | 137_L | 1.093 | 0.33 |
| 13_K | 42_Y | 1.091 | 0.33 |
| 238_L | 241_G | 1.089 | 0.33 |
| 32_V | 195_E | 1.089 | 0.33 |
| 138_L | 207_G | 1.083 | 0.33 |
| 16_H | 21_G | 1.081 | 0.32 |
| 119_D | 206_P | 1.077 | 0.32 |
| 26_Q | 258_D | 1.077 | 0.32 |
| 65_M | 78_E | 1.074 | 0.32 |
| 184_H | 187_A | 1.070 | 0.32 |
| 49_D | 205_G | 1.069 | 0.31 |
| 18_I | 107_I | 1.067 | 0.31 |
| 47_W | 261_W | 1.063 | 0.31 |
| 127_P | 154_I | 1.062 | 0.31 |
| 266_K | 269_G | 1.060 | 0.31 |
| 27_K | 31_V | 1.060 | 0.31 |
| 34_E | 94_P | 1.059 | 0.31 |
| 119_D | 268_P | 1.057 | 0.31 |
| 146_N | 158_K | 1.051 | 0.30 |
| 40_P | 249_F | 1.051 | 0.30 |
| 234_D | 241_G | 1.045 | 0.30 |
| 61_F | 71_T | 1.044 | 0.30 |
| 95_N | 99_V | 1.044 | 0.30 |
| 179_S | 182_F | 1.039 | 0.29 |
| 255_N | 258_D | 1.036 | 0.29 |
| 55_A | 103_L | 1.035 | 0.29 |
| 12_D | 156_C | 1.032 | 0.29 |
| 205_G | 269_G | 1.031 | 0.29 |
| 114_I | 194_G | 1.027 | 0.29 |
| 244_K | 247_D | 1.027 | 0.29 |
| 164_Q | 168_D | 1.025 | 0.28 |
| 235_Q | 242_S | 1.018 | 0.28 |
| 47_W | 115_Y | 1.018 | 0.28 |
| 215_K | 238_L | 1.017 | 0.28 |
| 184_H | 190_K | 1.017 | 0.28 |
| 105_L | 168_D | 1.014 | 0.28 |
| 135_G | 139_S | 1.012 | 0.28 |
| 159_G | 212_Q | 1.011 | 0.27 |
| 63_L | 80_V | 1.009 | 0.27 |
| 127_P | 192_T | 1.008 | 0.27 |
| 72_V | 216_M | 1.006 | 0.27 |
| 64_D | 68_K | 1.005 | 0.27 |
| 76_N | 79_G | 1.005 | 0.27 |
| 104_R | 112_G | 1.003 | 0.27 |
| 47_W | 200_T | 1.003 | 0.27 |
| 24_M | 32_V | 1.001 | 0.27 |
| 249_F | 266_K | 1.001 | 0.27 |
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 | |
| 4dmvA | 1 | 0.9576 | 100 | 0.441 | Contact Map |
| 2bvlA | 1 | 0.9576 | 100 | 0.462 | Contact Map |
| 2vk9A | 1 | 0.9435 | 100 | 0.478 | Contact Map |
| 4mixA | 2 | 0.7845 | 100 | 0.514 | Contact Map |
| 3jszA | 1 | 0.9258 | 98.2 | 0.871 | Contact Map |
| 3tztA | 2 | 0.7703 | 74.8 | 0.941 | Contact Map |
| 1ll2A | 1 | 0.8057 | 62.7 | 0.946 | Contact Map |
| 4uegA | 2 | 0.7951 | 46.1 | 0.951 | Contact Map |
| 1g9rA | 1 | 0.8269 | 43.3 | 0.952 | Contact Map |
| 3u2uA | 2 | 0.8375 | 41.9 | 0.952 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)