| 1B6TA |
| ID: | 1411598749 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 157 (154) | ||
| Sequences: | 7164 (5113.5) | ||
| Seq/Len: | 46.519 | ||
| Nf(neff/√len): | 412.1 |
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: 46.519).
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 |
| 29_H | 64_E | 4.727 | 1.00 |
| 12_I | 53_A | 3.118 | 1.00 |
| 45_T | 48_E | 2.892 | 1.00 |
| 132_E | 136_H | 2.533 | 1.00 |
| 24_T | 62_N | 2.518 | 1.00 |
| 149_H | 153_M | 2.178 | 1.00 |
| 52_L | 151_A | 2.145 | 1.00 |
| 32_L | 63_V | 2.087 | 1.00 |
| 48_E | 155_K | 2.039 | 1.00 |
| 51_A | 54_Q | 2.039 | 1.00 |
| 129_L | 133_V | 2.038 | 1.00 |
| 3_A | 27_F | 1.991 | 1.00 |
| 50_V | 54_Q | 1.953 | 1.00 |
| 66_V | 75_F | 1.947 | 1.00 |
| 23_A | 85_I | 1.936 | 1.00 |
| 10_D | 44_F | 1.909 | 1.00 |
| 140_V | 144_L | 1.876 | 1.00 |
| 150_Q | 154_A | 1.795 | 1.00 |
| 129_L | 132_E | 1.783 | 1.00 |
| 55_Q | 151_A | 1.775 | 1.00 |
| 48_E | 151_A | 1.724 | 1.00 |
| 22_R | 25_Q | 1.710 | 1.00 |
| 146_E | 149_H | 1.702 | 1.00 |
| 133_V | 138_G | 1.694 | 1.00 |
| 17_I | 57_T | 1.675 | 1.00 |
| 2_R | 29_H | 1.643 | 1.00 |
| 21_T | 59_H | 1.642 | 1.00 |
| 141_T | 149_H | 1.611 | 1.00 |
| 51_A | 55_Q | 1.552 | 1.00 |
| 44_F | 52_L | 1.460 | 1.00 |
| 12_I | 20_V | 1.449 | 1.00 |
| 18_D | 22_R | 1.436 | 1.00 |
| 146_E | 150_Q | 1.417 | 1.00 |
| 18_D | 21_T | 1.405 | 0.99 |
| 17_I | 145_P | 1.403 | 0.99 |
| 14_N | 17_I | 1.395 | 0.99 |
| 48_E | 51_A | 1.388 | 0.99 |
| 14_N | 145_P | 1.387 | 0.99 |
| 58_A | 147_N | 1.372 | 0.99 |
| 31_I | 66_V | 1.369 | 0.99 |
| 20_V | 32_L | 1.361 | 0.99 |
| 127_S | 131_K | 1.337 | 0.99 |
| 139_D | 142_H | 1.334 | 0.99 |
| 4_I | 76_A | 1.332 | 0.99 |
| 46_L | 50_V | 1.311 | 0.99 |
| 12_I | 56_A | 1.299 | 0.99 |
| 140_V | 149_H | 1.298 | 0.99 |
| 141_T | 153_M | 1.283 | 0.99 |
| 57_T | 65_V | 1.273 | 0.99 |
| 17_I | 21_T | 1.270 | 0.99 |
| 21_T | 60_L | 1.262 | 0.99 |
| 22_R | 26_M | 1.253 | 0.99 |
| 66_V | 79_Q | 1.215 | 0.98 |
| 141_T | 146_E | 1.205 | 0.98 |
| 10_D | 43_M | 1.191 | 0.98 |
| 27_F | 30_V | 1.186 | 0.98 |
| 75_F | 79_Q | 1.182 | 0.98 |
| 8_T | 42_P | 1.172 | 0.98 |
| 55_Q | 58_A | 1.168 | 0.97 |
| 50_V | 67_G | 1.164 | 0.97 |
| 148_V | 152_L | 1.144 | 0.97 |
| 55_Q | 147_N | 1.141 | 0.97 |
| 106_H | 142_H | 1.137 | 0.97 |
| 22_R | 112_E | 1.104 | 0.96 |
| 51_A | 151_A | 1.103 | 0.96 |
| 13_T | 130_V | 1.100 | 0.96 |
| 12_I | 17_I | 1.092 | 0.96 |
| 50_V | 63_V | 1.087 | 0.96 |
| 134_A | 140_V | 1.080 | 0.95 |
| 17_I | 56_A | 1.073 | 0.95 |
| 91_V | 99_Q | 1.029 | 0.94 |
| 99_Q | 102_H | 1.027 | 0.94 |
| 21_T | 25_Q | 1.026 | 0.94 |
| 10_D | 42_P | 1.000 | 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
- 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 | |
| 1qjcA | 2 | 1 | 100 | 0.088 | Contact Map |
| 4natA | 3 | 0.9745 | 100 | 0.098 | Contact Map |
| 1vlhA | 6 | 1 | 100 | 0.1 | Contact Map |
| 3nbkA | 4 | 0.9936 | 100 | 0.108 | Contact Map |
| 1o6bA | 1 | 1 | 100 | 0.11 | Contact Map |
| 3k9wA | 1 | 1 | 100 | 0.113 | Contact Map |
| 1od6A | 1 | 0.9682 | 100 | 0.115 | Contact Map |
| 4f3rA | 3 | 0.9363 | 100 | 0.12 | Contact Map |
| 3nd5A | 6 | 0.949 | 100 | 0.121 | Contact Map |
| 3nv7A | 1 | 0.9873 | 100 | 0.13 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)