| B_aln |
| ID: | 1420172437 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 207 (191) | ||
| Sequences: | 3909 (2970.6) | ||
| Seq/Len: | 20.466 | ||
| Nf(neff/√len): | 214.9 |
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: 20.466).
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 |
| 10_R | 14_F | 3.546 | 1.00 |
| 31_I | 98_L | 3.300 | 1.00 |
| 38_T | 88_K | 2.976 | 1.00 |
| 46_K | 58_K | 2.831 | 1.00 |
| 48_E | 56_V | 2.800 | 1.00 |
| 34_S | 89_V | 2.754 | 1.00 |
| 168_E | 172_K | 2.745 | 1.00 |
| 64_T | 93_L | 2.745 | 1.00 |
| 107_V | 145_I | 2.716 | 1.00 |
| 48_E | 58_K | 2.538 | 1.00 |
| 92_F | 96_T | 2.450 | 1.00 |
| 148_L | 152_T | 2.433 | 1.00 |
| 137_K | 171_E | 2.261 | 1.00 |
| 21_V | 105_W | 2.226 | 1.00 |
| 115_V | 146_T | 2.147 | 1.00 |
| 180_K | 184_R | 2.004 | 1.00 |
| 36_K | 41_G | 1.974 | 1.00 |
| 148_L | 168_E | 1.959 | 1.00 |
| 12_I | 16_G | 1.953 | 1.00 |
| 161_Q | 164_P | 1.929 | 1.00 |
| 51_G | 143_P | 1.896 | 1.00 |
| 18_L | 108_V | 1.844 | 1.00 |
| 32_A | 43_V | 1.838 | 1.00 |
| 128_Y | 131_Y | 1.793 | 1.00 |
| 31_I | 62_F | 1.731 | 1.00 |
| 31_I | 93_L | 1.710 | 1.00 |
| 36_K | 43_V | 1.652 | 1.00 |
| 60_L | 106_N | 1.636 | 1.00 |
| 44_F | 60_L | 1.630 | 1.00 |
| 46_K | 60_L | 1.630 | 1.00 |
| 17_S | 21_V | 1.629 | 1.00 |
| 141_M | 170_V | 1.624 | 1.00 |
| 115_V | 182_L | 1.622 | 1.00 |
| 35_I | 38_T | 1.605 | 1.00 |
| 13_D | 113_S | 1.600 | 1.00 |
| 16_G | 114_L | 1.570 | 1.00 |
| 28_L | 62_F | 1.536 | 1.00 |
| 42_P | 67_V | 1.530 | 1.00 |
| 50_L | 56_V | 1.514 | 1.00 |
| 35_I | 39_S | 1.514 | 1.00 |
| 127_K | 131_Y | 1.508 | 1.00 |
| 56_V | 122_P | 1.468 | 1.00 |
| 184_R | 188_K | 1.448 | 1.00 |
| 97_S | 154_R | 1.448 | 1.00 |
| 147_G | 150_Q | 1.426 | 1.00 |
| 30_I | 34_S | 1.406 | 0.99 |
| 9_K | 13_D | 1.399 | 0.99 |
| 24_I | 28_L | 1.376 | 0.99 |
| 153_V | 157_V | 1.367 | 0.99 |
| 20_G | 104_L | 1.366 | 0.99 |
| 17_S | 108_V | 1.363 | 0.99 |
| 89_V | 93_L | 1.354 | 0.99 |
| 14_F | 18_L | 1.351 | 0.99 |
| 20_G | 24_I | 1.335 | 0.99 |
| 149_T | 162_R | 1.334 | 0.99 |
| 105_W | 109_T | 1.333 | 0.99 |
| 187_Q | 191_K | 1.329 | 0.99 |
| 168_E | 177_L | 1.329 | 0.99 |
| 20_G | 114_L | 1.324 | 0.99 |
| 104_L | 114_L | 1.310 | 0.99 |
| 137_K | 140_E | 1.305 | 0.99 |
| 9_K | 178_D | 1.278 | 0.99 |
| 52_K | 142_K | 1.274 | 0.99 |
| 120_P | 127_K | 1.266 | 0.99 |
| 147_G | 162_R | 1.262 | 0.99 |
| 10_R | 17_S | 1.237 | 0.98 |
| 79_K | 149_T | 1.236 | 0.98 |
| 42_P | 63_R | 1.236 | 0.98 |
| 114_L | 182_L | 1.210 | 0.98 |
| 95_A | 192_R | 1.209 | 0.98 |
| 120_P | 159_W | 1.206 | 0.98 |
| 14_F | 108_V | 1.201 | 0.98 |
| 14_F | 17_S | 1.175 | 0.98 |
| 138_R | 166_D | 1.165 | 0.97 |
| 175_V | 179_I | 1.156 | 0.97 |
| 22_I | 25_S | 1.155 | 0.97 |
| 189_I | 194_S | 1.149 | 0.97 |
| 148_L | 181_I | 1.142 | 0.97 |
| 182_L | 186_I | 1.132 | 0.97 |
| 21_V | 25_S | 1.121 | 0.97 |
| 36_K | 39_S | 1.107 | 0.96 |
| 68_N | 72_I | 1.103 | 0.96 |
| 47_Q | 59_I | 1.100 | 0.96 |
| 169_Y | 178_D | 1.089 | 0.96 |
| 16_G | 20_G | 1.088 | 0.96 |
| 132_N | 135_Q | 1.088 | 0.96 |
| 97_S | 162_R | 1.084 | 0.96 |
| 45_F | 70_E | 1.082 | 0.96 |
| 150_Q | 166_D | 1.064 | 0.95 |
| 60_L | 109_T | 1.057 | 0.95 |
| 66_I | 69_A | 1.050 | 0.94 |
| 93_L | 96_T | 1.043 | 0.94 |
| 148_L | 177_L | 1.040 | 0.94 |
| 18_L | 22_I | 1.039 | 0.94 |
| 158_S | 161_Q | 1.031 | 0.94 |
| 101_L | 104_L | 1.025 | 0.93 |
| 5_N | 173_F | 1.021 | 0.93 |
| 120_P | 162_R | 1.006 | 0.93 |
| 121_V | 127_K | 1.005 | 0.93 |
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 | |
| 4f0qA | 4 | 0.5507 | 7.9 | 0.967 | Contact Map |
| 3hinA | 2 | 0.3382 | 3.5 | 0.972 | Contact Map |
| 2clyA | 2 | 0.0821 | 2.6 | 0.974 | Contact Map |
| 3wguG | 2 | 0.1691 | 2.6 | 0.974 | Contact Map |
| 2om2B | 2 | 0.1739 | 2.1 | 0.975 | Contact Map |
| 2y69E | 2 | 0.2319 | 2.1 | 0.975 | Contact Map |
| 3hd7A | 2 | 0.1498 | 2 | 0.975 | Contact Map |
| 2lk9A | 1 | 0.1159 | 1.9 | 0.976 | Contact Map |
| 2bzwB | 1 | 0.1304 | 1.8 | 0.976 | Contact Map |
| 1xqoA | 1 | 0.4879 | 1.7 | 0.976 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)