| T0831d1 -force run |
| ID: | 1404710370 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 264 (262) | ||
| Sequences: | 130 (107.6) | ||
| Seq/Len: | 0.496 | ||
| Nf(neff/√len): | 6.6 |
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: 0.496).
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 |
| 22_R | 30_G | 2.175 | 0.91 |
| 49_R | 68_Q | 1.905 | 0.82 |
| 233_R | 239_L | 1.896 | 0.81 |
| 52_L | 77_M | 1.882 | 0.80 |
| 233_R | 244_F | 1.859 | 0.79 |
| 22_R | 65_D | 1.793 | 0.76 |
| 21_H | 70_L | 1.725 | 0.72 |
| 1_T | 184_F | 1.688 | 0.69 |
| 22_R | 71_H | 1.687 | 0.69 |
| 69_R | 100_A | 1.684 | 0.69 |
| 29_N | 32_A | 1.614 | 0.64 |
| 70_L | 103_L | 1.586 | 0.62 |
| 48_Y | 71_H | 1.553 | 0.60 |
| 22_R | 48_Y | 1.521 | 0.58 |
| 6_L | 190_L | 1.492 | 0.55 |
| 48_Y | 68_Q | 1.475 | 0.54 |
| 227_A | 234_P | 1.461 | 0.53 |
| 71_H | 107_Y | 1.444 | 0.52 |
| 206_K | 225_E | 1.434 | 0.51 |
| 187_C | 194_L | 1.409 | 0.49 |
| 22_R | 33_G | 1.406 | 0.49 |
| 20_A | 198_M | 1.388 | 0.47 |
| 48_Y | 65_D | 1.387 | 0.47 |
| 21_H | 234_P | 1.386 | 0.47 |
| 22_R | 37_I | 1.379 | 0.47 |
| 224_I | 227_A | 1.368 | 0.46 |
| 22_R | 67_L | 1.351 | 0.45 |
| 18_E | 63_K | 1.350 | 0.45 |
| 21_H | 186_D | 1.349 | 0.44 |
| 56_E | 123_Y | 1.343 | 0.44 |
| 104_R | 197_Q | 1.322 | 0.42 |
| 13_C | 233_R | 1.314 | 0.42 |
| 18_E | 33_G | 1.304 | 0.41 |
| 48_Y | 201_L | 1.299 | 0.41 |
| 49_R | 93_D | 1.295 | 0.40 |
| 93_D | 96_L | 1.294 | 0.40 |
| 5_L | 26_C | 1.292 | 0.40 |
| 29_N | 71_H | 1.289 | 0.40 |
| 234_P | 239_L | 1.282 | 0.39 |
| 228_T | 233_R | 1.280 | 0.39 |
| 12_K | 18_E | 1.277 | 0.39 |
| 5_L | 232_L | 1.276 | 0.39 |
| 51_V | 72_A | 1.275 | 0.39 |
| 5_L | 231_H | 1.275 | 0.39 |
| 192_F | 208_V | 1.271 | 0.39 |
| 21_H | 58_H | 1.253 | 0.37 |
| 80_L | 143_W | 1.242 | 0.37 |
| 21_H | 244_F | 1.240 | 0.36 |
| 231_H | 244_F | 1.236 | 0.36 |
| 52_L | 159_L | 1.224 | 0.35 |
| 18_E | 30_G | 1.218 | 0.35 |
| 26_C | 30_G | 1.211 | 0.34 |
| 32_A | 107_Y | 1.211 | 0.34 |
| 56_E | 181_S | 1.209 | 0.34 |
| 33_G | 48_Y | 1.203 | 0.34 |
| 33_G | 71_H | 1.200 | 0.34 |
| 51_V | 215_L | 1.198 | 0.33 |
| 227_A | 232_L | 1.198 | 0.33 |
| 29_N | 48_Y | 1.197 | 0.33 |
| 49_R | 90_T | 1.194 | 0.33 |
| 18_E | 22_R | 1.192 | 0.33 |
| 3_E | 162_R | 1.190 | 0.33 |
| 227_A | 231_H | 1.190 | 0.33 |
| 227_A | 255_E | 1.189 | 0.33 |
| 68_Q | 71_H | 1.185 | 0.33 |
| 1_T | 38_K | 1.185 | 0.33 |
| 97_E | 167_I | 1.167 | 0.31 |
| 21_H | 233_R | 1.166 | 0.31 |
| 143_W | 239_L | 1.165 | 0.31 |
| 24_L | 27_A | 1.165 | 0.31 |
| 37_I | 71_H | 1.165 | 0.31 |
| 231_H | 240_N | 1.163 | 0.31 |
| 184_F | 190_L | 1.161 | 0.31 |
| 150_A | 253_E | 1.151 | 0.30 |
