| av1_cp |
| ID: | 1513917391 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 256 (254) | ||
| Sequences: | 259 (72.7) | ||
| Seq/Len: | 1.020 | ||
| Nf(neff/√len): | 4.6 |
HHblits Results: (2016_02)
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: 1.020).
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 |
| 147_D | 154_E | 2.021 | 0.96 |
| 146_V | 154_E | 1.943 | 0.95 |
| 138_F | 180_R | 1.921 | 0.94 |
| 213_Q | 228_M | 1.803 | 0.91 |
| 153_G | 158_M | 1.767 | 0.90 |
| 207_N | 210_V | 1.721 | 0.89 |
| 185_T | 194_K | 1.597 | 0.83 |
| 147_D | 151_D | 1.496 | 0.77 |
| 151_D | 155_V | 1.486 | 0.76 |
| 6_A | 10_I | 1.451 | 0.74 |
| 181_K | 185_T | 1.416 | 0.71 |
| 138_F | 148_K | 1.410 | 0.71 |
| 232_A | 236_A | 1.409 | 0.71 |
| 1_M | 4_R | 1.406 | 0.70 |
| 8_I | 12_T | 1.403 | 0.70 |
| 83_I | 88_K | 1.383 | 0.69 |
| 180_R | 185_T | 1.375 | 0.68 |
| 78_E | 92_I | 1.369 | 0.68 |
| 29_S | 32_A | 1.365 | 0.67 |
| 5_A | 8_I | 1.362 | 0.67 |
| 48_P | 52_K | 1.360 | 0.67 |
| 27_Y | 30_R | 1.357 | 0.67 |
| 17_V | 36_V | 1.349 | 0.66 |
| 119_K | 132_T | 1.346 | 0.66 |
| 151_D | 154_E | 1.345 | 0.66 |
| 240_V | 243_T | 1.336 | 0.65 |
| 101_L | 172_H | 1.333 | 0.65 |
| 13_P | 18_R | 1.323 | 0.64 |
| 138_F | 159_F | 1.322 | 0.64 |
| 238_N | 241_Y | 1.320 | 0.63 |
| 52_K | 56_Y | 1.317 | 0.63 |
| 68_C | 75_Q | 1.309 | 0.62 |
| 18_R | 26_P | 1.304 | 0.62 |
| 247_R | 252_D | 1.290 | 0.61 |
| 13_P | 25_S | 1.288 | 0.61 |
| 18_R | 24_G | 1.275 | 0.59 |
| 247_R | 251_Y | 1.275 | 0.59 |
| 14_A | 30_R | 1.269 | 0.59 |
| 130_N | 133_N | 1.251 | 0.57 |
| 68_C | 71_P | 1.250 | 0.57 |
| 44_W | 47_R | 1.237 | 0.56 |
| 201_K | 208_Y | 1.230 | 0.55 |
| 249_Y | 253_S | 1.221 | 0.55 |
| 236_A | 242_A | 1.206 | 0.53 |
| 138_F | 172_H | 1.201 | 0.53 |
| 232_A | 237_S | 1.198 | 0.52 |
| 81_H | 90_M | 1.194 | 0.52 |
| 224_E | 227_L | 1.190 | 0.52 |
| 171_V | 228_M | 1.189 | 0.52 |
| 7_D | 11_S | 1.179 | 0.51 |
| 234_T | 242_A | 1.176 | 0.50 |
| 3_K | 11_S | 1.174 | 0.50 |
| 219_Y | 225_N | 1.173 | 0.50 |
| 71_P | 75_Q | 1.165 | 0.49 |
| 174_D | 177_Q | 1.160 | 0.49 |
| 36_V | 61_S | 1.160 | 0.49 |
| 243_T | 250_F | 1.157 | 0.49 |
| 2_S | 8_I | 1.150 | 0.48 |
| 232_A | 242_A | 1.150 | 0.48 |
| 171_V | 213_Q | 1.148 | 0.48 |
| 237_S | 240_V | 1.146 | 0.48 |
| 55_M | 58_M | 1.140 | 0.47 |
| 101_L | 180_R | 1.136 | 0.47 |
| 5_A | 10_I | 1.135 | 0.47 |
| 55_M | 101_L | 1.134 | 0.46 |
| 47_R | 52_K | 1.131 | 0.46 |
| 141_R | 144_R | 1.129 | 0.46 |
| 163_P | 166_A | 1.128 | 0.46 |
| 13_P | 26_P | 1.127 | 0.46 |
| 103_H | 107_K | 1.122 | 0.45 |
| 129_K | 190_Q | 1.117 | 0.45 |
| 243_T | 247_R | 1.117 | 0.45 |
| 18_R | 25_S | 1.111 | 0.44 |
| 154_E | 171_V | 1.108 | 0.44 |
| 120_I | 132_T | 1.108 | 0.44 |
