| asdfsdf |
| ID: | 1421663976 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 216 (171) | ||
| Sequences: | 4941 (3006.1) | ||
| Seq/Len: | 28.895 | ||
| Nf(neff/√len): | 229.9 |
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: 28.895).
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 |
| 17_G | 98_E | 4.346 | 1.00 |
| 93_R | 136_E | 3.644 | 1.00 |
| 88_Y | 148_C | 3.397 | 1.00 |
| 25_L | 159_V | 2.718 | 1.00 |
| 138_R | 142_K | 2.610 | 1.00 |
| 92_S | 95_S | 2.597 | 1.00 |
| 86_L | 99_V | 2.586 | 1.00 |
| 120_V | 162_A | 2.498 | 1.00 |
| 25_L | 87_V | 2.477 | 1.00 |
| 134_P | 138_R | 2.476 | 1.00 |
| 137_G | 141_A | 2.383 | 1.00 |
| 90_I | 124_C | 2.309 | 1.00 |
| 149_I | 165_A | 2.273 | 1.00 |
| 87_V | 122_N | 2.271 | 1.00 |
| 137_G | 148_C | 2.186 | 1.00 |
| 124_C | 157_V | 2.158 | 1.00 |
| 140_L | 144_F | 2.157 | 1.00 |
| 139_D | 143_R | 2.120 | 1.00 |
| 28_Q | 156_R | 2.109 | 1.00 |
| 83_G | 166_V | 2.065 | 1.00 |
| 88_Y | 137_G | 2.044 | 1.00 |
| 51_I | 56_V | 1.986 | 1.00 |
| 130_R | 150_E | 1.985 | 1.00 |
| 100_S | 143_R | 1.980 | 1.00 |
| 103_H | 107_L | 1.886 | 1.00 |
| 14_V | 26_T | 1.847 | 1.00 |
| 28_Q | 32_S | 1.806 | 1.00 |
| 122_N | 153_A | 1.799 | 1.00 |
| 119_V | 146_A | 1.726 | 1.00 |
| 169_A | 172_R | 1.663 | 1.00 |
| 100_S | 140_L | 1.637 | 1.00 |
| 133_Q | 136_E | 1.629 | 1.00 |
| 90_I | 121_A | 1.607 | 1.00 |
| 158_N | 161_E | 1.568 | 1.00 |
| 13_V | 81_G | 1.563 | 1.00 |
| 59_L | 167_V | 1.558 | 1.00 |
| 118_V | 149_I | 1.507 | 1.00 |
| 121_A | 137_G | 1.482 | 1.00 |
| 53_D | 168_R | 1.453 | 1.00 |
| 93_R | 97_E | 1.421 | 1.00 |
| 16_G | 22_K | 1.412 | 1.00 |
| 83_G | 170_I | 1.396 | 0.99 |
| 34_F | 154_K | 1.383 | 0.99 |
| 103_H | 144_F | 1.373 | 0.99 |
| 10_Y | 170_I | 1.372 | 0.99 |
| 104_Q | 108_R | 1.327 | 0.99 |
| 85_L | 120_V | 1.324 | 0.99 |
| 16_G | 21_G | 1.272 | 0.99 |
| 151_T | 162_A | 1.269 | 0.99 |
| 65_A | 68_E | 1.259 | 0.99 |
| 36_D | 154_K | 1.251 | 0.99 |
| 160_D | 164_I | 1.241 | 0.98 |
| 29_F | 48_K | 1.241 | 0.98 |
| 52_I | 168_R | 1.240 | 0.98 |
| 29_F | 163_F | 1.240 | 0.98 |
| 93_R | 131_Q | 1.237 | 0.98 |
| 120_V | 149_I | 1.236 | 0.98 |
| 27_I | 31_Q | 1.233 | 0.98 |
| 89_S | 92_S | 1.229 | 0.98 |
| 11_K | 80_T | 1.225 | 0.98 |
| 104_Q | 107_L | 1.224 | 0.98 |
| 99_V | 119_V | 1.217 | 0.98 |
| 90_I | 130_R | 1.215 | 0.98 |
| 96_F | 132_V | 1.178 | 0.98 |
| 147_Q | 165_A | 1.174 | 0.98 |
| 78_M | 105_Q | 1.145 | 0.97 |
| 96_F | 140_L | 1.134 | 0.97 |
| 118_V | 147_Q | 1.117 | 0.96 |
| 165_A | 168_R | 1.107 | 0.96 |
| 165_A | 169_A | 1.101 | 0.96 |
| 121_A | 150_E | 1.076 | 0.95 |
| 94_S | 97_E | 1.066 | 0.95 |
| 88_Y | 121_A | 1.066 | 0.95 |
| 9_E | 60_D | 1.060 | 0.95 |
| 137_G | 140_L | 1.054 | 0.95 |
| 61_V | 163_F | 1.052 | 0.95 |
| 90_I | 127_E | 1.034 | 0.94 |
| 85_L | 162_A | 1.031 | 0.94 |
| 149_I | 158_N | 1.015 | 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 | |
| 3cpjB | 1 | 0.7546 | 100 | 0.368 | Contact Map |
| 2g3yA | 1 | 0.7685 | 100 | 0.37 | Contact Map |
| 4ku4A | 2 | 0.7778 | 100 | 0.377 | Contact Map |
| 4cymA | 3 | 0.7917 | 100 | 0.377 | Contact Map |
| 2bovA | 1 | 0.8009 | 100 | 0.378 | Contact Map |
| 2bcgY | 1 | 0.8935 | 100 | 0.379 | Contact Map |
| 2j0vA | 4 | 0.7917 | 100 | 0.382 | Contact Map |
| 1m7bA | 1 | 0.7593 | 100 | 0.382 | Contact Map |
| 3t5gA | 1 | 0.787 | 100 | 0.386 | Contact Map |
| 2cjwA | 1 | 0.8056 | 100 | 0.388 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)