| CobBSIRT2 |
| ID: | 1506350732 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 279 (242) | ||
| Sequences: | 4410 (2807.3) | ||
| Seq/Len: | 18.223 | ||
| Nf(neff/√len): | 180.5 |
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: 18.223).
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 |
| 54_E | 259_S | 3.256 | 1.00 |
| 55_S | 107_N | 3.178 | 1.00 |
| 136_E | 145_H | 2.702 | 1.00 |
| 125_L | 203_A | 2.695 | 1.00 |
| 152_K | 186_H | 2.535 | 1.00 |
| 115_K | 118_D | 2.473 | 1.00 |
| 213_I | 258_A | 2.434 | 1.00 |
| 155_C | 158_S | 2.431 | 1.00 |
| 108_A | 263_P | 2.372 | 1.00 |
| 256_G | 261_V | 2.270 | 1.00 |
| 71_R | 74_D | 2.269 | 1.00 |
| 257_P | 260_Q | 2.252 | 1.00 |
| 155_C | 177_C | 2.251 | 1.00 |
| 51_I | 109_A | 2.243 | 1.00 |
| 114_A | 118_D | 2.176 | 1.00 |
| 174_C | 177_C | 2.126 | 1.00 |
| 113_L | 126_L | 2.119 | 1.00 |
| 109_A | 262_V | 2.105 | 1.00 |
| 112_A | 266_V | 2.093 | 1.00 |
| 42_R | 206_M | 2.062 | 1.00 |
| 161_V | 186_H | 2.056 | 1.00 |
| 256_G | 260_Q | 2.035 | 1.00 |
| 220_Y | 224_G | 2.031 | 1.00 |
| 45_V | 113_L | 2.028 | 1.00 |
| 115_K | 119_A | 1.983 | 1.00 |
| 241_L | 257_P | 1.935 | 1.00 |
| 117_Q | 142_N | 1.904 | 1.00 |
| 162_L | 183_L | 1.832 | 1.00 |
| 45_V | 211_I | 1.809 | 1.00 |
| 54_E | 257_P | 1.802 | 1.00 |
| 112_A | 263_P | 1.800 | 1.00 |
| 77_T | 80_G | 1.742 | 1.00 |
| 149_E | 152_K | 1.740 | 1.00 |
| 105_Q | 137_R | 1.704 | 1.00 |
| 59_T | 62_A | 1.679 | 1.00 |
| 230_K | 251_A | 1.677 | 1.00 |
| 79_E | 191_G | 1.670 | 1.00 |
| 53_A | 59_T | 1.659 | 1.00 |
| 264_E | 267_E | 1.657 | 1.00 |
| 220_Y | 223_A | 1.636 | 1.00 |
| 158_S | 177_C | 1.631 | 1.00 |
| 42_R | 124_F | 1.620 | 1.00 |
| 133_N | 137_R | 1.611 | 1.00 |
| 229_A | 234_A | 1.602 | 1.00 |
| 209_I | 237_V | 1.601 | 1.00 |
| 239_L | 261_V | 1.593 | 1.00 |
| 44_L | 207_A | 1.590 | 1.00 |
| 160_Q | 175_H | 1.571 | 1.00 |
| 78_P | 82_D | 1.565 | 1.00 |
| 117_Q | 140_N | 1.559 | 1.00 |
| 154_R | 186_H | 1.557 | 1.00 |
| 109_A | 258_A | 1.554 | 1.00 |
| 125_L | 144_I | 1.551 | 1.00 |
| 144_I | 199_E | 1.545 | 1.00 |
| 47_T | 135_H | 1.543 | 1.00 |
| 108_A | 111_L | 1.527 | 1.00 |
| 201_Y | 228_E | 1.522 | 1.00 |
| 155_C | 174_C | 1.513 | 1.00 |
| 145_H | 149_E | 1.481 | 1.00 |
| 90_A | 94_A | 1.461 | 1.00 |
| 235_H | 252_E | 1.424 | 1.00 |
| 209_I | 235_H | 1.417 | 1.00 |
| 41_P | 208_D | 1.391 | 0.99 |
| 99_L | 104_I | 1.370 | 0.99 |
| 82_D | 156_S | 1.360 | 0.99 |
| 47_T | 126_L | 1.350 | 0.99 |
| 86_E | 90_A | 1.334 | 0.99 |