| 229_V | 244_F | 1.148 | 0.30 |
| 70_L | 216_E | 1.145 | 0.30 |
| 6_L | 30_G | 1.145 | 0.30 |
| 30_G | 208_V | 1.145 | 0.30 |
| 21_H | 68_Q | 1.138 | 0.29 |
| 14_G | 18_E | 1.135 | 0.29 |
| 25_V | 79_L | 1.135 | 0.29 |
| 237_L | 253_E | 1.135 | 0.29 |
| 28_L | 35_H | 1.133 | 0.29 |
| 119_Q | 223_V | 1.129 | 0.29 |
| 91_L | 123_Y | 1.125 | 0.29 |
| 204_C | 210_E | 1.125 | 0.29 |
| 13_C | 244_F | 1.120 | 0.28 |
| 248_D | 261_N | 1.118 | 0.28 |
| 50_E | 233_R | 1.112 | 0.28 |
| 10_Q | 39_G | 1.105 | 0.27 |
| 6_L | 19_E | 1.103 | 0.27 |
| 82_A | 215_L | 1.103 | 0.27 |
| 165_N | 258_L | 1.096 | 0.27 |
| 90_T | 93_D | 1.095 | 0.27 |
| 1_T | 36_I | 1.093 | 0.27 |
| 9_L | 16_E | 1.089 | 0.26 |
| 52_L | 131_E | 1.086 | 0.26 |
| 30_G | 71_H | 1.084 | 0.26 |
| 187_C | 220_S | 1.082 | 0.26 |
| 255_E | 259_F | 1.079 | 0.26 |
| 165_N | 202_N | 1.075 | 0.26 |
| 27_A | 103_L | 1.072 | 0.25 |
| 104_R | 118_A | 1.064 | 0.25 |
| 185_R | 249_E | 1.063 | 0.25 |
| 21_H | 205_Q | 1.062 | 0.25 |
| 48_Y | 107_Y | 1.062 | 0.25 |
| 50_E | 196_T | 1.060 | 0.25 |
| 4_E | 250_L | 1.059 | 0.25 |
| 58_H | 233_R | 1.059 | 0.25 |
| 29_N | 75_N | 1.058 | 0.25 |
| 122_L | 233_R | 1.053 | 0.24 |
| 5_L | 35_H | 1.053 | 0.24 |
| 32_A | 71_H | 1.053 | 0.24 |
| 100_A | 111_C | 1.051 | 0.24 |
| 251_F | 257_K | 1.051 | 0.24 |
| 18_E | 96_L | 1.049 | 0.24 |
| 9_L | 71_H | 1.047 | 0.24 |
| 232_L | 255_E | 1.041 | 0.24 |
| 231_H | 234_P | 1.038 | 0.24 |
| 74_H | 259_F | 1.037 | 0.23 |
| 69_R | 125_V | 1.034 | 0.23 |
| 6_L | 233_R | 1.033 | 0.23 |
| 34_I | 58_H | 1.028 | 0.23 |
| 118_A | 223_V | 1.027 | 0.23 |
| 62_L | 212_V | 1.026 | 0.23 |
| 223_V | 229_V | 1.025 | 0.23 |
| 162_R | 252_T | 1.018 | 0.22 |
| 1_T | 188_R | 1.015 | 0.22 |
| 229_V | 233_R | 1.015 | 0.22 |
| 118_A | 128_T | 1.014 | 0.22 |
| 240_N | 244_F | 1.013 | 0.22 |
| 158_E | 166_E | 1.012 | 0.22 |
| 29_N | 65_D | 1.011 | 0.22 |
| 49_R | 92_R | 1.009 | 0.22 |
| 10_Q | 194_L | 1.008 | 0.22 |
| 196_T | 210_E | 1.008 | 0.22 |
| 205_Q | 233_R | 1.005 | 0.22 |
| 6_L | 257_K | 1.001 | 0.22 |
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 | |
| 3qwwA | 1 | 0.4432 | 97.6 | 0.881 | Contact Map |
| 3qwpA | 1 | 0.4697 | 97.5 | 0.883 | Contact Map |
| 3n71A | 1 | 0.5379 | 96.9 | 0.894 | Contact Map |
| 3nf1A | 1 | 0.3598 | 95.4 | 0.907 | Contact Map |
| 3ro3A | 1 | 0.6023 | 94 | 0.914 | Contact Map |
| 4jhrA | 2 | 0.7083 | 93.8 | 0.915 | Contact Map |
| 3u3wA | 2 | 0.5644 | 92.9 | 0.918 | Contact Map |
| 2c2lA | 4 | 0.8409 | 92.4 | 0.919 | Contact Map |
| 3ro2A | 1 | 0.6591 | 92.1 | 0.92 | Contact Map |
| 1ihgA | 1 | 0.6061 | 90 | 0.924 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)