| 2y64 |
| ID: | 1453982806 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 167 (157) | ||
| Sequences: | 549 (452.1) | ||
| Seq/Len: | 3.497 | ||
| Nf(neff/√len): | 36.1 |
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: 3.497).
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 |
| 91_R | 161_G | 6.627 | 1.00 |
| 84_V | 166_D | 3.624 | 1.00 |
| 91_R | 127_P | 3.471 | 1.00 |
| 88_Y | 164_I | 3.446 | 1.00 |
| 87_T | 129_T | 3.017 | 1.00 |
| 92_A | 128_F | 2.846 | 1.00 |
| 93_R | 125_W | 2.796 | 1.00 |
| 87_T | 131_E | 2.373 | 1.00 |
| 87_T | 165_V | 1.971 | 1.00 |
| 91_R | 125_W | 1.966 | 1.00 |
| 7_N | 10_F | 1.938 | 1.00 |
| 81_R | 166_D | 1.882 | 1.00 |
| 92_A | 121_I | 1.838 | 0.99 |
| 93_R | 158_Y | 1.796 | 0.99 |
| 159_I | 162_L | 1.717 | 0.99 |
| 58_A | 158_Y | 1.695 | 0.99 |
| 81_R | 84_V | 1.671 | 0.99 |
| 67_N | 70_N | 1.447 | 0.96 |
| 85_T | 131_E | 1.381 | 0.94 |
| 85_T | 133_T | 1.345 | 0.93 |
| 90_I | 128_F | 1.323 | 0.92 |
| 21_L | 24_G | 1.317 | 0.92 |
| 113_Y | 134_V | 1.296 | 0.91 |
| 110_F | 139_T | 1.292 | 0.91 |
| 125_W | 160_D | 1.273 | 0.90 |
| 51_P | 91_R | 1.235 | 0.88 |
| 65_G | 72_Q | 1.228 | 0.88 |
| 77_P | 142_R | 1.225 | 0.88 |
| 142_R | 146_H | 1.223 | 0.88 |
| 93_R | 145_I | 1.217 | 0.87 |
| 82_P | 138_E | 1.211 | 0.87 |
| 7_N | 21_L | 1.206 | 0.87 |
| 53_G | 161_G | 1.187 | 0.86 |
| 98_G | 157_I | 1.161 | 0.84 |
| 37_T | 163_A | 1.159 | 0.84 |
| 129_T | 136_D | 1.150 | 0.83 |
| 121_I | 145_I | 1.125 | 0.81 |
| 59_V | 110_F | 1.123 | 0.81 |
| 28_W | 85_T | 1.120 | 0.81 |
| 72_Q | 146_H | 1.120 | 0.81 |
| 58_A | 156_T | 1.116 | 0.80 |
| 9_G | 12_S | 1.111 | 0.80 |
| 95_E | 155_N | 1.111 | 0.80 |
| 10_F | 21_L | 1.110 | 0.80 |
| 69_F | 146_H | 1.094 | 0.79 |
| 125_W | 158_Y | 1.090 | 0.78 |
| 46_E | 49_D | 1.088 | 0.78 |
| 110_F | 113_Y | 1.074 | 0.77 |
| 22_A | 160_D | 1.071 | 0.76 |
| 147_F | 154_G | 1.070 | 0.76 |
| 56_V | 125_W | 1.064 | 0.76 |
| 6_I | 12_S | 1.051 | 0.75 |
| 54_N | 158_Y | 1.051 | 0.75 |
| 26_E | 38_N | 1.050 | 0.74 |
| 104_T | 144_P | 1.049 | 0.74 |
| 19_T | 28_W | 1.048 | 0.74 |
| 89_T | 127_P | 1.040 | 0.73 |
| 26_E | 56_V | 1.039 | 0.73 |
| 105_V | 109_S | 1.037 | 0.73 |
| 89_T | 165_V | 1.028 | 0.72 |
| 122_T | 153_V | 1.027 | 0.72 |
| 53_G | 56_V | 1.010 | 0.70 |
| 89_T | 129_T | 1.002 | 0.69 |
| 104_T | 132_F | 1.001 | 0.69 |
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 | |
| 4bj0A | 1 | 0.988 | 99.9 | 0.393 | Contact Map |
| 1gu3A | 1 | 0.7964 | 99.9 | 0.428 | Contact Map |
| 1cx1A | 1 | 0.8323 | 99.8 | 0.435 | Contact Map |
| 3k4zA | 1 | 0.9102 | 99.8 | 0.444 | Contact Map |
| 4qpwA | 1 | 0.8323 | 99.8 | 0.449 | Contact Map |
| 1guiA | 1 | 0.9102 | 99.8 | 0.449 | Contact Map |
| 3p6bA | 2 | 0.9042 | 99.8 | 0.454 | Contact Map |
| 4mgqA | 1 | 0.7246 | 99.8 | 0.49 | Contact Map |
| 4d0qA | 1 | 0.9042 | 99.7 | 0.502 | Contact Map |
| 4xuoA | 2 | 0 | 99.6 | 0.563 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)