| group 1 |
| ID: | 1459261348 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 107 (107) | ||
| Sequences: | 2418 (1706.1) | ||
| Seq/Len: | 22.598 | ||
| Nf(neff/√len): | 164.9 |
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: 22.598).
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_Q | 39_A | 3.315 | 1.00 |
| 71_T | 74_Q | 3.253 | 1.00 |
| 19_K | 88_Q | 2.821 | 1.00 |
| 10_Q | 43_S | 2.753 | 1.00 |
| 19_K | 84_M | 2.521 | 1.00 |
| 23_D | 77_N | 2.258 | 1.00 |
| 15_S | 88_Q | 2.135 | 1.00 |
| 83_S | 100_L | 2.135 | 1.00 |
| 2_I | 98_Q | 2.107 | 1.00 |
| 15_S | 19_K | 2.101 | 1.00 |
| 6_D | 47_A | 2.007 | 1.00 |
| 15_S | 18_D | 1.876 | 1.00 |
| 21_F | 35_K | 1.843 | 1.00 |
| 25_T | 77_N | 1.757 | 1.00 |
| 6_D | 10_Q | 1.624 | 1.00 |
| 12_I | 89_Q | 1.463 | 1.00 |
| 27_S | 30_F | 1.455 | 1.00 |
| 10_Q | 40_K | 1.447 | 1.00 |
| 40_K | 44_R | 1.418 | 1.00 |
| 86_L | 96_I | 1.411 | 1.00 |
| 13_T | 46_F | 1.377 | 0.99 |
| 92_G | 95_H | 1.365 | 0.99 |
| 54_P | 58_L | 1.343 | 0.99 |
| 44_R | 55_N | 1.337 | 0.99 |
| 87_Q | 100_L | 1.307 | 0.99 |
| 15_S | 89_Q | 1.306 | 0.99 |
| 18_D | 39_A | 1.280 | 0.99 |
| 83_S | 87_Q | 1.264 | 0.99 |
| 77_N | 81_Y | 1.258 | 0.99 |
| 10_Q | 14_Q | 1.236 | 0.98 |
| 87_Q | 96_I | 1.228 | 0.98 |
| 60_I | 63_E | 1.225 | 0.98 |
| 2_I | 95_H | 1.225 | 0.98 |
| 11_K | 89_Q | 1.223 | 0.98 |
| 93_F | 97_R | 1.207 | 0.98 |
| 19_K | 85_T | 1.203 | 0.98 |
| 5_Q | 8_G | 1.190 | 0.98 |
| 47_A | 55_N | 1.179 | 0.98 |
| 44_R | 59_E | 1.179 | 0.98 |
| 8_G | 11_K | 1.154 | 0.97 |
| 16_M | 78_F | 1.137 | 0.97 |
| 29_Y | 74_Q | 1.136 | 0.97 |
| 7_V | 11_K | 1.094 | 0.96 |
| 25_T | 80_F | 1.082 | 0.96 |
| 50_I | 99_L | 1.066 | 0.95 |
| 103_M | 106_Y | 1.066 | 0.95 |
| 83_S | 104_D | 1.065 | 0.95 |
| 9_I | 13_T | 1.064 | 0.95 |
| 25_T | 74_Q | 1.055 | 0.95 |
| 14_Q | 43_S | 1.043 | 0.94 |
| 16_M | 82_L | 1.034 | 0.94 |
| 84_M | 88_Q | 1.033 | 0.94 |
| 64_R | 67_Q | 1.033 | 0.94 |
| 99_L | 103_M | 1.018 | 0.93 |
| 25_T | 73_V | 1.014 | 0.93 |
| 16_M | 20_I | 1.009 | 0.93 |
| 6_D | 43_S | 1.006 | 0.93 |
| 23_D | 81_Y | 1.006 | 0.93 |
| 39_A | 43_S | 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
- 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 | |
| 4uurA | 2 | 0 | 99.9 | 0.074 | Contact Map |
| 1dlyA | 1 | 1 | 99.9 | 0.085 | Contact Map |
| 2kscA | 1 | 1 | 99.9 | 0.101 | Contact Map |
| 4c0nA | 1 | 0.9907 | 99.9 | 0.102 | Contact Map |
| 1s69A | 1 | 1 | 99.9 | 0.104 | Contact Map |
| 1dlwA | 1 | 1 | 99.9 | 0.114 | Contact Map |
| 4nk2A | 2 | 0.9813 | 99.9 | 0.116 | Contact Map |
| 2ig3A | 2 | 0.972 | 99.9 | 0.116 | Contact Map |
| 3aq9A | 2 | 1 | 99.9 | 0.124 | Contact Map |
| 4uzvA | 1 | 1 | 99.9 | 0.135 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)