| 232_A | 235_H | 1.107 | 0.44 |
| 187_T | 192_A | 1.107 | 0.44 |
| 46_N | 52_K | 1.102 | 0.43 |
| 4_R | 11_S | 1.099 | 0.43 |
| 46_N | 49_M | 1.097 | 0.43 |
| 1_M | 11_S | 1.094 | 0.43 |
| 102_T | 107_K | 1.094 | 0.43 |
| 15_S | 18_R | 1.090 | 0.42 |
| 80_R | 153_G | 1.087 | 0.42 |
| 14_A | 29_S | 1.084 | 0.42 |
| 187_T | 197_A | 1.084 | 0.42 |
| 247_R | 250_F | 1.083 | 0.42 |
| 27_Y | 55_M | 1.083 | 0.42 |
| 225_N | 240_V | 1.080 | 0.41 |
| 138_F | 203_V | 1.078 | 0.41 |
| 243_T | 252_D | 1.076 | 0.41 |
| 249_Y | 252_D | 1.076 | 0.41 |
| 5_A | 9_V | 1.074 | 0.41 |
| 2_S | 6_A | 1.071 | 0.41 |
| 79_S | 90_M | 1.070 | 0.41 |
| 128_T | 190_Q | 1.070 | 0.41 |
| 236_A | 240_V | 1.068 | 0.40 |
| 146_V | 171_V | 1.067 | 0.40 |
| 7_D | 10_I | 1.064 | 0.40 |
| 81_H | 191_Y | 1.064 | 0.40 |
| 234_T | 237_S | 1.063 | 0.40 |
| 150_Q | 179_L | 1.062 | 0.40 |
| 75_Q | 94_D | 1.061 | 0.40 |
| 116_V | 172_H | 1.061 | 0.40 |
| 48_P | 56_Y | 1.061 | 0.40 |
| 28_T | 45_T | 1.059 | 0.40 |
| 78_E | 82_D | 1.059 | 0.40 |
| 243_T | 249_Y | 1.059 | 0.40 |
| 25_S | 35_I | 1.058 | 0.39 |
| 17_V | 30_R | 1.056 | 0.39 |
| 10_I | 17_V | 1.052 | 0.39 |
| 147_D | 176_Y | 1.051 | 0.39 |
| 186_V | 195_E | 1.050 | 0.39 |
| 139_L | 153_G | 1.047 | 0.38 |
| 28_T | 42_Q | 1.046 | 0.38 |
| 187_T | 190_Q | 1.042 | 0.38 |
| 129_K | 192_A | 1.040 | 0.38 |
| 77_F | 92_I | 1.040 | 0.38 |
| 14_A | 32_A | 1.038 | 0.38 |
| 117_L | 153_G | 1.037 | 0.38 |
| 78_E | 181_K | 1.035 | 0.37 |
| 1_M | 6_A | 1.034 | 0.37 |
| 56_Y | 63_D | 1.034 | 0.37 |
| 232_A | 240_V | 1.032 | 0.37 |
| 240_V | 250_F | 1.029 | 0.37 |
| 7_D | 12_T | 1.028 | 0.37 |
| 16_K | 30_R | 1.026 | 0.37 |
| 13_P | 24_G | 1.025 | 0.37 |
| 16_K | 29_S | 1.024 | 0.36 |
| 79_S | 86_I | 1.024 | 0.36 |
| 237_S | 242_A | 1.022 | 0.36 |
| 225_N | 229_L | 1.016 | 0.36 |
| 174_D | 178_V | 1.011 | 0.35 |
| 177_Q | 194_K | 1.010 | 0.35 |
| 222_H | 228_M | 1.009 | 0.35 |
| 2_S | 5_A | 1.006 | 0.35 |
| 92_I | 114_V | 1.006 | 0.35 |
| 238_N | 243_T | 1.005 | 0.35 |
| 103_H | 108_G | 1.004 | 0.35 |
| 72_C | 75_Q | 1.002 | 0.35 |
| 111_V | 114_V | 1.001 | 0.35 |
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 | |
| 3zqxA | 1 | 0.1914 | 5.6 | 0.985 | Contact Map |
| 2knpA | 1 | 0.125 | 5.3 | 0.985 | Contact Map |
| 2b4wA | 1 | 0.1992 | 3.9 | 0.986 | Contact Map |
| 3zucA | 1 | 0.2031 | 3.7 | 0.987 | Contact Map |
| 2dw0A | 2 | 0.2148 | 3.6 | 0.987 | Contact Map |
| 3k7nA | 1 | 0.2266 | 3.3 | 0.987 | Contact Map |
| 3k7lA | 1 | 0.2461 | 3.2 | 0.987 | Contact Map |
| 1a9xA | 4 | 0.2344 | 2.9 | 0.987 | Contact Map |
| 2plxB | 1 | 0.1016 | 2.8 | 0.987 | Contact Map |
| 2ddiA | 1 | 0.1289 | 2.8 | 0.987 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)