| sst3a_deltaC 1-230 |
| ID: | 1410247190 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 230 (213) | ||
| Sequences: | 1576 (1091.8) | ||
| Seq/Len: | 7.399 | ||
| Nf(neff/√len): | 74.8 |
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: 7.399).
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 |
| 30_S | 128_T | 3.503 | 1.00 |
| 123_F | 174_F | 2.784 | 1.00 |
| 135_T | 147_A | 2.749 | 1.00 |
| 126_F | 174_F | 2.705 | 1.00 |
| 178_L | 201_A | 2.658 | 1.00 |
| 130_V | 178_L | 2.596 | 1.00 |
| 135_T | 144_G | 2.569 | 1.00 |
| 137_E | 188_K | 2.328 | 1.00 |
| 27_A | 125_S | 2.251 | 1.00 |
| 169_E | 209_W | 2.223 | 1.00 |
| 50_P | 117_V | 2.180 | 1.00 |
| 140_D | 143_A | 2.160 | 1.00 |
| 136_K | 144_G | 2.068 | 1.00 |
| 128_T | 148_A | 2.056 | 1.00 |
| 137_E | 185_K | 2.015 | 1.00 |
| 131_T | 151_I | 1.800 | 1.00 |
| 27_A | 129_I | 1.788 | 1.00 |
| 127_T | 177_L | 1.769 | 1.00 |
| 133_H | 181_Y | 1.755 | 1.00 |
| 50_P | 209_W | 1.700 | 1.00 |
| 182_M | 201_A | 1.700 | 1.00 |
| 144_G | 147_A | 1.686 | 1.00 |
| 204_Y | 208_S | 1.630 | 1.00 |
| 132_Y | 136_K | 1.624 | 1.00 |
| 124_S | 161_S | 1.588 | 1.00 |
| 182_M | 197_K | 1.579 | 1.00 |
| 151_I | 157_Y | 1.566 | 1.00 |
| 31_F | 125_S | 1.521 | 0.99 |
| 31_F | 35_L | 1.506 | 0.99 |
| 122_L | 126_F | 1.489 | 0.99 |
| 132_Y | 148_A | 1.485 | 0.99 |
| 134_L | 181_Y | 1.469 | 0.99 |
| 197_K | 201_A | 1.452 | 0.99 |
| 134_L | 184_I | 1.432 | 0.99 |
| 23_L | 145_L | 1.431 | 0.99 |
| 114_N | 118_F | 1.424 | 0.99 |
| 135_T | 138_L | 1.423 | 0.99 |
| 132_Y | 141_A | 1.421 | 0.99 |
| 129_I | 133_H | 1.392 | 0.99 |
| 135_T | 143_A | 1.382 | 0.99 |
| 152_A | 158_I | 1.362 | 0.99 |
| 131_T | 147_A | 1.352 | 0.99 |
| 175_C | 201_A | 1.348 | 0.98 |
| 77_W | 82_R | 1.337 | 0.98 |
| 182_M | 194_W | 1.331 | 0.98 |
| 172_A | 205_M | 1.327 | 0.98 |
| 133_H | 136_K | 1.326 | 0.98 |
| 61_A | 97_A | 1.325 | 0.98 |
| 126_F | 130_V | 1.300 | 0.98 |
| 48_F | 51_Y | 1.291 | 0.98 |
| 169_E | 172_A | 1.282 | 0.98 |
| 99_I | 103_L | 1.273 | 0.98 |
| 28_V | 32_S | 1.273 | 0.98 |
| 57_T | 166_Y | 1.267 | 0.97 |
| 131_T | 157_Y | 1.249 | 0.97 |
| 130_V | 144_G | 1.244 | 0.97 |
| 130_V | 177_L | 1.233 | 0.97 |
| 128_T | 152_A | 1.225 | 0.97 |
| 88_I | 91_G | 1.213 | 0.96 |
| 149_A | 153_V | 1.212 | 0.96 |
| 53_N | 168_N | 1.209 | 0.96 |
| 127_T | 157_Y | 1.190 | 0.96 |
| 58_R | 62_E | 1.166 | 0.95 |
| 126_F | 129_I | 1.161 | 0.95 |
| 23_L | 148_A | 1.159 | 0.95 |
| 182_M | 198_C | 1.151 | 0.95 |
| 117_V | 169_E | 1.146 | 0.95 |
| 89_Y | 92_L | 1.144 | 0.95 |
| 172_A | 209_W | 1.140 | 0.95 |
| 77_W | 80_L | 1.131 | 0.94 |
| 136_K | 141_A | 1.114 | 0.94 |
| 131_T | 134_L | 1.113 | 0.94 |
| 221_L | 224_L | 1.111 | 0.93 |
| 38_V | 124_S | 1.106 | 0.93 |
| 125_S | 128_T | 1.102 | 0.93 |
| 117_V | 209_W | 1.102 | 0.93 |
| 146_L | 150_M | 1.102 | 0.93 |
| 115_V | 118_F | 1.096 | 0.93 |
| 135_T | 139_K | 1.086 | 0.92 |
| 31_F | 225_V | 1.082 | 0.92 |
| 176_M | 215_L | 1.070 | 0.92 |
| 117_V | 162_V | 1.066 | 0.92 |
| 22_I | 26_A | 1.064 | 0.91 |
| 130_V | 189_T | 1.054 | 0.91 |
| 55_R | 167_D | 1.044 | 0.90 |
| 121_P | 124_S | 1.044 | 0.90 |
| 32_S | 36_F | 1.041 | 0.90 |
| 28_V | 122_L | 1.035 | 0.90 |
| 61_A | 150_M | 1.030 | 0.90 |
| 192_I | 196_A | 1.029 | 0.90 |
| 209_W | 212_Y | 1.027 | 0.89 |
| 51_Y | 160_R | 1.025 | 0.89 |
| 57_T | 96_S | 1.024 | 0.89 |
| 168_N | 209_W | 1.017 | 0.89 |
| 73_D | 82_R | 1.013 | 0.89 |
| 51_Y | 56_T | 1.011 | 0.88 |
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 | |
| 3wajA | 1 | 0.8913 | 100 | 0.344 | Contact Map |
| 3rceA | 1 | 0.8913 | 99.9 | 0.425 | Contact Map |
| 2m8rA | 1 | 0.1652 | 2.9 | 0.955 | Contact Map |
| 2bs2C | 2 | 0.2609 | 1.9 | 0.959 | Contact Map |
| 2looA | 1 | 0.4217 | 1.8 | 0.96 | Contact Map |
| 2a2pA | 1 | 0.1913 | 1.4 | 0.962 | Contact Map |
| 2hztA | 4 | 0.2 | 1.4 | 0.962 | Contact Map |
| 2lzpA | 1 | 0.0565 | 1.3 | 0.963 | Contact Map |
| 2lbcA | 1 | 0.1826 | 1.2 | 0.964 | Contact Map |
| 4murA | 2 | 0.2348 | 1.2 | 0.964 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)