| 1CFBA |
| ID: | 1411603768 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 205 (196) | ||
| Sequences: | 7896 (5627.5) | ||
| Seq/Len: | 40.286 | ||
| Nf(neff/√len): | 402.0 |
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: 40.286).
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 |
| 168_I | 179_I | 3.950 | 1.00 |
| 143_S | 180_K | 3.359 | 1.00 |
| 41_Q | 78_R | 3.327 | 1.00 |
| 42_F | 77_F | 3.151 | 1.00 |
| 80_I | 90_P | 3.105 | 1.00 |
| 139_H | 184_I | 3.041 | 1.00 |
| 144_W | 168_I | 2.632 | 1.00 |
| 21_A | 97_C | 2.532 | 1.00 |
| 141_Y | 182_V | 2.531 | 1.00 |
| 145_K | 178_L | 2.458 | 1.00 |
| 37_H | 82_F | 2.452 | 1.00 |
| 144_W | 179_I | 2.419 | 1.00 |
| 182_V | 192_V | 2.396 | 1.00 |
| 43_N | 76_T | 2.249 | 1.00 |
| 39_T | 82_F | 2.219 | 1.00 |
| 182_V | 189_E | 2.203 | 1.00 |
| 110_N | 126_T | 2.200 | 1.00 |
| 141_Y | 184_I | 2.169 | 1.00 |
| 81_A | 88_S | 2.075 | 1.00 |
| 184_I | 189_E | 2.058 | 1.00 |
| 117_E | 120_N | 1.983 | 1.00 |
| 23_I | 77_F | 1.956 | 1.00 |
| 27_Q | 38_Y | 1.949 | 1.00 |
| 146_R | 172_P | 1.906 | 1.00 |
| 183_A | 190_S | 1.873 | 1.00 |
| 74_N | 98_T | 1.843 | 1.00 |
| 40_I | 79_V | 1.840 | 1.00 |
| 142_V | 181_V | 1.838 | 1.00 |
| 83_N | 86_G | 1.797 | 1.00 |
| 39_T | 80_I | 1.764 | 1.00 |
| 40_I | 65_F | 1.740 | 1.00 |
| 127_P | 140_Y | 1.729 | 1.00 |
| 17_Q | 20_K | 1.723 | 1.00 |
| 82_F | 87_A | 1.714 | 1.00 |
| 123_I | 179_I | 1.714 | 1.00 |
| 142_V | 166_I | 1.700 | 1.00 |
| 180_K | 192_V | 1.694 | 1.00 |
| 185_N | 188_G | 1.692 | 1.00 |
| 22_E | 66_V | 1.663 | 1.00 |
| 77_F | 97_C | 1.637 | 1.00 |
| 122_V | 167_V | 1.593 | 1.00 |
| 21_A | 77_F | 1.589 | 1.00 |
| 80_I | 87_A | 1.532 | 1.00 |
| 83_N | 185_N | 1.522 | 1.00 |
| 73_A | 99_T | 1.515 | 1.00 |
| 78_R | 90_P | 1.511 | 1.00 |
| 42_F | 144_W | 1.484 | 1.00 |
| 111_V | 123_I | 1.461 | 1.00 |
| 182_V | 190_S | 1.419 | 1.00 |
| 51_W | 78_R | 1.380 | 0.99 |
| 121_L | 179_I | 1.378 | 0.99 |
| 112_V | 124_S | 1.377 | 0.99 |
| 77_F | 179_I | 1.359 | 0.99 |
| 171_Q | 177_Y | 1.353 | 0.99 |
| 168_I | 171_Q | 1.348 | 0.99 |
| 43_N | 51_W | 1.340 | 0.99 |
| 146_R | 175_V | 1.320 | 0.99 |
| 147_D | 178_L | 1.297 | 0.99 |
| 39_T | 87_A | 1.288 | 0.99 |
| 122_V | 165_N | 1.284 | 0.99 |
| 111_V | 181_V | 1.265 | 0.99 |
| 171_Q | 175_V | 1.231 | 0.98 |
| 28_Q | 38_Y | 1.230 | 0.98 |
| 11_L | 79_V | 1.224 | 0.98 |
| 141_Y | 189_E | 1.214 | 0.98 |
| 143_S | 192_V | 1.212 | 0.98 |
| 74_N | 96_S | 1.197 | 0.98 |
| 28_Q | 35_I | 1.195 | 0.98 |
| 185_N | 189_E | 1.190 | 0.98 |
| 133_H | 137_N | 1.188 | 0.98 |
| 80_I | 88_S | 1.174 | 0.98 |
| 41_Q | 80_I | 1.167 | 0.97 |
| 41_Q | 90_P | 1.164 | 0.97 |
| 11_L | 23_I | 1.153 | 0.97 |
| 22_E | 64_S | 1.143 | 0.97 |
| 41_Q | 53_A | 1.131 | 0.97 |
| 143_S | 182_V | 1.124 | 0.97 |
| 14_I | 22_E | 1.113 | 0.96 |
| 172_P | 177_Y | 1.113 | 0.96 |
| 51_W | 153_W | 1.111 | 0.96 |
| 83_N | 87_A | 1.107 | 0.96 |
| 15_T | 22_E | 1.106 | 0.96 |
| 43_N | 145_K | 1.103 | 0.96 |
| 69_M | 99_T | 1.102 | 0.96 |
| 69_M | 75_Y | 1.101 | 0.96 |
| 44_T | 70_S | 1.094 | 0.96 |
| 78_R | 180_K | 1.094 | 0.96 |
| 72_W | 174_F | 1.084 | 0.96 |
| 116_T | 121_L | 1.081 | 0.95 |
| 153_W | 158_I | 1.078 | 0.95 |
| 130_E | 133_H | 1.053 | 0.95 |
| 136_P | 185_N | 1.044 | 0.94 |
| 72_W | 98_T | 1.044 | 0.94 |
| 145_K | 153_W | 1.043 | 0.94 |
| 25_W | 79_V | 1.039 | 0.94 |
| 82_F | 184_I | 1.038 | 0.94 |
| 12_T | 24_H | 1.032 | 0.94 |
| 127_P | 164_N | 1.030 | 0.94 |
| 13_G | 16_C | 1.011 | 0.93 |
| 119_N | 173_T | 1.009 | 0.93 |
| 114_Q | 124_S | 1.001 | 0.92 |
| 70_S | 75_Y | 1.001 | 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
- 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 | |
| 1cfbA | 1 | 1 | 100 | 0.022 | Contact Map |
| 3e0gA | 1 | 0.9659 | 99.9 | 0.217 | Contact Map |
| 2ibgA | 4 | 0.9756 | 99.9 | 0.234 | Contact Map |
| 2q7nA | 2 | 0.9659 | 99.9 | 0.246 | Contact Map |
| 4hljA | 1 | 0.961 | 99.9 | 0.258 | Contact Map |
| 3fl7A | 1 | 0.8976 | 99.9 | 0.261 | Contact Map |
| 2d9qB | 1 | 0.9512 | 99.9 | 0.261 | Contact Map |
| 3lpwA | 2 | 0.9463 | 99.9 | 0.266 | Contact Map |
| 2vkwA | 2 | 0.9415 | 99.9 | 0.268 | Contact Map |
| 3p4lA | 1 | 0.922 | 99.9 | 0.268 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)