| fox_140_295 |
| ID: | 1415377066 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 160 (145) | ||
| Sequences: | 883 (570.2) | ||
| Seq/Len: | 6.090 | ||
| Nf(neff/√len): | 47.4 |
Jackhmmer Results: (2014_04_16)
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: 6.090).
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 |
| 58_Q | 62_D | 2.591 | 1.00 |
| 41_M | 64_F | 2.135 | 1.00 |
| 60_I | 67_Y | 1.872 | 1.00 |
| 81_S | 84_F | 1.827 | 1.00 |
| 30_K | 85_N | 1.613 | 1.00 |
| 36_I | 86_D | 1.603 | 0.99 |
| 57_Y | 73_R | 1.568 | 0.99 |
| 146_G | 149_G | 1.537 | 0.99 |
| 51_L | 55_E | 1.532 | 0.99 |
| 46_A | 51_L | 1.531 | 0.99 |
| 9_G | 12_R | 1.505 | 0.99 |
| 76_N | 83_S | 1.433 | 0.99 |
| 138_G | 141_G | 1.407 | 0.98 |
| 118_C | 126_F | 1.401 | 0.98 |
| 145_S | 148_K | 1.321 | 0.97 |
| 142_S | 147_A | 1.311 | 0.97 |
| 136_G | 140_S | 1.295 | 0.97 |
| 147_A | 150_G | 1.291 | 0.97 |
| 141_G | 144_G | 1.273 | 0.96 |
| 143_G | 147_A | 1.261 | 0.96 |
| 144_G | 148_K | 1.259 | 0.96 |
| 144_G | 147_A | 1.258 | 0.96 |
| 140_S | 143_G | 1.252 | 0.96 |
| 119_Y | 122_R | 1.244 | 0.96 |
| 135_G | 138_G | 1.235 | 0.95 |
| 143_G | 146_G | 1.234 | 0.95 |
| 39_I | 78_I | 1.222 | 0.95 |
| 10_R | 13_A | 1.220 | 0.95 |
| 142_S | 146_G | 1.219 | 0.95 |
| 114_F | 117_G | 1.218 | 0.95 |
| 120_L | 126_F | 1.208 | 0.95 |
| 70_N | 75_Q | 1.200 | 0.94 |
| 134_A | 139_G | 1.191 | 0.94 |
| 31_P | 64_F | 1.187 | 0.94 |
| 76_N | 84_F | 1.182 | 0.94 |
| 8_L | 13_A | 1.180 | 0.94 |
| 132_P | 137_G | 1.171 | 0.94 |
| 142_S | 145_S | 1.167 | 0.93 |
| 148_K | 151_P | 1.166 | 0.93 |
| 13_A | 19_A | 1.156 | 0.93 |
| 140_S | 144_G | 1.154 | 0.93 |
| 143_G | 149_G | 1.132 | 0.92 |
| 30_K | 77_S | 1.130 | 0.92 |
| 120_L | 125_R | 1.130 | 0.92 |
| 144_G | 149_G | 1.128 | 0.92 |
| 35_Y | 81_S | 1.128 | 0.92 |
| 33_Y | 41_M | 1.118 | 0.91 |
| 115_E | 119_Y | 1.113 | 0.91 |
| 34_S | 84_F | 1.111 | 0.91 |
| 10_R | 14_G | 1.105 | 0.91 |
| 45_Q | 51_L | 1.100 | 0.90 |
| 13_A | 16_G | 1.099 | 0.90 |
| 144_G | 150_G | 1.094 | 0.90 |
| 7_N | 10_R | 1.093 | 0.90 |
| 134_A | 141_G | 1.085 | 0.90 |
| 147_A | 151_P | 1.082 | 0.89 |
| 138_G | 143_G | 1.082 | 0.89 |
| 129_E | 132_P | 1.072 | 0.89 |
| 138_G | 145_S | 1.066 | 0.88 |
| 41_M | 87_C | 1.064 | 0.88 |
| 7_N | 12_R | 1.062 | 0.88 |
| 35_Y | 79_R | 1.051 | 0.88 |
| 71_Q | 78_I | 1.044 | 0.87 |
| 67_Y | 75_Q | 1.044 | 0.87 |
| 139_G | 144_G | 1.042 | 0.87 |
| 32_P | 64_F | 1.041 | 0.87 |
| 137_G | 140_S | 1.041 | 0.87 |
| 9_G | 13_A | 1.040 | 0.87 |
| 79_R | 83_S | 1.039 | 0.87 |
| 59_W | 76_N | 1.027 | 0.86 |
| 79_R | 88_F | 1.025 | 0.86 |
| 134_A | 137_G | 1.025 | 0.86 |
| 34_S | 54_S | 1.023 | 0.86 |
| 135_G | 140_S | 1.018 | 0.85 |
| 146_G | 150_G | 1.016 | 0.85 |
| 141_G | 146_G | 1.013 | 0.85 |
| 33_Y | 64_F | 1.013 | 0.85 |
| 138_G | 142_S | 1.012 | 0.85 |
| 12_R | 18_D | 1.009 | 0.84 |
| 9_G | 15_G | 1.007 | 0.84 |
| 138_G | 144_G | 1.005 | 0.84 |
| 114_F | 121_R | 1.000 | 0.84 |
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 | |
| 2hfhA | 1 | 0.5813 | 100 | 0.2 | Contact Map |
| 1vtnC | 1 | 0.6375 | 100 | 0.206 | Contact Map |
| 2c6yA | 2 | 0.6125 | 100 | 0.206 | Contact Map |
| 2hdcA | 1 | 0.6062 | 100 | 0.212 | Contact Map |
| 1kq8A | 1 | 0.4625 | 100 | 0.217 | Contact Map |
| 1e17A | 1 | 0.5312 | 100 | 0.241 | Contact Map |
| 4lg0A | 1 | 0.525 | 100 | 0.248 | Contact Map |
| 2mbfA | 1 | 0.6 | 100 | 0.264 | Contact Map |
| 3l2cA | 1 | 0.5 | 100 | 0.265 | Contact Map |
| 3g73A | 2 | 0.5938 | 100 | 0.281 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)