| 47_T | 51_I | 1.310 | 0.99 |
| 81_F | 156_S | 1.299 | 0.99 |
| 243_P | 255_Y | 1.298 | 0.99 |
| 242_E | 255_Y | 1.289 | 0.99 |
| 264_E | 268_K | 1.288 | 0.99 |
| 158_S | 174_C | 1.283 | 0.99 |
| 42_R | 208_D | 1.277 | 0.99 |
| 213_I | 239_L | 1.258 | 0.99 |
| 154_R | 161_V | 1.253 | 0.99 |
| 202_M | 206_M | 1.244 | 0.98 |
| 235_H | 251_A | 1.243 | 0.98 |
| 112_A | 115_K | 1.234 | 0.98 |
| 112_A | 262_V | 1.233 | 0.98 |
| 256_G | 264_E | 1.224 | 0.98 |
| 160_Q | 176_C | 1.224 | 0.98 |
| 115_K | 266_V | 1.209 | 0.98 |
| 117_Q | 141_T | 1.208 | 0.98 |
| 58_R | 69_E | 1.196 | 0.98 |
| 133_N | 145_H | 1.192 | 0.98 |
| 105_Q | 111_L | 1.187 | 0.98 |
| 108_A | 112_A | 1.184 | 0.98 |
| 99_L | 150_L | 1.181 | 0.98 |
| 196_G | 199_E | 1.170 | 0.97 |
| 213_I | 262_V | 1.168 | 0.97 |
| 162_L | 175_H | 1.166 | 0.97 |
| 211_I | 237_V | 1.159 | 0.97 |
| 81_F | 184_R | 1.153 | 0.97 |
| 62_A | 68_E | 1.127 | 0.97 |
| 205_S | 228_E | 1.127 | 0.97 |
| 44_L | 210_F | 1.124 | 0.97 |
| 133_N | 149_E | 1.123 | 0.97 |
| 254_Y | 261_V | 1.122 | 0.97 |
| 92_Y | 95_R | 1.120 | 0.96 |
| 47_T | 113_L | 1.112 | 0.96 |
| 136_E | 143_V | 1.110 | 0.96 |
| 108_A | 259_S | 1.104 | 0.96 |
| 260_Q | 264_E | 1.098 | 0.96 |
| 254_Y | 268_K | 1.095 | 0.96 |
| 33_V | 237_V | 1.092 | 0.96 |
| 238_E | 247_G | 1.090 | 0.96 |
| 152_K | 161_V | 1.082 | 0.96 |
| 156_S | 182_P | 1.071 | 0.95 |
| 49_A | 52_S | 1.070 | 0.95 |
| 42_R | 203_A | 1.068 | 0.95 |
| 146_M | 222_A | 1.068 | 0.95 |
| 88_V | 92_Y | 1.067 | 0.95 |
| 111_L | 115_K | 1.059 | 0.95 |
| 70_H | 87_L | 1.059 | 0.95 |
| 89_Q | 172_D | 1.053 | 0.95 |
| 74_D | 83_R | 1.049 | 0.94 |
| 116_L | 266_V | 1.044 | 0.94 |
| 76_A | 189_W | 1.037 | 0.94 |
| 74_D | 87_L | 1.037 | 0.94 |
| 57_I | 104_I | 1.035 | 0.94 |
| 67_W | 76_A | 1.032 | 0.94 |
| 238_E | 250_F | 1.017 | 0.93 |
| 114_A | 138_A | 1.016 | 0.93 |
| 133_N | 151_L | 1.012 | 0.93 |
| 199_E | 202_M | 1.010 | 0.93 |
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 | |
| 1m2kA | 1 | 0.8781 | 100 | 0.214 | Contact Map |
| 1yc5A | 1 | 0.8136 | 100 | 0.222 | Contact Map |
| 4twjA | 1 | 0.8172 | 100 | 0.228 | Contact Map |
| 3riyA | 2 | 0.871 | 100 | 0.228 | Contact Map |
| 3u31A | 1 | 0.8961 | 100 | 0.228 | Contact Map |
| 1s5pA | 1 | 0.8065 | 100 | 0.232 | Contact Map |
| 5btrA | 3 | 0 | 100 | 0.249 | Contact Map |
| 4iaoA | 2 | 0.957 | 100 | 0.253 | Contact Map |
| 4kxqA | 1 | 0.9032 | 100 | 0.255 | Contact Map |
| 2hjhA | 2 | 0.9427 | 100 | 0.258 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)