| gremlindata enrich iter1 |
| ID: | 1412139915 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 310 (291) | ||
| Sequences: | 22672 (10303.2) | ||
| Seq/Len: | 77.911 | ||
| Nf(neff/√len): | 604.0 |
HHblits Results: (2013_03)
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: 77.911).
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 |
| 46_T | 82_A | 4.914 | 1.00 |
| 73_S | 156_W | 3.867 | 1.00 |
| 203_L | 207_R | 2.919 | 1.00 |
| 103_V | 107_I | 2.728 | 1.00 |
| 125_A | 155_V | 2.718 | 1.00 |
| 73_S | 122_H | 2.663 | 1.00 |
| 98_W | 101_G | 2.428 | 1.00 |
| 146_K | 150_C | 2.380 | 1.00 |
| 131_Y | 136_Q | 2.331 | 1.00 |
| 57_V | 72_V | 2.286 | 1.00 |
| 102_K | 106_G | 2.251 | 1.00 |
| 63_L | 68_N | 2.233 | 1.00 |
| 125_A | 151_I | 2.224 | 1.00 |
| 164_S | 168_L | 2.194 | 1.00 |
| 33_A | 37_A | 2.121 | 1.00 |
| 207_R | 210_Q | 2.103 | 1.00 |
| 114_L | 160_A | 2.047 | 1.00 |
| 54_V | 72_V | 1.977 | 1.00 |
| 110_A | 114_L | 1.953 | 1.00 |
| 283_N | 287_Y | 1.878 | 1.00 |
| 106_G | 171_D | 1.871 | 1.00 |
| 242_V | 286_I | 1.871 | 1.00 |
| 74_L | 78_D | 1.862 | 1.00 |
| 247_W | 276_G | 1.842 | 1.00 |
| 105_C | 177_C | 1.817 | 1.00 |
| 88_F | 92_N | 1.787 | 1.00 |
| 131_Y | 135_T | 1.777 | 1.00 |
| 60_S | 297_A | 1.746 | 1.00 |
| 235_V | 290_F | 1.725 | 1.00 |
| 69_L | 152_I | 1.725 | 1.00 |
| 151_I | 155_V | 1.721 | 1.00 |
| 122_H | 152_I | 1.715 | 1.00 |
| 205_Y | 208_I | 1.694 | 1.00 |
| 149_K | 153_V | 1.674 | 1.00 |
| 252_F | 256_L | 1.672 | 1.00 |
| 260_C | 263_Y | 1.671 | 1.00 |
| 129_D | 143_R | 1.657 | 1.00 |
| 65_A | 68_N | 1.648 | 1.00 |
| 150_C | 154_I | 1.646 | 1.00 |
| 206_I | 210_Q | 1.623 | 1.00 |
| 80_L | 115_F | 1.622 | 1.00 |
| 46_T | 281_S | 1.616 | 1.00 |
| 118_S | 159_S | 1.607 | 1.00 |
| 129_D | 133_S | 1.598 | 1.00 |
| 72_V | 76_T | 1.586 | 1.00 |
| 51_I | 79_I | 1.584 | 1.00 |
| 144_T | 147_R | 1.577 | 1.00 |
| 200_I | 204_V | 1.571 | 1.00 |
| 77_A | 118_S | 1.540 | 1.00 |
| 51_I | 55_I | 1.538 | 1.00 |
| 47_V | 82_A | 1.497 | 1.00 |
| 58_L | 72_V | 1.496 | 1.00 |
| 43_I | 83_T | 1.488 | 1.00 |
| 110_A | 167_L | 1.472 | 1.00 |
| 77_A | 119_S | 1.469 | 1.00 |
| 76_T | 80_L | 1.454 | 1.00 |
| 101_G | 104_W | 1.440 | 1.00 |
| 131_Y | 207_R | 1.423 | 1.00 |
| 132_W | 142_K | 1.419 | 1.00 |
| 73_S | 152_I | 1.404 | 0.99 |
| 237_A | 241_G | 1.386 | 0.99 |
| 202_I | 206_I | 1.380 | 0.99 |
| 297_A | 300_K | 1.369 | 0.99 |
| 52_L | 56_A | 1.353 | 0.99 |
| 53_V | 288_T | 1.351 | 0.99 |
| 47_V | 79_I | 1.340 | 0.99 |
| 120_I | 197_P | 1.294 | 0.99 |
| 120_I | 124_C | 1.292 | 0.99 |
| 278_C | 282_L | 1.284 | 0.99 |
| 166_P | 169_S | 1.271 | 0.99 |
| 53_V | 57_V | 1.257 | 0.99 |
| 49_G | 75_A | 1.252 | 0.99 |
| 84_L | 87_P | 1.246 | 0.98 |
| 86_M | 89_S | 1.234 | 0.98 |
