| 3c7t_default |
| ID: | 1453987843 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 259 (255) | ||
| Sequences: | 531 (334.2) | ||
| Seq/Len: | 2.082 | ||
| Nf(neff/√len): | 20.9 |
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: 2.082).
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 |
| 89_R | 117_E | 2.448 | 1.00 |
| 10_G | 57_L | 2.387 | 1.00 |
| 157_E | 165_R | 2.169 | 1.00 |
| 169_A | 173_A | 2.076 | 0.99 |
| 84_A | 109_I | 2.065 | 0.99 |
| 85_S | 89_R | 1.988 | 0.99 |
| 188_G | 193_L | 1.959 | 0.99 |
| 82_V | 94_A | 1.910 | 0.99 |
| 11_E | 60_L | 1.851 | 0.98 |
| 117_E | 190_A | 1.841 | 0.98 |
| 9_H | 117_E | 1.827 | 0.98 |
| 117_E | 189_H | 1.826 | 0.98 |
| 89_R | 189_H | 1.816 | 0.98 |
| 197_V | 230_M | 1.631 | 0.95 |
| 169_A | 196_M | 1.615 | 0.95 |
| 15_L | 224_Y | 1.598 | 0.94 |
| 83_Y | 110_K | 1.528 | 0.93 |
| 117_E | 225_C | 1.495 | 0.91 |
| 65_A | 69_G | 1.494 | 0.91 |
| 247_N | 250_S | 1.419 | 0.88 |
| 110_K | 143_D | 1.404 | 0.88 |
| 12_R | 15_L | 1.401 | 0.88 |
| 83_Y | 235_W | 1.382 | 0.87 |
| 117_E | 230_M | 1.371 | 0.86 |
| 58_T | 126_G | 1.351 | 0.85 |
| 9_H | 64_Q | 1.341 | 0.84 |
| 56_P | 92_E | 1.338 | 0.84 |
| 245_S | 248_S | 1.332 | 0.84 |
| 82_V | 108_K | 1.327 | 0.83 |
| 242_C | 245_S | 1.324 | 0.83 |
| 250_S | 253_F | 1.324 | 0.83 |
| 10_G | 188_G | 1.320 | 0.83 |
| 85_S | 189_H | 1.312 | 0.82 |
| 131_T | 134_E | 1.310 | 0.82 |
| 248_S | 256_R | 1.308 | 0.82 |
| 12_R | 189_H | 1.301 | 0.82 |
| 215_I | 226_A | 1.299 | 0.82 |
| 61_G | 85_S | 1.288 | 0.81 |
| 66_Q | 99_D | 1.282 | 0.80 |
| 63_F | 67_L | 1.277 | 0.80 |
| 11_E | 20_W | 1.275 | 0.80 |
| 231_R | 237_V | 1.268 | 0.79 |
| 240_P | 255_W | 1.264 | 0.79 |
| 12_R | 190_A | 1.263 | 0.79 |
| 11_E | 88_L | 1.258 | 0.79 |
| 188_G | 226_A | 1.253 | 0.78 |
| 76_G | 80_K | 1.246 | 0.78 |
| 249_S | 252_R | 1.242 | 0.77 |
| 62_W | 96_G | 1.241 | 0.77 |
| 71_G | 227_L | 1.231 | 0.77 |
| 88_L | 92_E | 1.230 | 0.76 |
| 3_W | 229_A | 1.219 | 0.76 |
| 12_R | 224_Y | 1.211 | 0.75 |
| 89_R | 224_Y | 1.210 | 0.75 |
| 17_Y | 20_W | 1.209 | 0.75 |
| 115_L | 186_F | 1.202 | 0.74 |
| 129_F | 187_I | 1.199 | 0.74 |
| 24_C | 30_Y | 1.198 | 0.74 |
| 82_V | 96_G | 1.190 | 0.73 |
| 61_G | 64_Q | 1.189 | 0.73 |
| 250_S | 254_D | 1.186 | 0.73 |
| 243_P | 247_N | 1.183 | 0.72 |
| 6_A | 186_F | 1.181 | 0.72 |
| 69_G | 107_V | 1.180 | 0.72 |
| 44_R | 47_G | 1.179 | 0.72 |
| 12_R | 117_E | 1.178 | 0.72 |
| 9_H | 189_H | 1.178 | 0.72 |
| 251_G | 255_W | 1.164 | 0.71 |
| 32_R | 70_E | 1.161 | 0.70 |
| 225_C | 230_M | 1.153 | 0.70 |
| 65_A | 74_M | 1.150 | 0.69 |
| 8_R | 89_R | 1.148 | 0.69 |
| 80_K | 182_G | 1.146 | 0.69 |
| 250_S | 255_W | 1.139 | 0.68 |
| 249_S | 255_W | 1.139 | 0.68 |
| 129_F | 143_D | 1.139 | 0.68 |
