| Chain 2 |
| ID: | 1450296191 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 220 (211) | ||
| Sequences: | 9952 (6778.1) | ||
| Seq/Len: | 47.166 | ||
| Nf(neff/√len): | 466.6 |
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: 47.166).
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 |
| 12_V | 86_L | 4.614 | 1.00 |
| 162_N | 204_N | 3.631 | 1.00 |
| 67_R | 90_D | 3.038 | 1.00 |
| 147_C | 203_C | 2.919 | 1.00 |
| 17_S | 84_N | 2.781 | 1.00 |
| 13_Q | 16_G | 2.714 | 1.00 |
| 22_C | 96_C | 2.705 | 1.00 |
| 37_V | 97_S | 2.580 | 1.00 |
| 18_L | 116_V | 2.549 | 1.00 |
| 20_L | 116_V | 2.495 | 1.00 |
| 144_A | 190_T | 2.400 | 1.00 |
| 19_R | 82_Q | 2.372 | 1.00 |
| 12_V | 18_L | 2.350 | 1.00 |
| 17_S | 82_Q | 2.300 | 1.00 |
| 38_R | 92_A | 2.235 | 1.00 |
| 144_A | 188_V | 2.210 | 1.00 |
| 207_H | 210_S | 2.185 | 1.00 |
| 93_V | 115_L | 2.124 | 1.00 |
| 19_R | 80_Y | 2.010 | 1.00 |
| 149_V | 159_V | 1.986 | 1.00 |
| 26_G | 32_T | 1.909 | 1.00 |
| 36_W | 81_L | 1.902 | 1.00 |
| 146_G | 188_V | 1.825 | 1.00 |
| 21_S | 80_Y | 1.791 | 1.00 |
| 95_Y | 113_G | 1.786 | 1.00 |
| 162_N | 202_I | 1.780 | 1.00 |
| 69_T | 84_N | 1.735 | 1.00 |
| 100_G | 103_G | 1.718 | 1.00 |
| 93_V | 113_G | 1.676 | 1.00 |
| 71_S | 82_Q | 1.664 | 1.00 |
| 142_T | 192_P | 1.660 | 1.00 |
| 206_N | 211_N | 1.655 | 1.00 |
| 159_V | 187_S | 1.653 | 1.00 |
| 161_W | 187_S | 1.641 | 1.00 |
| 158_T | 206_N | 1.634 | 1.00 |
| 35_H | 99_W | 1.623 | 1.00 |
| 24_A | 34_I | 1.606 | 1.00 |
| 38_R | 94_Y | 1.603 | 1.00 |
| 142_T | 190_T | 1.594 | 1.00 |
| 95_Y | 111_G | 1.586 | 1.00 |
| 20_L | 36_W | 1.584 | 1.00 |
| 35_H | 97_S | 1.574 | 1.00 |
| 17_S | 85_S | 1.568 | 1.00 |
| 9_G | 115_L | 1.543 | 1.00 |
| 69_T | 82_Q | 1.515 | 1.00 |
| 163_S | 199_Q | 1.511 | 1.00 |
| 160_S | 206_N | 1.489 | 1.00 |
| 148_L | 186_S | 1.465 | 1.00 |
| 71_S | 78_T | 1.464 | 1.00 |
| 160_S | 204_N | 1.430 | 1.00 |
| 163_S | 201_Y | 1.388 | 0.99 |
| 91_T | 118_V | 1.380 | 0.99 |
| 38_R | 90_D | 1.372 | 0.99 |
| 34_I | 96_C | 1.348 | 0.99 |
| 14_P | 88_A | 1.319 | 0.99 |
| 204_N | 213_K | 1.318 | 0.99 |
| 145_L | 161_W | 1.290 | 0.99 |
| 204_N | 211_N | 1.278 | 0.99 |
| 99_W | 104_F | 1.273 | 0.99 |
| 163_S | 166_L | 1.272 | 0.99 |
