| adk |
| ID: | 1494971990 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 217 (214) | ||
| Sequences: | 2816 (1578.9) | ||
| Seq/Len: | 13.159 | ||
| Nf(neff/√len): | 107.9 |
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: 13.159).
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 |
| 117_K | 176_M | 3.242 | 1.00 |
| 122_E | 140_V | 3.001 | 1.00 |
| 50_K | 54_D | 2.978 | 1.00 |
| 48_E | 51_S | 2.919 | 1.00 |
| 35_F | 64_T | 2.864 | 1.00 |
| 97_E | 189_K | 2.780 | 1.00 |
| 69_K | 102_E | 2.689 | 1.00 |
| 23_D | 209_K | 2.609 | 1.00 |
| 161_A | 164_N | 2.535 | 1.00 |
| 71_R | 76_D | 2.531 | 1.00 |
| 52_Y | 60_P | 2.515 | 1.00 |
| 128_R | 139_L | 2.436 | 1.00 |
| 65_I | 86_F | 2.434 | 1.00 |
| 199_Q | 207_D | 2.412 | 1.00 |
| 38_A | 70_E | 2.411 | 1.00 |
| 199_Q | 203_D | 2.339 | 1.00 |
| 113_I | 197_G | 2.265 | 1.00 |
| 37_A | 41_E | 2.229 | 1.00 |
| 173_E | 177_K | 2.214 | 1.00 |
| 131_S | 155_G | 2.213 | 1.00 |
| 126_G | 138_H | 2.194 | 1.00 |
| 131_S | 158_Y | 2.181 | 1.00 |
| 44_P | 48_E | 2.168 | 1.00 |
| 19_R | 205_Y | 2.136 | 1.00 |
| 114_E | 194_N | 2.124 | 1.00 |
| 130_C | 133_C | 2.031 | 1.00 |
| 112_N | 194_N | 2.000 | 1.00 |
| 187_S | 194_N | 1.959 | 1.00 |
| 42_E | 47_L | 1.879 | 1.00 |
| 65_I | 95_A | 1.822 | 1.00 |
| 75_D | 78_E | 1.788 | 1.00 |
| 44_P | 47_L | 1.783 | 1.00 |
| 97_E | 185_F | 1.761 | 1.00 |
| 170_K | 173_E | 1.703 | 1.00 |
| 48_E | 66_G | 1.684 | 1.00 |
| 39_M | 53_I | 1.677 | 1.00 |
| 24_Y | 209_K | 1.671 | 1.00 |
| 109_Y | 193_A | 1.652 | 1.00 |
| 165_E | 169_S | 1.649 | 1.00 |
| 150_C | 153_D | 1.646 | 1.00 |
| 149_I | 156_E | 1.643 | 1.00 |
| 146_T | 149_I | 1.612 | 1.00 |
| 132_V | 153_D | 1.602 | 1.00 |
| 124_L | 168_V | 1.597 | 1.00 |
| 38_A | 67_I | 1.588 | 1.00 |
| 60_P | 63_V | 1.487 | 1.00 |
| 130_C | 153_D | 1.472 | 1.00 |
| 130_C | 150_C | 1.458 | 1.00 |
| 203_D | 207_D | 1.455 | 1.00 |
| 174_V | 178_Q | 1.447 | 1.00 |
| 206_A | 210_D | 1.442 | 1.00 |
| 180_Q | 184_D | 1.421 | 1.00 |
| 193_A | 211_L | 1.401 | 0.99 |
| 131_S | 156_E | 1.399 | 0.99 |
| 8_L | 175_N | 1.394 | 0.99 |
| 19_R | 202_Q | 1.394 | 0.99 |
| 133_C | 153_D | 1.377 | 0.99 |
| 38_A | 43_T | 1.358 | 0.99 |
| 116_D | 198_Q | 1.354 | 0.99 |
| 133_C | 150_C | 1.350 | 0.99 |
