| 1N88 |
| ID: | 1429462789 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 96 (93) | ||
| Sequences: | 1683 (990.4) | ||
| Seq/Len: | 18.097 | ||
| Nf(neff/√len): | 102.7 |
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: 18.097).
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 |
| 39_I | 56_T | 4.013 | 1.00 |
| 10_A | 29_W | 2.926 | 1.00 |
| 61_G | 75_D | 2.564 | 1.00 |
| 32_P | 58_H | 2.450 | 1.00 |
| 56_T | 77_K | 2.255 | 1.00 |
| 52_V | 84_A | 2.132 | 1.00 |
| 57_L | 80_I | 2.113 | 1.00 |
| 25_K | 80_I | 2.030 | 1.00 |
| 9_L | 31_H | 2.006 | 1.00 |
| 59_V | 76_R | 1.951 | 1.00 |
| 50_K | 84_A | 1.903 | 1.00 |
| 50_K | 87_Q | 1.896 | 1.00 |
| 44_E | 50_K | 1.869 | 1.00 |
| 59_V | 78_K | 1.866 | 1.00 |
| 12_V | 29_W | 1.686 | 1.00 |
| 29_W | 76_R | 1.658 | 1.00 |
| 26_Y | 89_I | 1.645 | 1.00 |
| 63_K | 72_K | 1.641 | 1.00 |
| 38_E | 41_N | 1.623 | 1.00 |
| 35_T | 38_E | 1.557 | 1.00 |
| 63_K | 70_L | 1.547 | 1.00 |
| 66_L | 69_Y | 1.525 | 1.00 |
| 55_N | 82_Q | 1.520 | 1.00 |
| 8_I | 46_A | 1.513 | 1.00 |
| 41_N | 45_T | 1.493 | 1.00 |
| 2_K | 38_E | 1.359 | 0.99 |
| 27_T | 80_I | 1.351 | 0.99 |
| 30_V | 39_I | 1.350 | 0.99 |
| 37_T | 40_K | 1.329 | 0.99 |
| 72_K | 75_D | 1.328 | 0.99 |
| 43_V | 81_V | 1.292 | 0.99 |
| 37_T | 41_N | 1.257 | 0.99 |
| 4_A | 45_T | 1.242 | 0.98 |
| 25_K | 55_N | 1.239 | 0.98 |
| 44_E | 51_V | 1.220 | 0.98 |
| 32_P | 75_D | 1.180 | 0.98 |
| 17_A | 27_T | 1.179 | 0.98 |
| 14_S | 18_Y | 1.151 | 0.97 |
| 52_V | 82_Q | 1.142 | 0.97 |
| 62_K | 73_R | 1.109 | 0.96 |
| 52_V | 55_N | 1.077 | 0.95 |
| 12_V | 27_T | 1.066 | 0.95 |
| 56_T | 79_A | 1.052 | 0.95 |
| 9_L | 29_W | 1.028 | 0.94 |
| 83_V | 87_Q | 1.028 | 0.94 |
| 57_L | 78_K | 1.024 | 0.93 |
| 43_V | 51_V | 1.019 | 0.93 |
| 29_W | 78_K | 1.010 | 0.93 |
| 51_V | 84_A | 1.007 | 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 | |
| 3j3wT | 1 | 0.9792 | 100 | 0.033 | Contact Map |
| 2zjrQ | 1 | 0.9688 | 100 | 0.059 | Contact Map |
| 4wweX | 1 | 0.9583 | 100 | 0.066 | Contact Map |
| 4uy8T | 1 | 0.9271 | 100 | 0.102 | Contact Map |
| 2go54 | 1 | 0.8229 | 99.9 | 0.222 | Contact Map |
| 2wwbK | 1 | 0.8438 | 99.9 | 0.235 | Contact Map |
| 1vq8S | 1 | 0.8125 | 99.9 | 0.266 | Contact Map |
| 4ce4X | 1 | 0.6875 | 99.9 | 0.295 | Contact Map |
| 3j7yU | 1 | 0.9375 | 99.9 | 0.316 | Contact Map |
| 3j7a1 | 1 | 0.8854 | 24.8 | 0.905 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)