| CC_scpA |
| ID: | 1446319175 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 274 (243) | ||
| Sequences: | 2207 (1462.9) | ||
| Seq/Len: | 9.082 | ||
| Nf(neff/√len): | 93.8 |
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: 9.082).
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 |
| 200_R | 249_V | 3.736 | 1.00 |
| 27_D | 32_E | 3.104 | 1.00 |
| 256_E | 259_Q | 2.902 | 1.00 |
| 245_V | 252_A | 2.567 | 1.00 |
| 209_W | 264_R | 2.484 | 1.00 |
| 31_Y | 40_A | 2.479 | 1.00 |
| 254_Q | 261_I | 2.286 | 1.00 |
| 43_R | 123_D | 2.222 | 1.00 |
| 251_E | 264_R | 2.211 | 1.00 |
| 56_R | 59_E | 2.208 | 1.00 |
| 113_A | 117_F | 2.142 | 1.00 |
| 213_T | 260_D | 2.134 | 1.00 |
| 162_D | 165_G | 2.060 | 1.00 |
| 200_R | 244_L | 2.021 | 1.00 |
| 195_A | 233_Y | 2.015 | 1.00 |
| 195_A | 237_T | 2.000 | 1.00 |
| 195_A | 198_R | 1.985 | 1.00 |
| 254_Q | 258_F | 1.961 | 1.00 |
| 191_P | 194_D | 1.882 | 1.00 |
| 196_R | 244_L | 1.835 | 1.00 |
| 18_A | 21_G | 1.809 | 1.00 |
| 241_S | 263_L | 1.754 | 1.00 |
| 81_V | 85_W | 1.736 | 1.00 |
| 211_V | 260_D | 1.728 | 1.00 |
| 121_K | 124_V | 1.701 | 1.00 |
| 127_K | 130_E | 1.672 | 1.00 |
| 47_V | 53_S | 1.656 | 1.00 |
| 77_A | 87_A | 1.605 | 1.00 |
| 112_A | 116_A | 1.601 | 1.00 |
| 68_A | 75_L | 1.584 | 1.00 |
| 254_Q | 259_Q | 1.582 | 1.00 |
| 49_L | 89_L | 1.582 | 1.00 |
| 190_Y | 195_A | 1.570 | 1.00 |
| 63_A | 67_Q | 1.540 | 1.00 |
| 42_A | 48_D | 1.520 | 1.00 |
| 209_W | 262_Y | 1.472 | 1.00 |
| 30_G | 47_V | 1.468 | 1.00 |
| 188_T | 236_S | 1.453 | 1.00 |
| 241_S | 250_L | 1.450 | 1.00 |
| 93_L | 112_A | 1.445 | 1.00 |
| 54_I | 57_L | 1.444 | 0.99 |
| 251_E | 266_R | 1.440 | 0.99 |
| 163_L | 167_M | 1.440 | 0.99 |
| 53_S | 116_A | 1.410 | 0.99 |
| 59_E | 63_A | 1.395 | 0.99 |
| 48_D | 51_Q | 1.385 | 0.99 |
| 145_R | 148_P | 1.376 | 0.99 |
| 127_K | 131_A | 1.371 | 0.99 |
| 50_L | 120_A | 1.333 | 0.99 |
| 145_R | 149_D | 1.325 | 0.99 |
| 65_V | 75_L | 1.323 | 0.99 |
| 192_L | 203_L | 1.307 | 0.99 |
| 194_D | 198_R | 1.301 | 0.99 |
| 18_A | 22_A | 1.298 | 0.99 |
| 114_Q | 118_R | 1.292 | 0.99 |
| 58_A | 111_M | 1.284 | 0.99 |
| 39_L | 119_L | 1.279 | 0.99 |
| 52_L | 112_A | 1.277 | 0.98 |
| 66_Q | 69_R | 1.264 | 0.98 |
| 165_G | 168_S | 1.241 | 0.98 |
| 165_G | 169_A | 1.236 | 0.98 |