| 135_T | 152_K | 1.346 | 0.99 |
| 63_V | 66_G | 1.338 | 0.99 |
| 51_S | 55_K | 1.330 | 0.99 |
| 6_M | 183_L | 1.312 | 0.99 |
| 11_A | 115_V | 1.307 | 0.99 |
| 23_D | 205_Y | 1.299 | 0.99 |
| 16_Q | 208_V | 1.291 | 0.99 |
| 119_V | 198_Q | 1.286 | 0.99 |
| 199_Q | 204_V | 1.281 | 0.99 |
| 125_T | 165_E | 1.280 | 0.99 |
| 91_A | 94_E | 1.270 | 0.99 |
| 126_G | 139_L | 1.264 | 0.99 |
| 184_D | 188_E | 1.255 | 0.99 |
| 115_V | 197_G | 1.244 | 0.98 |
| 121_M | 125_T | 1.223 | 0.98 |
| 117_K | 173_E | 1.199 | 0.98 |
| 2_N | 105_K | 1.193 | 0.98 |
| 119_V | 122_E | 1.174 | 0.98 |
| 121_M | 169_S | 1.174 | 0.98 |
| 164_N | 167_T | 1.174 | 0.98 |
| 117_K | 169_S | 1.162 | 0.97 |
| 6_M | 182_L | 1.159 | 0.97 |
| 138_H | 141_F | 1.156 | 0.97 |
| 98_E | 102_E | 1.146 | 0.97 |
| 25_G | 79_R | 1.142 | 0.97 |
| 145_K | 151_D | 1.135 | 0.97 |
| 4_V | 107_I | 1.135 | 0.97 |
| 205_Y | 209_K | 1.115 | 0.96 |
| 24_Y | 213_G | 1.113 | 0.96 |
| 48_E | 62_E | 1.111 | 0.96 |
| 200_D | 203_D | 1.091 | 0.96 |
| 196_N | 199_Q | 1.077 | 0.95 |
| 5_L | 82_L | 1.074 | 0.95 |
| 71_R | 74_K | 1.070 | 0.95 |
| 111_I | 208_V | 1.062 | 0.95 |
| 182_L | 192_L | 1.059 | 0.95 |
| 112_N | 183_L | 1.054 | 0.95 |
| 185_F | 189_K | 1.049 | 0.94 |
| 184_D | 187_S | 1.043 | 0.94 |
| 18_E | 22_E | 1.036 | 0.94 |
| 69_K | 73_G | 1.035 | 0.94 |
| 21_V | 28_H | 1.034 | 0.94 |
| 94_E | 98_E | 1.030 | 0.94 |
| 135_T | 153_D | 1.020 | 0.93 |
| 35_F | 39_M | 1.016 | 0.93 |
| 144_P | 151_D | 1.014 | 0.93 |
| 129_I | 136_T | 1.013 | 0.93 |
| 34_M | 38_A | 1.011 | 0.93 |
| 203_D | 206_A | 1.009 | 0.93 |
| 176_M | 180_Q | 1.002 | 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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 4qbgB | 1 | 1 | 100 | 0.334 | Contact Map |
| 3be4A | 1 | 0.9677 | 100 | 0.371 | Contact Map |
| 3tlxA | 4 | 0.9862 | 100 | 0.373 | Contact Map |
| 4jzkA | 2 | 0.9631 | 100 | 0.373 | Contact Map |
| 3gmtA | 2 | 0.8894 | 100 | 0.375 | Contact Map |
| 2xb4A | 1 | 0.977 | 100 | 0.378 | Contact Map |
| 4pzlA | 4 | 0.9724 | 100 | 0.379 | Contact Map |
| 1ak2A | 1 | 1 | 100 | 0.381 | Contact Map |
| 1akyA | 1 | 0.9908 | 100 | 0.391 | Contact Map |
| 4nu0A | 2 | 0.9724 | 100 | 0.408 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)