| 1CC8A |
| ID: | 1411602551 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 72 (65) | ||
| Sequences: | 8291 (6605.7) | ||
| Seq/Len: | 127.554 | ||
| Nf(neff/√len): | 819.3 |
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: 127.554).
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 |
| 14_C | 17_C | 3.119 | 1.00 |
| 22_N | 26_T | 2.368 | 1.00 |
| 7_Q | 43_L | 2.175 | 1.00 |
| 11_V | 65_E | 2.163 | 1.00 |
| 18_S | 39_L | 2.138 | 1.00 |
| 51_P | 54_F | 1.943 | 1.00 |
| 34_K | 47_Y | 1.863 | 1.00 |
| 7_Q | 45_D | 1.825 | 1.00 |
| 5_H | 47_Y | 1.694 | 1.00 |
| 25_L | 44_V | 1.642 | 1.00 |
| 6_Y | 48_T | 1.602 | 1.00 |
| 10_V | 44_V | 1.571 | 1.00 |
| 11_V | 42_Q | 1.549 | 1.00 |
| 38_S | 41_K | 1.498 | 1.00 |
| 28_L | 58_K | 1.485 | 1.00 |
| 28_L | 31_D | 1.468 | 1.00 |
| 24_V | 62_T | 1.420 | 1.00 |
| 56_L | 66_V | 1.419 | 1.00 |
| 59_I | 65_E | 1.393 | 0.99 |
| 9_N | 67_R | 1.356 | 0.99 |
| 11_V | 67_R | 1.330 | 0.99 |
| 33_S | 47_Y | 1.322 | 0.99 |
| 53_D | 57_E | 1.283 | 0.99 |
| 60_K | 65_E | 1.194 | 0.98 |
| 6_Y | 52_Y | 1.182 | 0.98 |
| 12_M | 37_I | 1.146 | 0.97 |
| 15_S | 18_S | 1.119 | 0.96 |
| 52_Y | 56_L | 1.119 | 0.96 |
| 5_H | 45_D | 1.115 | 0.96 |
| 24_V | 58_K | 1.110 | 0.96 |
| 15_S | 19_G | 1.098 | 0.96 |
| 56_L | 60_K | 1.092 | 0.96 |
| 18_S | 22_N | 1.089 | 0.96 |
| 13_T | 20_A | 1.046 | 0.94 |
| 19_G | 23_K | 1.041 | 0.94 |
| 12_M | 21_V | 1.032 | 0.94 |
| 54_F | 57_E | 1.010 | 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 | |
| 1jk9B | 2 | 0.9722 | 98.1 | 0.153 | Contact Map |
| 1cc8A | 1 | 1 | 98.1 | 0.168 | Contact Map |
| 1qupA | 2 | 0.9861 | 98.1 | 0.169 | Contact Map |
| 2crlA | 1 | 0.9861 | 97.9 | 0.196 | Contact Map |
| 2lqbA | 1 | 0.9583 | 97.9 | 0.198 | Contact Map |
| 1osdA | 2 | 0.9444 | 97.9 | 0.201 | Contact Map |
| 2k2pA | 1 | 0.875 | 97.8 | 0.213 | Contact Map |
| 3iwlA | 1 | 0.9167 | 97.8 | 0.215 | Contact Map |
| 2roeA | 1 | 0.9028 | 97.8 | 0.216 | Contact Map |
| 2ew9A | 1 | 0.9583 | 97.8 | 0.216 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)