| 211_V | 214_S | 1.234 | 0.98 |
| 45_Q | 56_R | 1.233 | 0.98 |
| 203_L | 250_L | 1.233 | 0.98 |
| 35_L | 39_L | 1.223 | 0.98 |
| 133_K | 137_I | 1.212 | 0.98 |
| 123_D | 244_L | 1.203 | 0.98 |
| 250_L | 263_L | 1.200 | 0.97 |
| 212_L | 216_A | 1.198 | 0.97 |
| 241_S | 252_A | 1.196 | 0.97 |
| 51_Q | 54_I | 1.195 | 0.97 |
| 43_R | 77_A | 1.194 | 0.97 |
| 61_Y | 81_V | 1.192 | 0.97 |
| 40_A | 44_S | 1.182 | 0.97 |
| 93_L | 111_M | 1.175 | 0.97 |
| 34_P | 37_V | 1.172 | 0.97 |
| 53_S | 93_L | 1.149 | 0.96 |
| 133_K | 136_P | 1.144 | 0.96 |
| 88_Y | 91_S | 1.128 | 0.96 |
| 47_V | 167_M | 1.127 | 0.96 |
| 81_V | 143_F | 1.126 | 0.96 |
| 19_E | 22_A | 1.107 | 0.95 |
| 124_V | 248_G | 1.106 | 0.95 |
| 51_Q | 112_A | 1.105 | 0.95 |
| 134_E | 137_I | 1.097 | 0.95 |
| 31_Y | 84_A | 1.093 | 0.95 |
| 243_E | 246_K | 1.093 | 0.95 |
| 229_S | 233_Y | 1.079 | 0.95 |
| 64_F | 68_A | 1.073 | 0.94 |
| 139_K | 150_A | 1.071 | 0.94 |
| 28_I | 31_Y | 1.067 | 0.94 |
| 170_Y | 174_R | 1.061 | 0.94 |
| 167_M | 171_I | 1.059 | 0.94 |
| 72_R | 75_L | 1.058 | 0.94 |
| 210_T | 214_S | 1.057 | 0.94 |
| 115_L | 118_R | 1.053 | 0.94 |
| 40_A | 61_Y | 1.049 | 0.93 |
| 89_L | 116_A | 1.037 | 0.93 |
| 18_A | 268_E | 1.036 | 0.93 |
| 43_R | 76_A | 1.035 | 0.93 |
| 69_R | 75_L | 1.026 | 0.92 |
| 116_A | 120_A | 1.025 | 0.92 |
| 131_A | 135_R | 1.021 | 0.92 |
| 53_S | 111_M | 1.016 | 0.92 |
| 190_Y | 236_S | 1.016 | 0.92 |
| 132_L | 135_R | 1.012 | 0.92 |
| 199_L | 237_T | 1.011 | 0.92 |
| 43_R | 79_Y | 1.010 | 0.92 |
| 117_F | 121_K | 1.009 | 0.92 |
| 46_K | 65_V | 1.005 | 0.91 |
| 162_D | 175_K | 1.002 | 0.91 |
| 83_A | 235_A | 1.001 | 0.91 |
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 | |
| 4i98A | 1 | 0.5365 | 100 | 0.426 | Contact Map |
| 3w6jA | 2 | 0.5547 | 100 | 0.432 | Contact Map |
| 3zgxC | 2 | 0.2445 | 100 | 0.609 | Contact Map |
| 4i99C | 2 | 0.2409 | 99.3 | 0.8 | Contact Map |
| 1w1wE | 4 | 0.2555 | 95.8 | 0.906 | Contact Map |
| 2l02A | 2 | 0.2701 | 64.9 | 0.942 | Contact Map |
| 2l01A | 2 | 0.2774 | 19.7 | 0.957 | Contact Map |
| 4y66A | 3 | 0.2628 | 8 | 0.964 | Contact Map |
| 3j39U | 1 | 0.3723 | 5.2 | 0.967 | Contact Map |
| 2w2uA | 2 | 0.2628 | 4.7 | 0.967 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)