| 142_V | 147_K | 1.134 | 0.68 |
| 44_R | 170_M | 1.134 | 0.68 |
| 248_S | 258_L | 1.132 | 0.68 |
| 6_A | 110_K | 1.131 | 0.68 |
| 93_T | 225_C | 1.126 | 0.67 |
| 7_L | 60_L | 1.122 | 0.67 |
| 142_V | 146_Y | 1.120 | 0.66 |
| 251_G | 257_I | 1.114 | 0.66 |
| 173_A | 198_G | 1.109 | 0.65 |
| 253_F | 256_R | 1.101 | 0.64 |
| 112_E | 115_L | 1.098 | 0.64 |
| 34_D | 38_P | 1.097 | 0.64 |
| 80_K | 84_A | 1.091 | 0.63 |
| 182_G | 226_A | 1.089 | 0.63 |
| 171_Q | 175_N | 1.087 | 0.63 |
| 10_G | 180_D | 1.082 | 0.62 |
| 87_A | 190_A | 1.080 | 0.62 |
| 69_G | 98_L | 1.080 | 0.62 |
| 3_W | 231_R | 1.078 | 0.62 |
| 92_E | 223_P | 1.077 | 0.62 |
| 230_M | 235_W | 1.077 | 0.62 |
| 4_V | 233_K | 1.071 | 0.61 |
| 248_S | 251_G | 1.070 | 0.61 |
| 157_E | 161_E | 1.070 | 0.61 |
| 15_L | 57_L | 1.069 | 0.61 |
| 241_P | 247_N | 1.065 | 0.61 |
| 18_G | 193_L | 1.064 | 0.61 |
| 251_G | 258_L | 1.063 | 0.60 |
| 113_P | 116_F | 1.059 | 0.60 |
| 252_R | 255_W | 1.056 | 0.60 |
| 17_Y | 90_C | 1.056 | 0.60 |
| 10_G | 19_P | 1.053 | 0.59 |
| 252_R | 257_I | 1.052 | 0.59 |
| 112_E | 157_E | 1.049 | 0.59 |
| 249_S | 254_D | 1.045 | 0.59 |
| 42_A | 246_I | 1.045 | 0.59 |
| 8_R | 12_R | 1.043 | 0.58 |
| 69_G | 73_R | 1.042 | 0.58 |
| 12_R | 89_R | 1.040 | 0.58 |
| 33_K | 37_L | 1.038 | 0.58 |
| 52_V | 161_E | 1.038 | 0.58 |
| 248_S | 252_R | 1.034 | 0.57 |
| 197_V | 201_H | 1.033 | 0.57 |
| 80_K | 108_K | 1.032 | 0.57 |
| 2_R | 235_W | 1.030 | 0.57 |
| 253_F | 258_L | 1.028 | 0.57 |
| 65_A | 96_G | 1.028 | 0.57 |
| 61_G | 89_R | 1.027 | 0.57 |
| 72_M | 166_G | 1.025 | 0.56 |
| 234_P | 238_V | 1.024 | 0.56 |
| 130_M | 190_A | 1.023 | 0.56 |
| 92_E | 187_I | 1.022 | 0.56 |
| 240_P | 250_S | 1.020 | 0.56 |
| 83_Y | 177_T | 1.020 | 0.56 |
| 6_A | 230_M | 1.018 | 0.56 |
| 254_D | 258_L | 1.015 | 0.55 |
| 11_E | 17_Y | 1.014 | 0.55 |
| 87_A | 232_G | 1.013 | 0.55 |
| 11_E | 173_A | 1.011 | 0.55 |
| 57_L | 231_R | 1.010 | 0.55 |
| 249_S | 257_I | 1.009 | 0.55 |
| 6_A | 193_L | 1.006 | 0.54 |
| 55_T | 224_Y | 1.005 | 0.54 |
| 18_G | 230_M | 1.004 | 0.54 |
| 240_P | 247_N | 1.004 | 0.54 |
| 195_Q | 221_K | 1.001 | 0.54 |
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 | |
| 3c7tA | 4 | 0.9884 | 100 | 0.326 | Contact Map |
| 3d4iA | 4 | 0.9846 | 100 | 0.333 | Contact Map |
| 3mbkA | 2 | 0.9807 | 100 | 0.344 | Contact Map |
| 2yn2A | 1 | 0.8764 | 100 | 0.517 | Contact Map |
| 2yn0A | 1 | 0.8764 | 100 | 0.522 | Contact Map |
| 4pzaA | 2 | 0.7722 | 100 | 0.539 | Contact Map |
| 3gp3A | 4 | 0.7761 | 100 | 0.542 | Contact Map |
| 1fztA | 1 | 0.7761 | 100 | 0.542 | Contact Map |
| 3kkkA | 4 | 0.7761 | 100 | 0.548 | Contact Map |
| 4eo9A | 1 | 0.8185 | 100 | 0.549 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)