| 20 |
| ID: | 1410187111 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 145 (144) | ||
| Sequences: | 189 (137.5) | ||
| Seq/Len: | 1.312 | ||
| Nf(neff/√len): | 11.5 |
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: 1.312).
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 |
| 34_F | 38_L | 2.477 | 1.00 |
| 69_F | 112_Q | 2.217 | 0.99 |
| 27_K | 31_D | 2.165 | 0.99 |
| 71_L | 75_Q | 1.489 | 0.83 |
| 48_A | 84_G | 1.445 | 0.80 |
| 107_L | 111_Q | 1.419 | 0.78 |
| 141_E | 145_E | 1.416 | 0.78 |
| 18_I | 22_I | 1.415 | 0.78 |
| 75_Q | 92_H | 1.399 | 0.77 |
| 71_L | 92_H | 1.396 | 0.77 |
| 132_R | 136_A | 1.355 | 0.74 |
| 17_F | 114_L | 1.343 | 0.73 |
| 142_D | 145_E | 1.331 | 0.72 |
| 90_V | 109_V | 1.323 | 0.71 |
| 116_P | 119_F | 1.321 | 0.71 |
| 7_A | 11_G | 1.313 | 0.70 |
| 11_G | 14_G | 1.311 | 0.70 |
| 67_Q | 81_L | 1.287 | 0.68 |
| 105_Q | 108_Q | 1.286 | 0.68 |
| 139_L | 144_V | 1.280 | 0.68 |
| 135_S | 139_L | 1.276 | 0.67 |
| 18_I | 72_E | 1.273 | 0.67 |
| 11_G | 62_D | 1.268 | 0.67 |
| 129_I | 137_Q | 1.266 | 0.66 |
| 96_A | 106_L | 1.263 | 0.66 |
| 33_N | 83_Q | 1.254 | 0.65 |
| 134_V | 137_Q | 1.253 | 0.65 |
| 58_P | 111_Q | 1.225 | 0.63 |
| 54_L | 58_P | 1.225 | 0.63 |
| 136_A | 142_D | 1.219 | 0.62 |
| 137_Q | 142_D | 1.208 | 0.61 |
| 85_E | 121_M | 1.207 | 0.61 |
| 42_R | 92_H | 1.197 | 0.60 |
| 140_A | 144_V | 1.187 | 0.59 |
| 97_I | 110_L | 1.185 | 0.59 |
| 73_E | 92_H | 1.160 | 0.56 |
| 92_H | 95_N | 1.157 | 0.56 |
| 63_A | 122_L | 1.153 | 0.56 |
| 38_L | 106_L | 1.146 | 0.55 |
| 89_G | 112_Q | 1.135 | 0.54 |
| 9_A | 19_G | 1.124 | 0.53 |
| 128_T | 135_S | 1.121 | 0.52 |
| 136_A | 141_E | 1.108 | 0.51 |
| 26_R | 30_S | 1.099 | 0.50 |
| 100_C | 110_L | 1.098 | 0.50 |
| 136_A | 139_L | 1.094 | 0.50 |
| 13_C | 48_A | 1.087 | 0.49 |
| 76_L | 111_Q | 1.086 | 0.49 |
| 22_I | 74_I | 1.084 | 0.49 |
| 14_G | 74_I | 1.084 | 0.49 |
| 67_Q | 127_P | 1.082 | 0.49 |
| 8_I | 118_V | 1.080 | 0.48 |
| 76_L | 82_A | 1.070 | 0.47 |
| 14_G | 68_K | 1.070 | 0.47 |
| 29_R | 78_E | 1.067 | 0.47 |
| 71_L | 115_P | 1.065 | 0.47 |
| 111_Q | 122_L | 1.065 | 0.47 |
| 136_A | 140_A | 1.065 | 0.47 |
| 132_R | 135_S | 1.063 | 0.47 |
| 9_A | 17_F | 1.061 | 0.47 |
| 137_Q | 144_V | 1.050 | 0.45 |
| 76_L | 102_Q | 1.043 | 0.45 |
| 42_R | 45_Q | 1.040 | 0.44 |
| 27_K | 32_P | 1.040 | 0.44 |
| 131_Q | 135_S | 1.038 | 0.44 |
| 95_N | 100_C | 1.034 | 0.44 |
| 62_D | 65_A | 1.031 | 0.44 |
| 10_A | 26_R | 1.029 | 0.43 |
| 134_V | 144_V | 1.022 | 0.43 |
| 135_S | 138_S | 1.022 | 0.43 |
| 40_E | 122_L | 1.020 | 0.42 |
| 32_P | 46_K | 1.019 | 0.42 |
| 66_V | 73_E | 1.019 | 0.42 |
| 31_D | 84_G | 1.018 | 0.42 |
| 94_T | 130_S | 1.016 | 0.42 |
| 108_Q | 119_F | 1.013 | 0.42 |
| 15_A | 64_E | 1.012 | 0.42 |
| 85_E | 88_K | 1.012 | 0.42 |
| 21_C | 90_V | 1.009 | 0.41 |
| 67_Q | 110_L | 1.005 | 0.41 |
| 17_F | 99_V | 1.002 | 0.41 |
| 11_G | 84_G | 1.001 | 0.41 |
| 128_T | 134_V | 1.000 | 0.41 |
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 | |
| 1om2A | 1 | 0.6552 | 100 | 0.439 | Contact Map |
| 3ax2A | 4 | 0.4828 | 99.9 | 0.52 | Contact Map |
| 2j5lA | 1 | 0 | 28.9 | 0.941 | Contact Map |
| 3sf4A | 3 | 0.5517 | 22.8 | 0.944 | Contact Map |
| 1u11A | 2 | 0.3586 | 19.1 | 0.946 | Contact Map |
| 2l2tA | 2 | 0.2483 | 17.7 | 0.947 | Contact Map |
| 4ay3A | 4 | 0.3586 | 17.6 | 0.947 | Contact Map |
| 1d2tA | 1 | 0.331 | 17 | 0.947 | Contact Map |
| 3fp2A | 1 | 0.6276 | 16.3 | 0.948 | Contact Map |
| 4grdA | 4 | 0.3724 | 16.2 | 0.948 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)