| 201_M | 205_Y | 1.234 | 0.98 |
| 117_T | 193_S | 1.226 | 0.98 |
| 248_F | 252_F | 1.223 | 0.98 |
| 110_A | 160_A | 1.219 | 0.98 |
| 57_V | 64_K | 1.212 | 0.98 |
| 119_S | 246_C | 1.212 | 0.98 |
| 201_M | 240_M | 1.208 | 0.98 |
| 207_R | 211_V | 1.208 | 0.98 |
| 87_P | 90_L | 1.205 | 0.98 |
| 82_A | 86_M | 1.205 | 0.98 |
| 190_S | 195_F | 1.189 | 0.98 |
| 123_L | 201_M | 1.184 | 0.98 |
| 19_A | 180_N | 1.169 | 0.97 |
| 70_F | 148_V | 1.168 | 0.97 |
| 34_S | 38_L | 1.165 | 0.97 |
| 184_W | 188_S | 1.164 | 0.97 |
| 107_I | 111_L | 1.161 | 0.97 |
| 215_R | 219_I | 1.159 | 0.97 |
| 133_S | 138_V | 1.157 | 0.97 |
| 57_V | 63_L | 1.156 | 0.97 |
| 150_C | 153_V | 1.152 | 0.97 |
| 133_S | 137_A | 1.146 | 0.97 |
| 232_F | 235_V | 1.139 | 0.97 |
| 198_C | 244_V | 1.136 | 0.97 |
| 153_V | 157_L | 1.128 | 0.97 |
| 121_V | 158_I | 1.121 | 0.97 |
| 193_S | 197_P | 1.116 | 0.96 |
| 113_V | 163_S | 1.113 | 0.96 |
| 229_E | 233_T | 1.112 | 0.96 |
| 53_V | 283_N | 1.110 | 0.96 |
| 103_V | 106_G | 1.100 | 0.96 |
| 121_V | 193_S | 1.098 | 0.96 |
| 34_S | 37_A | 1.096 | 0.96 |
| 124_C | 200_I | 1.094 | 0.96 |
| 209_Y | 213_K | 1.091 | 0.96 |
| 49_G | 281_S | 1.091 | 0.96 |
| 186_I | 189_S | 1.090 | 0.96 |
| 126_I | 236_L | 1.090 | 0.96 |
| 238_V | 286_I | 1.088 | 0.96 |
| 21_W | 24_D | 1.087 | 0.96 |
| 286_I | 290_F | 1.086 | 0.96 |
| 244_V | 248_F | 1.084 | 0.96 |
| 120_I | 243_F | 1.080 | 0.95 |
| 75_A | 78_D | 1.078 | 0.95 |
| 69_L | 149_K | 1.072 | 0.95 |
| 246_C | 249_P | 1.071 | 0.95 |
| 84_L | 88_F | 1.070 | 0.95 |
| 85_V | 89_S | 1.061 | 0.95 |
| 256_L | 268_T | 1.058 | 0.95 |
| 134_V | 138_V | 1.053 | 0.95 |
| 121_V | 155_V | 1.053 | 0.95 |
| 188_S | 192_A | 1.053 | 0.95 |
| 60_S | 63_L | 1.051 | 0.94 |
| 44_L | 48_V | 1.046 | 0.94 |
| 242_V | 282_L | 1.045 | 0.94 |
| 190_S | 255_S | 1.035 | 0.94 |
| 89_S | 93_E | 1.034 | 0.94 |
| 194_F | 251_F | 1.030 | 0.94 |
| 88_F | 104_W | 1.026 | 0.94 |
| 283_N | 291_N | 1.018 | 0.93 |
| 69_L | 73_S | 1.016 | 0.93 |
| 27_Y | 31_A | 1.011 | 0.93 |
| 17_L | 180_N | 1.010 | 0.93 |
| 85_V | 112_D | 1.004 | 0.93 |
| 86_M | 277_Y | 1.001 | 0.92 |
| 55_I | 59_T | 1.001 | 0.92 |
| 131_Y | 203_L | 1.001 | 0.92 |
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 | |
| 4iarA | 1 | 0.9 | 100 | 0.152 | Contact Map |
| 1u19A | 2 | 1 | 100 | 0.16 | Contact Map |
| 2r4rA | 1 | 0.6742 | 100 | 0.174 | Contact Map |
| 4buoA | 2 | 0.929 | 100 | 0.192 | Contact Map |
| 3uonA | 1 | 0.8871 | 100 | 0.192 | Contact Map |
| 2rh1A | 1 | 0.8903 | 100 | 0.193 | Contact Map |
| 4grvA | 1 | 0.8903 | 100 | 0.194 | Contact Map |
| 4phuA | 1 | 0.8226 | 100 | 0.196 | Contact Map |
| 4pxzA | 1 | 0.8613 | 100 | 0.197 | Contact Map |
| 4bvnA | 1 | 0.8742 | 100 | 0.197 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)