| i-spanin homologs |
| ID: | 1450318677 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 145 (143) | ||
| Sequences: | 356 (224.1) | ||
| Seq/Len: | 2.490 | ||
| Nf(neff/√len): | 18.7 |
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: 2.490).
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 |
| 103_G | 134_Y | 2.640 | 1.00 |
| 128_I | 132_V | 2.146 | 1.00 |
| 100_S | 134_Y | 2.055 | 1.00 |
| 109_G | 115_E | 1.969 | 0.99 |
| 129_T | 132_V | 1.801 | 0.98 |
| 100_S | 103_G | 1.685 | 0.97 |
| 122_R | 125_I | 1.665 | 0.97 |
| 118_Y | 121_L | 1.662 | 0.97 |
| 116_L | 124_G | 1.586 | 0.96 |
| 112_A | 124_G | 1.579 | 0.96 |
| 33_Y | 36_Q | 1.576 | 0.96 |
| 128_I | 131_Q | 1.566 | 0.95 |
| 71_T | 76_R | 1.534 | 0.95 |
| 121_L | 131_Q | 1.506 | 0.94 |
| 113_D | 124_G | 1.488 | 0.94 |
| 78_D | 84_K | 1.476 | 0.93 |
| 112_A | 116_L | 1.401 | 0.91 |
| 46_D | 50_R | 1.387 | 0.90 |
| 118_Y | 131_Q | 1.384 | 0.90 |
| 32_T | 35_T | 1.379 | 0.90 |
| 8_I | 18_C | 1.365 | 0.89 |
| 115_E | 118_Y | 1.351 | 0.88 |
| 78_D | 83_R | 1.322 | 0.87 |
| 18_C | 22_A | 1.317 | 0.87 |
| 7_I | 10_A | 1.297 | 0.85 |
| 121_L | 132_V | 1.286 | 0.85 |
| 27_R | 31_M | 1.283 | 0.85 |
| 29_N | 33_Y | 1.280 | 0.84 |
| 63_K | 67_D | 1.277 | 0.84 |
| 5_T | 14_C | 1.269 | 0.84 |
| 120_R | 131_Q | 1.269 | 0.84 |
| 104_D | 111_T | 1.267 | 0.84 |
| 124_G | 128_I | 1.252 | 0.83 |
| 19_L | 23_V | 1.233 | 0.81 |
| 130_A | 139_I | 1.216 | 0.80 |
| 120_R | 124_G | 1.210 | 0.80 |
| 125_I | 128_I | 1.184 | 0.77 |
| 20_S | 23_V | 1.182 | 0.77 |
| 58_D | 62_T | 1.179 | 0.77 |
| 7_I | 12_V | 1.175 | 0.77 |
| 35_T | 39_K | 1.171 | 0.76 |
| 64_E | 82_G | 1.164 | 0.76 |
| 78_D | 85_R | 1.164 | 0.76 |
| 10_A | 14_C | 1.161 | 0.75 |
| 6_A | 18_C | 1.148 | 0.74 |
| 6_A | 14_C | 1.143 | 0.74 |
| 8_I | 14_C | 1.135 | 0.73 |
| 131_Q | 134_Y | 1.132 | 0.73 |
| 128_I | 133_N | 1.116 | 0.71 |
| 79_V | 119_Y | 1.114 | 0.71 |
| 16_I | 19_L | 1.113 | 0.71 |
| 74_S | 77_A | 1.111 | 0.71 |
| 128_I | 134_Y | 1.092 | 0.69 |
| 121_L | 127_R | 1.078 | 0.67 |
| 109_G | 124_G | 1.077 | 0.67 |
| 30_A | 36_Q | 1.073 | 0.67 |
| 115_E | 131_Q | 1.072 | 0.67 |
| 137_E | 141_T | 1.064 | 0.66 |
| 79_V | 86_L | 1.064 | 0.66 |
| 115_E | 124_G | 1.062 | 0.66 |
| 108_P | 118_Y | 1.058 | 0.65 |
| 52_R | 55_A | 1.052 | 0.65 |
| 57_L | 61_Y | 1.049 | 0.64 |
| 4_V | 7_I | 1.046 | 0.64 |
| 79_V | 82_G | 1.044 | 0.64 |
| 125_I | 135_L | 1.040 | 0.63 |
| 29_N | 36_Q | 1.034 | 0.63 |
| 9_S | 16_I | 1.028 | 0.62 |
| 117_N | 130_A | 1.027 | 0.62 |
| 126_D | 131_Q | 1.024 | 0.62 |
| 12_V | 15_I | 1.024 | 0.62 |
| 71_T | 74_S | 1.023 | 0.62 |
| 124_G | 134_Y | 1.019 | 0.61 |
| 44_I | 47_M | 1.016 | 0.61 |
| 30_A | 33_Y | 1.014 | 0.61 |
| 12_V | 16_I | 1.004 | 0.59 |
| 9_S | 18_C | 1.002 | 0.59 |
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 | |
| 4q4gX | 1 | 0 | 73 | 0.902 | Contact Map |
| 4cgkA | 2 | 0.4759 | 63.5 | 0.909 | Contact Map |
| 4bgnA | 2 | 0.269 | 23.6 | 0.929 | Contact Map |
| 1scfA | 4 | 0 | 20 | 0.932 | Contact Map |
| 3rvyA | 2 | 0.1793 | 16.5 | 0.934 | Contact Map |
| 4ltoA | 4 | 0.4828 | 14.5 | 0.936 | Contact Map |
| 1fzcA | 2 | 0.1931 | 13.3 | 0.937 | Contact Map |
| 5a2fA | 1 | 0 | 10.1 | 0.94 | Contact Map |
| 4gipD | 3 | 0.3724 | 7.5 | 0.944 | Contact Map |
| 4cbcA | 4 | 0.1793 | 7.1 | 0.944 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)