| Austin Day |
| ID: | 1453242864 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 109 (108) | ||
| Sequences: | 6948 (3700.3) | ||
| Seq/Len: | 64.333 | ||
| Nf(neff/√len): | 356.1 |
HHblits Results: (2015_06)
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: 64.333).
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 |
| 13_A | 78_L | 2.959 | 1.00 |
| 56_G | 59_P | 2.223 | 1.00 |
| 37_Q | 84_A | 2.154 | 1.00 |
| 36_Y | 46_L | 1.963 | 1.00 |
| 13_A | 19_V | 1.920 | 1.00 |
| 14_S | 17_D | 1.896 | 1.00 |
| 48_I | 64_G | 1.874 | 1.00 |
| 62_F | 75_I | 1.854 | 1.00 |
| 99_F | 102_G | 1.849 | 1.00 |
| 100_G | 103_T | 1.816 | 1.00 |
| 103_T | 107_M | 1.797 | 1.00 |
| 38_Q | 44_P | 1.793 | 1.00 |
| 102_G | 105_L | 1.560 | 1.00 |
| 13_A | 17_D | 1.527 | 1.00 |
| 98_T | 108_K | 1.510 | 1.00 |
| 54_L | 58_V | 1.500 | 1.00 |
| 33_I | 71_F | 1.476 | 1.00 |
| 97_I | 101_Q | 1.464 | 1.00 |
| 95_P | 98_T | 1.455 | 1.00 |
| 37_Q | 45_K | 1.426 | 1.00 |
| 97_I | 104_R | 1.423 | 1.00 |
| 18_R | 74_T | 1.391 | 0.99 |
| 104_R | 108_K | 1.376 | 0.99 |
| 98_T | 101_Q | 1.347 | 0.99 |
| 95_P | 104_R | 1.346 | 0.99 |
| 61_R | 82_D | 1.334 | 0.99 |
| 20_S | 74_T | 1.330 | 0.99 |
| 61_R | 75_I | 1.318 | 0.99 |
| 20_S | 72_T | 1.313 | 0.99 |
| 34_N | 49_H | 1.300 | 0.99 |
| 23_C | 35_W | 1.294 | 0.99 |
| 39_K | 42_K | 1.284 | 0.99 |
| 96_P | 104_R | 1.264 | 0.99 |
| 55_V | 58_V | 1.209 | 0.98 |
| 19_V | 105_L | 1.184 | 0.98 |
| 98_T | 106_E | 1.167 | 0.97 |
| 47_L | 62_F | 1.164 | 0.97 |
| 96_P | 105_L | 1.164 | 0.97 |
| 95_P | 99_F | 1.159 | 0.97 |
| 101_Q | 108_K | 1.143 | 0.97 |
| 15_V | 80_P | 1.114 | 0.96 |
| 97_I | 106_E | 1.108 | 0.96 |
| 63_S | 76_S | 1.107 | 0.96 |
| 35_W | 73_L | 1.105 | 0.96 |
| 42_K | 45_K | 1.102 | 0.96 |
| 99_F | 104_R | 1.101 | 0.96 |
| 97_I | 100_G | 1.086 | 0.96 |
| 34_N | 89_Q | 1.077 | 0.95 |
| 102_G | 107_M | 1.067 | 0.95 |
| 24_R | 70_D | 1.063 | 0.95 |
| 47_L | 58_V | 1.052 | 0.95 |
| 54_L | 60_S | 1.047 | 0.94 |
| 50_A | 71_F | 1.047 | 0.94 |
| 25_P | 33_I | 1.045 | 0.94 |
| 101_Q | 104_R | 1.033 | 0.94 |
| 46_L | 55_V | 1.031 | 0.94 |
| 99_F | 105_L | 1.026 | 0.94 |
| 63_S | 74_T | 1.016 | 0.93 |
| 18_R | 78_L | 1.016 | 0.93 |
| 32_Y | 49_H | 1.004 | 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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 1dqtA | 4 | 0.9817 | 99.8 | 0.191 | Contact Map |
| 4ut7H | 1 | 0.9817 | 99.8 | 0.21 | Contact Map |
| 4pfeA | 2 | 0 | 99.8 | 0.212 | Contact Map |
| 4aj0A | 4 | 0.9817 | 99.8 | 0.226 | Contact Map |
| 4qgyA | 2 | 0.9908 | 99.8 | 0.234 | Contact Map |
| 3k3qA | 1 | 0.9908 | 99.8 | 0.237 | Contact Map |
| 1yjdC | 1 | 0.9541 | 99.8 | 0.237 | Contact Map |
| 4n8pA | 1 | 0.9541 | 99.8 | 0.241 | Contact Map |
| 4i13B | 1 | 0.9908 | 99.8 | 0.241 | Contact Map |
| 1zvyA | 1 | 0.9725 | 99.8 | 0.242 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)