| 1ayaA |
| ID: | 1507296321 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 101 (96) | ||
| Sequences: | 4610 (2615) | ||
| Seq/Len: | 48.021 | ||
| Nf(neff/√len): | 266.9 |
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: 48.021).
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 |
| 42_S | 51_H | 2.928 | 1.00 |
| 18_L | 42_S | 2.530 | 1.00 |
| 71_T | 74_E | 2.452 | 1.00 |
| 60_Y | 70_A | 2.324 | 1.00 |
| 5_F | 31_P | 2.255 | 1.00 |
| 4_W | 29_A | 2.046 | 1.00 |
| 90_N | 93_V | 2.043 | 1.00 |
| 7_P | 31_P | 2.039 | 1.00 |
| 13_E | 16_N | 1.927 | 1.00 |
| 10_T | 13_E | 1.906 | 1.00 |
| 43_V | 52_I | 1.879 | 1.00 |
| 69_F | 78_Y | 1.875 | 1.00 |
| 70_A | 74_E | 1.841 | 1.00 |
| 24_D | 45_R | 1.829 | 1.00 |
| 24_D | 46_N | 1.780 | 1.00 |
| 32_S | 40_T | 1.722 | 1.00 |
| 69_F | 79_Y | 1.656 | 1.00 |
| 40_T | 53_K | 1.628 | 1.00 |
| 60_Y | 68_K | 1.624 | 1.00 |
| 11_G | 30_R | 1.596 | 1.00 |
| 2_R | 73_A | 1.545 | 1.00 |
| 8_N | 31_P | 1.513 | 1.00 |
| 11_G | 51_H | 1.512 | 1.00 |
| 57_T | 60_Y | 1.472 | 1.00 |
| 31_P | 37_G | 1.406 | 0.99 |
| 27_F | 80_M | 1.396 | 0.99 |
| 77_Q | 80_M | 1.354 | 0.99 |
| 22_G | 26_S | 1.352 | 0.99 |
| 29_A | 76_V | 1.330 | 0.99 |
| 30_R | 42_S | 1.325 | 0.99 |
| 88_E | 91_G | 1.284 | 0.99 |
| 6_H | 9_I | 1.267 | 0.99 |
| 80_M | 84_G | 1.206 | 0.98 |
| 6_H | 17_L | 1.196 | 0.98 |
| 12_V | 15_E | 1.183 | 0.98 |
| 41_L | 54_I | 1.171 | 0.98 |
| 54_I | 61_Y | 1.163 | 0.97 |
| 92_D | 95_E | 1.149 | 0.97 |
| 14_A | 18_L | 1.144 | 0.97 |
| 40_T | 51_H | 1.111 | 0.96 |
| 35_N | 38_D | 1.108 | 0.96 |
| 15_E | 51_H | 1.089 | 0.96 |
| 26_S | 44_R | 1.081 | 0.95 |
| 6_H | 28_L | 1.064 | 0.95 |
| 19_L | 49_V | 1.060 | 0.95 |
| 29_A | 54_I | 1.057 | 0.95 |
| 38_D | 53_K | 1.050 | 0.94 |
| 90_N | 96_L | 1.026 | 0.94 |
| 73_A | 77_Q | 1.016 | 0.93 |
| 23_V | 26_S | 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 | |
| 3ps5A | 1 | 1 | 99.9 | 0.101 | Contact Map |
| 2b3oA | 1 | 0.9901 | 99.9 | 0.105 | Contact Map |
| 4fl3A | 1 | 1 | 99.9 | 0.112 | Contact Map |
| 2ozoA | 1 | 1 | 99.9 | 0.127 | Contact Map |
| 2shpA | 2 | 1 | 99.9 | 0.134 | Contact Map |
| 3eazA | 1 | 0.9505 | 99.9 | 0.138 | Contact Map |
| 2oq1A | 1 | 1 | 99.9 | 0.14 | Contact Map |
| 2ysxA | 1 | 1 | 99.9 | 0.14 | Contact Map |
| 3us4A | 1 | 0.9406 | 99.9 | 0.141 | Contact Map |
| 1rjaA | 1 | 0.9703 | 99.9 | 0.143 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)