| 1an0 |
| ID: | 1506711061 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 188 (170) | ||
| Sequences: | 38465 (20728.7) | ||
| Seq/Len: | 226.265 | ||
| Nf(neff/√len): | 1589.8 |
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: 226.265).
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 |
| 21_S | 161_Q | 3.273 | 1.00 |
| 154_V | 170_E | 3.081 | 1.00 |
| 10_D | 91_N | 2.819 | 1.00 |
| 83_V | 113_G | 2.783 | 1.00 |
| 18_L | 80_C | 2.474 | 1.00 |
| 78_L | 112_V | 2.471 | 1.00 |
| 80_C | 114_T | 2.462 | 1.00 |
| 170_E | 173_L | 2.317 | 1.00 |
| 112_V | 167_V | 2.316 | 1.00 |
| 170_E | 174_A | 2.152 | 1.00 |
| 152_K | 170_E | 2.148 | 1.00 |
| 112_V | 156_C | 2.100 | 1.00 |
| 116_I | 155_E | 2.072 | 1.00 |
| 113_G | 155_E | 1.966 | 1.00 |
| 6_V | 74_T | 1.911 | 1.00 |
| 17_C | 158_A | 1.859 | 1.00 |
| 116_I | 162_K | 1.840 | 1.00 |
| 97_V | 109_F | 1.796 | 1.00 |
| 114_T | 158_A | 1.764 | 1.00 |
| 78_L | 171_A | 1.744 | 1.00 |
| 83_V | 116_I | 1.739 | 1.00 |
| 7_V | 19_L | 1.736 | 1.00 |
| 79_V | 97_V | 1.715 | 1.00 |
| 76_V | 171_A | 1.688 | 1.00 |
| 81_F | 111_L | 1.688 | 1.00 |
| 4_K | 53_G | 1.684 | 1.00 |
| 81_F | 153_Y | 1.667 | 1.00 |
| 163_G | 166_N | 1.664 | 1.00 |
| 142_E | 146_R | 1.633 | 1.00 |
| 3_I | 175_A | 1.609 | 1.00 |
| 156_C | 167_V | 1.554 | 1.00 |
| 18_L | 167_V | 1.550 | 1.00 |
| 52_L | 172_I | 1.544 | 1.00 |
| 110_L | 154_V | 1.539 | 1.00 |
| 78_L | 110_L | 1.528 | 1.00 |
| 18_L | 164_L | 1.510 | 1.00 |
| 84_V | 118_L | 1.487 | 1.00 |
| 138_P | 142_E | 1.486 | 1.00 |
| 143_K | 147_D | 1.477 | 1.00 |
| 42_T | 51_T | 1.467 | 1.00 |
| 110_L | 170_E | 1.450 | 1.00 |
| 21_S | 164_L | 1.381 | 0.99 |
| 82_S | 115_Q | 1.372 | 0.99 |
| 7_V | 78_L | 1.372 | 0.99 |
| 76_V | 110_L | 1.357 | 0.99 |
| 50_Y | 172_I | 1.286 | 0.99 |
| 81_F | 113_G | 1.283 | 0.99 |
| 97_V | 101_T | 1.282 | 0.99 |
| 82_S | 85_S | 1.269 | 0.99 |
| 141_A | 145_A | 1.242 | 0.98 |
| 86_P | 140_T | 1.232 | 0.98 |
| 165_K | 169_D | 1.221 | 0.98 |
| 79_V | 92_V | 1.214 | 0.98 |
| 5_C | 76_V | 1.204 | 0.98 |
| 22_Y | 168_F | 1.202 | 0.98 |
| 44_M | 49_P | 1.192 | 0.98 |
| 20_I | 28_P | 1.181 | 0.98 |
| 137_T | 140_T | 1.180 | 0.98 |
| 166_N | 169_D | 1.179 | 0.98 |
| 113_G | 153_Y | 1.170 | 0.97 |
| 98_P | 102_H | 1.167 | 0.97 |
| 174_A | 177_E | 1.141 | 0.97 |
| 2_T | 53_G | 1.134 | 0.97 |
| 85_S | 88_S | 1.127 | 0.97 |
| 108_P | 174_A | 1.126 | 0.97 |
| 144_L | 148_L | 1.117 | 0.96 |
| 164_L | 168_F | 1.116 | 0.96 |
| 18_L | 22_Y | 1.103 | 0.96 |
| 152_K | 174_A | 1.100 | 0.96 |
| 172_I | 176_L | 1.084 | 0.96 |
| 78_L | 167_V | 1.081 | 0.95 |
| 112_V | 154_V | 1.071 | 0.95 |
| 168_F | 171_A | 1.071 | 0.95 |
| 117_D | 157_S | 1.067 | 0.95 |
| 18_L | 158_A | 1.067 | 0.95 |
| 169_D | 173_L | 1.060 | 0.95 |
| 166_N | 170_E | 1.059 | 0.95 |
| 115_Q | 118_L | 1.040 | 0.94 |
| 77_F | 107_T | 1.035 | 0.94 |
| 4_K | 9_G | 1.030 | 0.94 |
| 99_E | 102_H | 1.030 | 0.94 |
| 56_D | 59_G | 1.027 | 0.94 |
| 143_K | 146_R | 1.016 | 0.93 |
| 87_S | 90_E | 1.013 | 0.93 |
| 4_K | 55_F | 1.011 | 0.93 |
| 83_V | 119_R | 1.003 | 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 | |
| 1mh1A | 1 | 0.9574 | 100 | 0.18 | Contact Map |
| 1m7bA | 1 | 0.9468 | 100 | 0.184 | Contact Map |
| 2atxA | 2 | 0.9468 | 100 | 0.19 | Contact Map |
| 2j0vA | 4 | 0.9415 | 100 | 0.192 | Contact Map |
| 3regA | 2 | 0.9043 | 100 | 0.192 | Contact Map |
| 2q3hA | 1 | 0.9096 | 100 | 0.194 | Contact Map |
| 4mitA | 4 | 0.9468 | 100 | 0.195 | Contact Map |
| 3bwdD | 1 | 0.8298 | 100 | 0.201 | Contact Map |
| 2j1lA | 1 | 0.8298 | 100 | 0.213 | Contact Map |
| 2wkqA | 1 | 0.9415 | 100 | 0.215 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)