| hellf again |
| ID: | 1428596878 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 206 (198) | ||
| Sequences: | 1839 (1658.8) | ||
| Seq/Len: | 9.288 | ||
| Nf(neff/√len): | 117.9 |
Jackhmmer Results: (2015_01_07)
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: 9.288).
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 |
| 2_D | 5_S | 4.390 | 1.00 |
| 15_T | 19_Q | 3.499 | 1.00 |
| 3_P | 7_T | 2.483 | 1.00 |
| 37_S | 119_D | 2.369 | 1.00 |
| 85_K | 89_Q | 2.225 | 1.00 |
| 44_L | 126_N | 2.023 | 1.00 |
| 94_A | 121_K | 1.988 | 1.00 |
| 27_L | 116_Y | 1.977 | 1.00 |
| 4_L | 9_S | 1.968 | 1.00 |
| 130_A | 134_R | 1.898 | 1.00 |
| 6_V | 9_S | 1.890 | 1.00 |
| 6_V | 10_A | 1.832 | 1.00 |
| 12_A | 15_T | 1.788 | 1.00 |
| 56_A | 60_E | 1.740 | 1.00 |
| 130_A | 133_Q | 1.671 | 1.00 |
| 188_D | 192_E | 1.579 | 1.00 |
| 11_V | 16_A | 1.567 | 1.00 |
| 4_L | 8_A | 1.524 | 1.00 |
| 44_L | 133_Q | 1.501 | 1.00 |
| 133_Q | 138_M | 1.491 | 1.00 |
| 5_S | 8_A | 1.486 | 1.00 |
| 25_H | 29_D | 1.484 | 1.00 |
| 48_T | 129_L | 1.411 | 0.99 |
| 190_I | 193_G | 1.398 | 0.99 |
| 5_S | 12_A | 1.381 | 0.99 |
| 195_S | 198_R | 1.367 | 0.99 |
| 12_A | 19_Q | 1.347 | 0.99 |
| 48_T | 84_T | 1.347 | 0.99 |
| 91_F | 125_L | 1.337 | 0.99 |
| 35_P | 112_R | 1.337 | 0.99 |
| 148_S | 151_T | 1.335 | 0.99 |
| 174_A | 177_S | 1.322 | 0.99 |
| 123_N | 127_R | 1.304 | 0.99 |
| 186_D | 190_I | 1.283 | 0.99 |
| 182_E | 187_D | 1.281 | 0.99 |
| 92_T | 96_T | 1.273 | 0.99 |
| 2_D | 6_V | 1.267 | 0.98 |
| 192_E | 196_S | 1.258 | 0.98 |
| 179_R | 182_E | 1.247 | 0.98 |
| 163_A | 167_K | 1.247 | 0.98 |
| 8_A | 11_V | 1.246 | 0.98 |
| 173_S | 179_R | 1.243 | 0.98 |
| 39_S | 43_S | 1.239 | 0.98 |
| 193_G | 196_S | 1.234 | 0.98 |
| 151_T | 155_I | 1.228 | 0.98 |
| 158_L | 166_E | 1.224 | 0.98 |
| 37_S | 115_V | 1.218 | 0.98 |
| 190_I | 195_S | 1.218 | 0.98 |
| 9_S | 12_A | 1.205 | 0.98 |
| 186_D | 191_A | 1.197 | 0.98 |
| 189_G | 193_G | 1.172 | 0.97 |
| 194_D | 198_R | 1.165 | 0.97 |
| 8_A | 13_L | 1.157 | 0.97 |
| 182_E | 186_D | 1.150 | 0.97 |
| 21_A | 25_H | 1.149 | 0.97 |
| 30_G | 119_D | 1.138 | 0.96 |
| 138_M | 141_S | 1.137 | 0.96 |
| 49_Q | 53_G | 1.136 | 0.96 |
| 3_P | 6_V | 1.130 | 0.96 |
| 3_P | 9_S | 1.127 | 0.96 |
| 146_I | 150_R | 1.121 | 0.96 |
| 122_I | 126_N | 1.118 | 0.96 |
| 182_E | 192_E | 1.110 | 0.96 |
| 51_T | 133_Q | 1.109 | 0.96 |
| 191_A | 196_S | 1.107 | 0.96 |
| 137_T | 141_S | 1.103 | 0.95 |
| 161_Q | 166_E | 1.103 | 0.95 |
| 192_E | 195_S | 1.102 | 0.95 |
| 177_S | 183_S | 1.097 | 0.95 |
| 152_S | 156_D | 1.095 | 0.95 |
| 182_E | 188_D | 1.094 | 0.95 |
| 184_Q | 195_S | 1.093 | 0.95 |
| 182_E | 185_A | 1.091 | 0.95 |
| 44_L | 130_A | 1.084 | 0.95 |
| 40_H | 128_D | 1.081 | 0.95 |
| 8_A | 12_A | 1.079 | 0.95 |
| 178_I | 182_E | 1.078 | 0.95 |
| 28_V | 32_A | 1.078 | 0.95 |
| 38_V | 98_V | 1.073 | 0.95 |
| 115_V | 126_N | 1.068 | 0.94 |
| 184_Q | 187_D | 1.063 | 0.94 |
| 160_T | 163_A | 1.060 | 0.94 |
| 10_A | 14_A | 1.059 | 0.94 |
| 87_I | 132_C | 1.057 | 0.94 |
| 133_Q | 137_T | 1.048 | 0.94 |
| 14_A | 17_A | 1.042 | 0.93 |
| 166_E | 169_L | 1.041 | 0.93 |
| 184_Q | 190_I | 1.040 | 0.93 |
| 115_V | 122_I | 1.033 | 0.93 |
| 119_D | 123_N | 1.031 | 0.93 |
| 155_I | 159_Q | 1.030 | 0.93 |
| 17_A | 21_A | 1.029 | 0.93 |
| 186_D | 189_G | 1.029 | 0.93 |
| 190_I | 196_S | 1.025 | 0.93 |
| 172_L | 180_E | 1.025 | 0.93 |
| 11_V | 15_T | 1.024 | 0.93 |
| 106_H | 110_R | 1.015 | 0.92 |
| 81_L | 88_C | 1.011 | 0.92 |
| 13_L | 16_A | 1.010 | 0.92 |
| 185_A | 188_D | 1.004 | 0.92 |
| 187_D | 190_I | 1.003 | 0.92 |
| 44_L | 51_T | 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 | |
| 4btfA | 1 | 0.7136 | 96.3 | 0.774 | Contact Map |
| 2wvqA | 2 | 0.8641 | 96.2 | 0.778 | Contact Map |
| 2msvA | 1 | 0.7476 | 94.6 | 0.8 | Contact Map |
| 4q4gX | 1 | 0 | 84.3 | 0.842 | Contact Map |
| 4cgkA | 2 | 0.7524 | 75.5 | 0.855 | Contact Map |
| 3qflA | 1 | 0.5243 | 58.8 | 0.87 | Contact Map |
| 3ojaB | 1 | 0.6553 | 37.9 | 0.886 | Contact Map |
| 1i84S | 2 | 0 | 36.6 | 0.887 | Contact Map |
| 3na7A | 1 | 0.8301 | 29.7 | 0.892 | Contact Map |
| 2ljbA | 4 | 0.1456 | 22.6 | 0.898 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)