| T0831d2 -force run |
| ID: | 1404710438 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 155 (145) | ||
| Sequences: | 104 (82.5) | ||
| Seq/Len: | 0.717 | ||
| Nf(neff/√len): | 6.9 |
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: 0.717).
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 |
| 75_L | 86_V | 1.970 | 0.91 |
| 32_S | 95_A | 1.943 | 0.90 |
| 35_E | 72_Y | 1.823 | 0.86 |
| 95_A | 102_R | 1.715 | 0.81 |
| 41_I | 61_S | 1.586 | 0.73 |
| 42_L | 58_G | 1.544 | 0.70 |
| 79_W | 82_L | 1.499 | 0.67 |
| 25_T | 95_A | 1.474 | 0.65 |
| 100_R | 106_E | 1.460 | 0.64 |
| 148_L | 152_N | 1.440 | 0.63 |
| 86_V | 112_P | 1.421 | 0.61 |
| 29_W | 72_Y | 1.411 | 0.60 |
| 145_G | 149_Y | 1.393 | 0.59 |
| 33_E | 69_K | 1.389 | 0.58 |
| 37_S | 65_F | 1.378 | 0.58 |
| 73_K | 79_W | 1.372 | 0.57 |
| 20_R | 23_T | 1.359 | 0.56 |
| 48_H | 96_T | 1.354 | 0.56 |
| 59_S | 95_A | 1.348 | 0.55 |
| 82_L | 86_V | 1.338 | 0.54 |
| 30_A | 96_T | 1.325 | 0.53 |
| 75_L | 152_N | 1.309 | 0.52 |
| 35_E | 69_K | 1.308 | 0.52 |
| 95_A | 100_R | 1.307 | 0.52 |
| 41_I | 83_R | 1.298 | 0.51 |
| 69_K | 87_S | 1.267 | 0.48 |
| 29_W | 129_L | 1.266 | 0.48 |
| 27_G | 94_M | 1.252 | 0.47 |
| 70_K | 100_R | 1.251 | 0.47 |
| 79_W | 152_N | 1.247 | 0.47 |
| 12_D | 16_L | 1.245 | 0.46 |
| 87_S | 137_T | 1.228 | 0.45 |
| 109_P | 122_V | 1.227 | 0.45 |
| 45_A | 99_L | 1.214 | 0.44 |
| 56_D | 59_S | 1.213 | 0.44 |
| 70_K | 76_H | 1.213 | 0.44 |
| 71_E | 150_L | 1.208 | 0.43 |
| 89_V | 140_L | 1.191 | 0.42 |
| 114_L | 142_K | 1.188 | 0.42 |
| 69_K | 140_L | 1.177 | 0.41 |
| 32_S | 146_Q | 1.165 | 0.40 |
| 63_D | 69_K | 1.160 | 0.39 |
| 27_G | 73_K | 1.158 | 0.39 |
| 84_N | 148_L | 1.150 | 0.38 |
| 12_D | 15_G | 1.148 | 0.38 |
| 33_E | 145_G | 1.147 | 0.38 |
| 34_T | 85_R | 1.147 | 0.38 |
| 47_S | 149_Y | 1.146 | 0.38 |
| 44_F | 132_D | 1.138 | 0.38 |
| 83_R | 86_V | 1.130 | 0.37 |
| 66_E | 69_K | 1.129 | 0.37 |
| 101_V | 149_Y | 1.125 | 0.36 |
| 64_L | 68_W | 1.121 | 0.36 |
| 74_L | 99_L | 1.112 | 0.35 |
| 77_E | 83_R | 1.103 | 0.35 |
| 137_T | 152_N | 1.102 | 0.35 |
| 33_E | 77_E | 1.101 | 0.35 |
| 41_I | 77_E | 1.084 | 0.33 |
| 73_K | 86_V | 1.082 | 0.33 |
| 35_E | 58_G | 1.079 | 0.33 |
| 87_S | 101_V | 1.068 | 0.32 |
| 31_I | 69_K | 1.059 | 0.31 |
| 31_I | 62_M | 1.056 | 0.31 |
| 37_S | 104_P | 1.056 | 0.31 |
| 61_S | 129_L | 1.055 | 0.31 |
| 82_L | 152_N | 1.049 | 0.31 |
| 45_A | 105_R | 1.044 | 0.30 |
| 46_K | 133_K | 1.042 | 0.30 |
| 75_L | 148_L | 1.040 | 0.30 |
| 97_E | 116_I | 1.038 | 0.30 |
| 68_W | 115_H | 1.036 | 0.30 |
| 30_A | 100_R | 1.032 | 0.30 |
| 105_R | 108_K | 1.025 | 0.29 |
| 43_S | 67_A | 1.017 | 0.28 |
| 15_G | 46_K | 1.011 | 0.28 |
| 117_I | 143_K | 1.011 | 0.28 |
| 13_E | 17_V | 1.010 | 0.28 |
| 41_I | 44_F | 1.009 | 0.28 |
| 39_K | 59_S | 1.007 | 0.28 |
| 100_R | 116_I | 1.002 | 0.27 |
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 | |
| 2lr1B | 1 | 0.1355 | 3.7 | 0.954 | Contact Map |
| 2o1kA | 2 | 0.2645 | 3.1 | 0.956 | Contact Map |
| 4b4tT | 1 | 0.2129 | 2.4 | 0.958 | Contact Map |
| 4b4tM | 1 | 0.1484 | 2.4 | 0.959 | Contact Map |
| 3ghgA | 4 | 0.9226 | 2.3 | 0.959 | Contact Map |
| 2lm4A | 1 | 0.3355 | 2.1 | 0.96 | Contact Map |
| 2vhjA | 3 | 0.5742 | 2.1 | 0.96 | Contact Map |
| 2gtvX | 1 | 0.3806 | 2 | 0.96 | Contact Map |
| 3mpxA | 1 | 0.2129 | 1.6 | 0.963 | Contact Map |
| 3eg5B | 2 | 0.5484 | 1.6 | 0.963 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)