| 686_1 |
| ID: | 1433411730 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 92 (88) | ||
| Sequences: | 691 (546.8) | ||
| Seq/Len: | 7.852 | ||
| Nf(neff/√len): | 58.3 |
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: 7.852).
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 |
| 74_Q | 79_R | 4.112 | 1.00 |
| 59_E | 78_N | 3.042 | 1.00 |
| 31_D | 34_K | 3.029 | 1.00 |
| 19_H | 65_Q | 2.593 | 1.00 |
| 5_R | 49_E | 2.374 | 1.00 |
| 38_L | 48_V | 2.040 | 1.00 |
| 23_D | 58_I | 1.971 | 1.00 |
| 18_F | 64_L | 1.923 | 1.00 |
| 66_D | 70_K | 1.885 | 1.00 |
| 40_W | 44_H | 1.873 | 1.00 |
| 40_W | 43_G | 1.753 | 1.00 |
| 35_A | 63_V | 1.722 | 1.00 |
| 61_K | 78_N | 1.707 | 1.00 |
| 21_V | 63_V | 1.697 | 1.00 |
| 10_R | 64_L | 1.676 | 1.00 |
| 24_D | 58_I | 1.593 | 1.00 |
| 55_N | 83_T | 1.414 | 0.99 |
| 20_L | 48_V | 1.405 | 0.99 |
| 58_I | 81_V | 1.384 | 0.99 |
| 52_L | 83_T | 1.384 | 0.99 |
| 23_D | 29_L | 1.349 | 0.99 |
| 3_R | 51_D | 1.297 | 0.98 |
| 3_R | 49_E | 1.255 | 0.98 |
| 23_D | 59_E | 1.253 | 0.98 |
| 36_V | 48_V | 1.251 | 0.98 |
| 73_W | 78_N | 1.249 | 0.98 |
| 7_V | 47_T | 1.249 | 0.98 |
| 16_Q | 66_D | 1.228 | 0.97 |
| 84_G | 87_A | 1.223 | 0.97 |
| 22_G | 27_L | 1.185 | 0.96 |
| 42_E | 47_T | 1.165 | 0.96 |
| 19_H | 35_A | 1.162 | 0.96 |
| 25_P | 29_L | 1.128 | 0.95 |
| 21_V | 32_P | 1.113 | 0.94 |
| 32_P | 63_V | 1.111 | 0.94 |
| 37_P | 65_Q | 1.109 | 0.94 |
| 21_V | 73_W | 1.104 | 0.94 |
| 19_H | 37_P | 1.079 | 0.93 |
| 39_D | 44_H | 1.078 | 0.93 |
| 17_S | 37_P | 1.068 | 0.92 |
| 41_S | 47_T | 1.063 | 0.92 |
| 59_E | 73_W | 1.060 | 0.92 |
| 12_C | 18_F | 1.038 | 0.91 |
| 12_C | 44_H | 1.033 | 0.91 |
| 19_H | 63_V | 1.032 | 0.91 |
| 12_C | 15_G | 1.003 | 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 | |
| 2vn4A | 1 | 1 | 99.9 | 0.086 | Contact Map |
| 4jcmA | 1 | 1 | 99.9 | 0.124 | Contact Map |
| 1cygA | 1 | 1 | 99.9 | 0.131 | Contact Map |
| 1gcyA | 1 | 0 | 99.9 | 0.141 | Contact Map |
| 1ac0A | 1 | 1 | 99.9 | 0.146 | Contact Map |
| 4jclA | 1 | 0.9891 | 99.9 | 0.151 | Contact Map |
| 1qhoA | 1 | 0.9891 | 99.9 | 0.153 | Contact Map |
| 1d3cA | 1 | 0.9891 | 99.9 | 0.159 | Contact Map |
| 1vemA | 1 | 0.9891 | 99.9 | 0.173 | Contact Map |
| 3bmvA | 1 | 0.9783 | 99.9 | 0.173 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)