| 138_T | 194_S | 1.270 | 0.99 |
| 48_V | 55_N | 1.258 | 0.99 |
| 68_F | 83_M | 1.245 | 0.98 |
| 37_V | 95_Y | 1.233 | 0.98 |
| 151_D | 159_V | 1.227 | 0.98 |
| 86_L | 91_T | 1.217 | 0.98 |
| 149_V | 205_V | 1.217 | 0.98 |
| 11_L | 117_T | 1.206 | 0.98 |
| 23_A | 78_T | 1.192 | 0.98 |
| 86_L | 118_V | 1.192 | 0.98 |
| 10_G | 18_L | 1.188 | 0.98 |
| 21_S | 78_T | 1.185 | 0.98 |
| 24_A | 79_A | 1.184 | 0.98 |
| 135_S | 138_T | 1.172 | 0.98 |
| 11_L | 119_S | 1.171 | 0.98 |
| 83_M | 90_D | 1.162 | 0.97 |
| 34_I | 79_A | 1.155 | 0.97 |
| 17_S | 86_L | 1.145 | 0.97 |
| 30_K | 100_G | 1.141 | 0.97 |
| 142_T | 193_S | 1.123 | 0.97 |
| 149_V | 153_F | 1.122 | 0.97 |
| 146_G | 186_S | 1.117 | 0.96 |
| 20_L | 114_T | 1.104 | 0.96 |
| 193_S | 201_Y | 1.097 | 0.96 |
| 39_Q | 93_V | 1.090 | 0.96 |
| 13_Q | 119_S | 1.090 | 0.96 |
| 191_V | 198_T | 1.081 | 0.95 |
| 164_G | 167_T | 1.080 | 0.95 |
| 161_W | 189_V | 1.078 | 0.95 |
| 24_A | 98_R | 1.076 | 0.95 |
| 64_V | 68_F | 1.076 | 0.95 |
| 9_G | 114_T | 1.069 | 0.95 |
| 151_D | 155_E | 1.063 | 0.95 |
| 175_A | 198_T | 1.063 | 0.95 |
| 33_Y | 99_W | 1.063 | 0.95 |
| 153_F | 157_V | 1.062 | 0.95 |
| 147_C | 161_W | 1.059 | 0.95 |
| 164_G | 202_I | 1.052 | 0.95 |
| 9_G | 117_T | 1.050 | 0.94 |
| 10_G | 21_S | 1.049 | 0.94 |
| 134_S | 137_S | 1.041 | 0.94 |
| 143_A | 191_V | 1.039 | 0.94 |
| 45_L | 48_V | 1.031 | 0.94 |
| 194_S | 201_Y | 1.026 | 0.94 |
| 210_S | 213_K | 1.026 | 0.94 |
| 39_Q | 95_Y | 1.025 | 0.93 |
| 18_L | 114_T | 1.007 | 0.93 |
| 81_L | 90_D | 1.006 | 0.93 |
| 26_G | 30_K | 1.001 | 0.92 |
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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 4ydjH | 2 | 0 | 99.9 | 0.137 | Contact Map |
| 4nzuH | 1 | 0.9909 | 99.9 | 0.139 | Contact Map |
| 1c1eH | 1 | 0.9909 | 99.9 | 0.143 | Contact Map |
| 3tv3H | 1 | 0.9864 | 99.9 | 0.147 | Contact Map |
| 1mjuH | 1 | 0.9455 | 99.9 | 0.148 | Contact Map |
| 4jamH | 2 | 0.9864 | 99.9 | 0.149 | Contact Map |
| 3qhzH | 2 | 0.9682 | 99.9 | 0.15 | Contact Map |
| 3t65B | 1 | 0.9955 | 99.9 | 0.152 | Contact Map |
| 3lizH | 1 | 0.9636 | 99.9 | 0.154 | Contact Map |
| 3baeH | 1 | 0.9636 | 99.9 | 0.158 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)