| 2npo |
| ID: | 1452701049 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 198 (191) | ||
| Sequences: | 1458 (1257.4) | ||
| Seq/Len: | 7.634 | ||
| Nf(neff/√len): | 91.0 |
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: 7.634).
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 |
| 152_N | 170_D | 3.359 | 1.00 |
| 144_A | 157_I | 3.300 | 1.00 |
| 116_G | 134_F | 2.775 | 1.00 |
| 183_Q | 189_F | 2.768 | 1.00 |
| 114_E | 133_E | 2.375 | 1.00 |
| 79_N | 99_I | 2.344 | 1.00 |
| 132_G | 151_K | 2.269 | 1.00 |
| 115_K | 133_E | 2.233 | 1.00 |
| 155_L | 159_S | 2.197 | 1.00 |
| 67_Y | 116_G | 2.172 | 1.00 |
| 162_L | 175_G | 2.055 | 1.00 |
| 119_L | 123_S | 1.996 | 1.00 |
| 9_I | 25_A | 1.978 | 1.00 |
| 8_K | 31_K | 1.946 | 1.00 |
| 64_K | 151_K | 1.934 | 1.00 |
| 96_N | 115_K | 1.913 | 1.00 |
| 150_G | 169_D | 1.907 | 1.00 |
| 71_S | 97_A | 1.856 | 1.00 |
| 64_K | 152_N | 1.845 | 1.00 |
| 94_E | 112_K | 1.844 | 1.00 |
| 19_L | 110_K | 1.840 | 1.00 |
| 24_V | 80_L | 1.809 | 1.00 |
| 153_C | 171_S | 1.808 | 1.00 |
| 117_V | 135_S | 1.792 | 1.00 |
| 64_K | 68_Q | 1.785 | 1.00 |
| 178_T | 192_V | 1.781 | 1.00 |
| 25_A | 80_L | 1.775 | 1.00 |
| 11_I | 56_A | 1.748 | 1.00 |
| 77_I | 116_G | 1.677 | 1.00 |
| 27_N | 82_H | 1.675 | 1.00 |
| 184_D | 187_G | 1.646 | 1.00 |
| 143_C | 149_I | 1.636 | 1.00 |
| 173_L | 179_L | 1.629 | 1.00 |
| 169_D | 185_E | 1.624 | 1.00 |
| 95_E | 99_I | 1.609 | 1.00 |
| 107_I | 111_A | 1.573 | 1.00 |
| 146_N | 164_N | 1.568 | 1.00 |
| 97_A | 115_K | 1.558 | 1.00 |
| 64_K | 134_F | 1.548 | 1.00 |
| 99_I | 117_V | 1.499 | 0.99 |
| 168_A | 185_E | 1.494 | 0.99 |
| 148_K | 166_S | 1.487 | 0.99 |
| 153_C | 185_E | 1.481 | 0.99 |
| 79_N | 115_K | 1.462 | 0.99 |
| 173_L | 183_Q | 1.444 | 0.99 |
| 99_I | 133_E | 1.432 | 0.99 |
| 82_H | 103_P | 1.429 | 0.99 |
| 22_E | 35_F | 1.410 | 0.99 |
| 151_K | 169_D | 1.402 | 0.99 |
| 19_L | 128_E | 1.400 | 0.99 |
| 124_V | 142_K | 1.396 | 0.99 |
| 112_K | 130_V | 1.392 | 0.99 |
| 187_G | 196_R | 1.376 | 0.99 |
| 170_D | 186_K | 1.376 | 0.99 |
| 99_I | 115_K | 1.367 | 0.99 |
| 135_S | 153_C | 1.365 | 0.99 |
| 191_G | 194_A | 1.361 | 0.99 |
| 27_N | 83_K | 1.347 | 0.99 |
| 117_V | 151_K | 1.346 | 0.99 |
| 190_V | 197_M | 1.336 | 0.98 |
| 54_F | 100_L | 1.315 | 0.98 |
| 67_Y | 134_F | 1.311 | 0.98 |
| 171_S | 183_Q | 1.296 | 0.98 |
| 20_V | 108_N | 1.295 | 0.98 |
| 189_F | 196_R | 1.294 | 0.98 |
| 18_G | 35_F | 1.291 | 0.98 |
| 70_I | 75_F | 1.264 | 0.98 |
| 130_V | 148_K | 1.251 | 0.97 |
| 127_H | 145_G | 1.245 | 0.97 |
| 157_I | 160_C | 1.236 | 0.97 |
| 166_S | 182_N | 1.232 | 0.97 |
| 133_E | 151_K | 1.218 | 0.97 |
| 177_A | 194_A | 1.215 | 0.97 |
| 18_G | 22_E | 1.210 | 0.97 |
| 79_N | 95_E | 1.201 | 0.96 |
| 90_S | 93_V | 1.199 | 0.96 |
| 168_A | 187_G | 1.184 | 0.96 |
| 142_K | 157_I | 1.180 | 0.96 |
| 129_C | 143_C | 1.175 | 0.96 |
| 141_A | 159_S | 1.175 | 0.96 |
| 14_A | 35_F | 1.169 | 0.96 |
| 168_A | 189_F | 1.145 | 0.95 |
| 137_V | 155_L | 1.143 | 0.95 |
| 54_F | 78_V | 1.140 | 0.95 |
| 84_S | 104_Y | 1.136 | 0.95 |
| 189_F | 194_A | 1.118 | 0.94 |
| 55_I | 67_Y | 1.117 | 0.94 |
| 14_A | 18_G | 1.115 | 0.94 |
| 110_K | 128_E | 1.114 | 0.94 |
| 184_D | 189_F | 1.114 | 0.94 |
| 53_F | 77_I | 1.110 | 0.94 |
| 132_G | 148_K | 1.109 | 0.94 |
| 131_I | 137_V | 1.108 | 0.94 |
| 120_N | 139_V | 1.099 | 0.93 |
| 57_I | 66_I | 1.065 | 0.92 |
| 162_L | 165_L | 1.063 | 0.92 |
| 53_F | 75_F | 1.046 | 0.91 |
| 118_I | 136_H | 1.043 | 0.91 |
| 17_H | 20_V | 1.041 | 0.91 |
| 137_V | 141_A | 1.038 | 0.91 |
| 179_L | 194_A | 1.034 | 0.90 |
| 18_G | 38_D | 1.021 | 0.90 |
| 121_T | 126_E | 1.019 | 0.89 |
| 168_A | 184_D | 1.016 | 0.89 |
| 138_S | 154_F | 1.013 | 0.89 |
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 | |
| 3bfpA | 1 | 0.9192 | 100 | 0.296 | Contact Map |
| 4m98A | 1 | 0.9596 | 100 | 0.316 | Contact Map |
| 4ea9A | 1 | 0.9798 | 100 | 0.324 | Contact Map |
| 4m9cA | 6 | 0.9697 | 100 | 0.331 | Contact Map |
| 4r36A | 2 | 0 | 99.9 | 0.558 | Contact Map |
| 3pmoA | 1 | 0.9899 | 99.9 | 0.56 | Contact Map |
| 3r8yA | 6 | 0.899 | 99.9 | 0.564 | Contact Map |
| 4mzuA | 12 | 0.6768 | 99.9 | 0.569 | Contact Map |
| 3mqgA | 6 | 0.6111 | 99.9 | 0.573 | Contact Map |
| 3vbiA | 3 | 0.6869 | 99.9 | 0.577 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)