| 4m5bA |
| ID: | 1491921322 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 214 (212) | ||
| Sequences: | 1187 (786.3) | ||
| Seq/Len: | 5.599 | ||
| Nf(neff/√len): | 54.0 |
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: 5.599).
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 |
| 140_A | 199_A | 4.147 | 1.00 |
| 112_N | 157_E | 3.634 | 1.00 |
| 116_I | 153_A | 2.877 | 1.00 |
| 87_L | 114_A | 2.777 | 1.00 |
| 20_M | 111_F | 2.768 | 1.00 |
| 88_T | 110_S | 2.743 | 1.00 |
| 24_L | 88_T | 2.251 | 1.00 |
| 120_V | 149_A | 2.069 | 1.00 |
| 66_A | 194_A | 2.039 | 1.00 |
| 177_Y | 181_V | 1.970 | 1.00 |
| 139_S | 203_G | 1.924 | 1.00 |
| 73_L | 205_V | 1.917 | 1.00 |
| 47_S | 86_S | 1.895 | 1.00 |
| 20_M | 24_L | 1.872 | 1.00 |
| 135_K | 210_L | 1.851 | 1.00 |
| 16_M | 111_F | 1.831 | 1.00 |
| 143_G | 202_T | 1.826 | 1.00 |
| 74_L | 83_A | 1.822 | 1.00 |
| 152_L | 187_M | 1.696 | 1.00 |
| 123_G | 127_L | 1.682 | 1.00 |
| 128_M | 138_S | 1.678 | 1.00 |
| 140_A | 203_G | 1.671 | 1.00 |
| 121_G | 146_G | 1.653 | 1.00 |
| 13_C | 17_G | 1.646 | 1.00 |
| 126_R | 130_S | 1.594 | 0.99 |
| 191_L | 196_I | 1.492 | 0.99 |
| 81_W | 119_F | 1.488 | 0.99 |
| 69_I | 117_A | 1.454 | 0.98 |
| 66_A | 190_H | 1.442 | 0.98 |
| 16_M | 108_A | 1.440 | 0.98 |
| 20_M | 110_S | 1.424 | 0.98 |
| 128_M | 133_L | 1.420 | 0.98 |
| 17_G | 103_I | 1.409 | 0.98 |
| 26_V | 29_K | 1.408 | 0.98 |
| 170_G | 175_F | 1.383 | 0.98 |
| 196_I | 200_V | 1.361 | 0.97 |
| 136_V | 203_G | 1.356 | 0.97 |
| 31_V | 85_I | 1.336 | 0.97 |
| 64_T | 185_A | 1.335 | 0.97 |
| 197_V | 201_I | 1.334 | 0.97 |
| 121_G | 142_G | 1.318 | 0.97 |
| 128_M | 141_I | 1.306 | 0.96 |
| 20_M | 115_F | 1.299 | 0.96 |
| 29_K | 33_K | 1.294 | 0.96 |
| 144_Y | 191_L | 1.276 | 0.96 |
| 50_A | 74_L | 1.274 | 0.96 |
| 46_G | 77_T | 1.273 | 0.96 |
| 10_P | 14_A | 1.234 | 0.95 |
| 23_V | 27_A | 1.224 | 0.94 |
| 50_A | 83_A | 1.223 | 0.94 |
| 113_M | 150_A | 1.217 | 0.94 |
| 24_L | 110_S | 1.209 | 0.94 |
| 144_Y | 148_N | 1.207 | 0.94 |
| 19_A | 111_F | 1.191 | 0.93 |
| 92_F | 106_L | 1.187 | 0.93 |
| 106_L | 110_S | 1.180 | 0.93 |
| 208_Y | 212_H | 1.179 | 0.93 |
| 120_V | 145_V | 1.178 | 0.93 |
| 9_S | 12_T | 1.176 | 0.93 |
| 14_A | 18_A | 1.172 | 0.93 |
| 7_Y | 64_T | 1.167 | 0.92 |
| 57_N | 100_D | 1.166 | 0.92 |
| 17_G | 21_V | 1.164 | 0.92 |
| 148_N | 187_M | 1.163 | 0.92 |
| 112_N | 153_A | 1.161 | 0.92 |
| 27_A | 85_I | 1.151 | 0.92 |
| 126_R | 129_L | 1.148 | 0.92 |
| 23_V | 115_F | 1.148 | 0.92 |
| 26_V | 30_K | 1.143 | 0.91 |
| 76_T | 139_S | 1.113 | 0.90 |
| 137_L | 140_A | 1.099 | 0.89 |
| 129_L | 135_K | 1.098 | 0.89 |
| 146_G | 150_A | 1.091 | 0.89 |
| 69_I | 150_A | 1.088 | 0.88 |
| 50_A | 71_A | 1.067 | 0.87 |
| 41_P | 213_H | 1.066 | 0.87 |
| 185_A | 194_A | 1.065 | 0.87 |
| 76_T | 142_G | 1.061 | 0.87 |
| 139_S | 143_G | 1.060 | 0.87 |
| 73_L | 202_T | 1.059 | 0.86 |
| 21_V | 26_V | 1.053 | 0.86 |
| 159_G | 177_Y | 1.052 | 0.86 |
| 152_L | 156_I | 1.052 | 0.86 |
| 8_L | 108_A | 1.045 | 0.85 |
| 167_T | 170_G | 1.031 | 0.84 |
| 53_I | 68_A | 1.028 | 0.84 |
| 23_V | 119_F | 1.027 | 0.84 |
| 39_D | 42_A | 1.020 | 0.84 |
| 15_V | 18_A | 1.020 | 0.84 |
| 154_T | 158_L | 1.019 | 0.83 |
| 116_I | 149_A | 1.014 | 0.83 |
| 4_P | 7_Y | 1.011 | 0.83 |
| 111_F | 116_I | 1.009 | 0.83 |
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 | |
| 4m5bA | 1 | 1 | 100 | 0.18 | Contact Map |
| 3p5nA | 2 | 0.729 | 98.6 | 0.831 | Contact Map |
| 4huqS | 1 | 0.729 | 98.5 | 0.837 | Contact Map |
| 3rlbA | 2 | 0.757 | 98.2 | 0.851 | Contact Map |
| 4rfsS | 1 | 0.757 | 98 | 0.859 | Contact Map |
| 4tkrA | 2 | 0.7804 | 98 | 0.861 | Contact Map |
| 4hzuS | 1 | 0.7243 | 97.8 | 0.865 | Contact Map |
| 4z7fA | 6 | 0 | 97.8 | 0.865 | Contact Map |
| 4dveA | 3 | 0.7944 | 97.5 | 0.874 | Contact Map |
| 4r1iA | 2 | 0.2757 | 21.6 | 0.952 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)