| 4dbb |
| ID: | 1453972417 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 162 (149) | ||
| Sequences: | 394 (239.2) | ||
| Seq/Len: | 2.644 | ||
| Nf(neff/√len): | 19.6 |
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: 2.644).
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 |
| 78_H | 95_L | 2.150 | 1.00 |
| 84_S | 87_A | 2.105 | 1.00 |
| 126_G | 129_F | 2.098 | 1.00 |
| 133_Y | 136_F | 1.674 | 0.98 |
| 118_A | 127_Q | 1.657 | 0.97 |
| 18_S | 111_H | 1.654 | 0.97 |
| 15_Y | 18_S | 1.599 | 0.97 |
| 11_F | 59_I | 1.579 | 0.96 |
| 58_F | 67_L | 1.572 | 0.96 |
| 89_I | 94_V | 1.541 | 0.95 |
| 38_E | 41_S | 1.479 | 0.94 |
| 145_E | 149_Q | 1.436 | 0.93 |
| 121_I | 133_Y | 1.423 | 0.92 |
| 89_I | 93_V | 1.422 | 0.92 |
| 4_D | 7_D | 1.399 | 0.91 |
| 125_I | 135_E | 1.362 | 0.90 |
| 78_H | 83_I | 1.360 | 0.90 |
| 32_R | 55_V | 1.349 | 0.89 |
| 15_Y | 111_H | 1.340 | 0.89 |
| 2_P | 5_L | 1.332 | 0.88 |
| 2_P | 6_I | 1.323 | 0.88 |
| 59_I | 93_V | 1.323 | 0.88 |
| 3_E | 144_P | 1.306 | 0.87 |
| 134_Q | 137_L | 1.305 | 0.87 |
| 40_V | 44_K | 1.302 | 0.87 |
| 7_D | 11_F | 1.298 | 0.87 |
| 144_P | 148_S | 1.275 | 0.85 |
| 53_T | 68_N | 1.271 | 0.85 |
| 146_D | 149_Q | 1.265 | 0.85 |
| 123_Q | 133_Y | 1.253 | 0.84 |
| 121_I | 127_Q | 1.248 | 0.84 |
| 33_M | 37_Q | 1.235 | 0.83 |
| 80_L | 132_A | 1.220 | 0.82 |
| 63_R | 83_I | 1.218 | 0.82 |
| 110_C | 113_F | 1.215 | 0.81 |
| 38_E | 42_R | 1.212 | 0.81 |
| 95_L | 108_M | 1.195 | 0.80 |
| 56_D | 69_A | 1.188 | 0.79 |
| 3_E | 7_D | 1.186 | 0.79 |
| 55_V | 75_M | 1.179 | 0.79 |
| 66_V | 76_M | 1.175 | 0.78 |
| 1_D | 4_D | 1.172 | 0.78 |
| 78_H | 86_I | 1.168 | 0.78 |
| 78_H | 112_V | 1.156 | 0.77 |
| 11_F | 121_I | 1.154 | 0.76 |
| 83_I | 112_V | 1.149 | 0.76 |
| 97_A | 125_I | 1.147 | 0.76 |
| 83_I | 113_F | 1.144 | 0.76 |
| 93_V | 125_I | 1.140 | 0.75 |
| 26_T | 96_M | 1.139 | 0.75 |
| 118_A | 121_I | 1.127 | 0.74 |
| 66_V | 131_V | 1.122 | 0.74 |
| 98_R | 108_M | 1.120 | 0.73 |
| 118_A | 129_F | 1.119 | 0.73 |
| 96_M | 119_Q | 1.109 | 0.72 |
| 16_L | 19_T | 1.104 | 0.72 |
| 76_M | 98_R | 1.104 | 0.72 |
| 65_K | 69_A | 1.100 | 0.71 |
| 4_D | 9_I | 1.086 | 0.70 |
| 9_I | 97_A | 1.085 | 0.70 |
| 138_R | 144_P | 1.078 | 0.69 |
| 12_A | 71_T | 1.071 | 0.69 |
| 15_Y | 115_S | 1.068 | 0.68 |
| 80_L | 89_I | 1.065 | 0.68 |
| 47_G | 60_S | 1.062 | 0.68 |
| 54_E | 70_D | 1.059 | 0.67 |
| 104_S | 147_L | 1.050 | 0.66 |
| 27_P | 113_F | 1.038 | 0.65 |
| 76_M | 86_I | 1.037 | 0.65 |
| 95_L | 125_I | 1.034 | 0.65 |
| 122_A | 133_Y | 1.031 | 0.64 |
| 68_N | 71_T | 1.027 | 0.64 |
| 143_N | 147_L | 1.026 | 0.64 |
| 143_N | 146_D | 1.019 | 0.63 |
| 66_V | 75_M | 1.012 | 0.62 |
| 75_M | 95_L | 1.011 | 0.62 |
| 123_Q | 132_A | 1.008 | 0.62 |
| 48_E | 51_P | 1.000 | 0.61 |
| 87_A | 135_E | 1.000 | 0.61 |
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 | |
| 4dbbA | 1 | 0.9259 | 100 | 0.174 | Contact Map |
| 3suzA | 1 | 1 | 100 | 0.249 | Contact Map |
| 1aqcA | 2 | 0.821 | 100 | 0.266 | Contact Map |
| 1n3hA | 1 | 0.8272 | 100 | 0.363 | Contact Map |
| 2elaA | 2 | 0.8457 | 100 | 0.368 | Contact Map |
| 2ej8A | 2 | 0.7901 | 100 | 0.375 | Contact Map |
| 2dyqA | 1 | 0.7346 | 100 | 0.378 | Contact Map |
| 2m38A | 1 | 0.7593 | 100 | 0.385 | Contact Map |
| 3so6A | 1 | 0.7963 | 100 | 0.399 | Contact Map |
| 3f0wA | 1 | 0.7778 | 100 | 0.402 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)