| IL4 -force run |
| ID: | 1475264254 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 153 (145) | ||
| Sequences: | 58 (32.9) | ||
| Seq/Len: | 0.400 | ||
| Nf(neff/√len): | 2.7 |
HHblits Results: (2016_02)
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: 0.400).
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 |
| 77_R | 80_Y | 1.891 | 0.75 |
| 116_G | 124_P | 1.634 | 0.59 |
| 73_A | 118_A | 1.598 | 0.57 |
| 16_A | 73_A | 1.552 | 0.53 |
| 133_L | 137_L | 1.515 | 0.51 |
| 17_C | 50_E | 1.507 | 0.50 |
| 22_V | 56_I | 1.504 | 0.50 |
| 12_F | 47_L | 1.497 | 0.49 |
| 41_L | 74_T | 1.467 | 0.47 |
| 24_G | 75_V | 1.412 | 0.43 |
| 62_N | 71_R | 1.400 | 0.42 |
| 141_K | 149_S | 1.379 | 0.41 |
| 27_C | 68_T | 1.378 | 0.41 |
| 41_L | 45_K | 1.371 | 0.40 |
| 24_G | 138_E | 1.344 | 0.38 |
| 4_T | 8_L | 1.338 | 0.38 |
| 105_R | 116_G | 1.323 | 0.37 |
| 134_E | 138_E | 1.301 | 0.36 |
| 113_N | 118_A | 1.299 | 0.35 |
| 145_R | 151_C | 1.297 | 0.35 |
| 47_L | 88_R | 1.282 | 0.34 |
| 12_F | 122_S | 1.271 | 0.34 |
| 15_L | 33_E | 1.255 | 0.33 |
| 60_S | 117_L | 1.254 | 0.32 |
| 13_F | 109_R | 1.238 | 0.31 |
| 49_T | 129_N | 1.217 | 0.30 |
| 76_L | 114_L | 1.213 | 0.30 |
| 74_T | 124_P | 1.209 | 0.30 |
| 51_L | 117_L | 1.199 | 0.29 |
| 85_K | 88_R | 1.175 | 0.28 |
| 48_C | 133_L | 1.168 | 0.27 |
| 17_C | 53_V | 1.167 | 0.27 |
| 24_G | 35_I | 1.163 | 0.27 |
| 57_F | 145_R | 1.159 | 0.27 |
| 67_E | 105_R | 1.155 | 0.27 |
| 125_V | 143_I | 1.153 | 0.26 |
| 21_F | 51_L | 1.152 | 0.26 |
| 12_F | 46_T | 1.151 | 0.26 |
| 24_G | 127_E | 1.142 | 0.26 |
| 34_I | 75_V | 1.141 | 0.26 |
| 32_Q | 35_I | 1.139 | 0.26 |
| 42_T | 126_K | 1.138 | 0.26 |
| 134_E | 148_Y | 1.136 | 0.25 |
| 85_K | 102_Q | 1.128 | 0.25 |
| 95_Q | 150_K | 1.126 | 0.25 |
| 57_F | 96_Q | 1.124 | 0.25 |
| 78_Q | 124_P | 1.117 | 0.24 |
| 81_S | 86_D | 1.109 | 0.24 |
| 96_Q | 102_Q | 1.093 | 0.23 |
| 23_H | 67_E | 1.092 | 0.23 |
| 46_T | 85_K | 1.090 | 0.23 |
| 50_E | 53_V | 1.083 | 0.23 |
| 24_G | 39_N | 1.078 | 0.22 |
| 13_F | 132_T | 1.078 | 0.22 |
| 56_I | 81_S | 1.076 | 0.22 |
| 12_F | 88_R | 1.074 | 0.22 |
| 68_T | 86_D | 1.073 | 0.22 |
| 133_L | 136_F | 1.069 | 0.22 |
| 20_N | 65_E | 1.067 | 0.22 |
| 80_Y | 118_A | 1.062 | 0.22 |
| 4_T | 68_T | 1.060 | 0.21 |
| 73_A | 114_L | 1.058 | 0.21 |
| 70_C | 76_L | 1.052 | 0.21 |
| 131_S | 136_F | 1.052 | 0.21 |
| 50_E | 138_E | 1.049 | 0.21 |
| 146_E | 150_K | 1.047 | 0.21 |
| 71_R | 78_Q | 1.044 | 0.21 |
| 75_V | 138_E | 1.039 | 0.20 |
| 21_F | 36_K | 1.038 | 0.20 |
| 132_T | 147_K | 1.038 | 0.20 |
| 144_M | 149_S | 1.038 | 0.20 |
| 30_T | 49_T | 1.035 | 0.20 |
| 19_G | 30_T | 1.032 | 0.20 |
| 25_H | 69_F | 1.026 | 0.20 |
| 119_G | 126_K | 1.026 | 0.20 |
| 51_L | 60_S | 1.022 | 0.20 |
| 2_G | 112_R | 1.021 | 0.20 |
| 128_A | 150_K | 1.021 | 0.20 |
| 73_A | 113_N | 1.017 | 0.19 |
| 65_E | 77_R | 1.015 | 0.19 |
| 135_N | 139_R | 1.013 | 0.19 |
| 142_T | 149_S | 1.008 | 0.19 |
| 74_T | 78_Q | 1.007 | 0.19 |
| 26_K | 131_S | 1.006 | 0.19 |
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 | |
| 2d48A | 1 | 0.8431 | 100 | 0.265 | Contact Map |
| 3lb6A | 1 | 0.6863 | 99.4 | 0.779 | Contact Map |
| 4i77Z | 1 | 0.634 | 96.7 | 0.893 | Contact Map |
| 3bpoA | 1 | 0.6405 | 96.4 | 0.897 | Contact Map |
| 1ax8A | 1 | 0.7059 | 65 | 0.939 | Contact Map |
| 2oqpA | 1 | 0.7582 | 59.3 | 0.941 | Contact Map |
| 2gmfA | 2 | 0.7255 | 27 | 0.952 | Contact Map |
| 3pivA | 2 | 0.7255 | 26.9 | 0.952 | Contact Map |
| 1au1A | 2 | 0.7712 | 25.7 | 0.952 | Contact Map |
| 1wu3I | 1 | 0.8105 | 20.6 | 0.955 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)