| 1soy |
| ID: | 1467500459 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 106 (106) | ||
| Sequences: | 979 (630.5) | ||
| Seq/Len: | 9.236 | ||
| Nf(neff/√len): | 61.2 |
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: 9.236).
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 |
| 59_Q | 72_D | 3.375 | 1.00 |
| 85_E | 93_Q | 2.780 | 1.00 |
| 2_N | 5_E | 2.754 | 1.00 |
| 3_D | 58_H | 2.171 | 1.00 |
| 7_H | 11_D | 1.989 | 1.00 |
| 64_T | 94_A | 1.740 | 1.00 |
| 6_F | 55_E | 1.726 | 1.00 |
| 71_F | 83_S | 1.696 | 1.00 |
| 40_T | 48_K | 1.675 | 1.00 |
| 92_E | 96_T | 1.663 | 1.00 |
| 7_H | 53_R | 1.566 | 1.00 |
| 39_L | 43_F | 1.536 | 1.00 |
| 34_I | 80_C | 1.491 | 1.00 |
| 64_T | 67_G | 1.459 | 1.00 |
| 77_E | 86_T | 1.428 | 0.99 |
| 17_I | 20_R | 1.374 | 0.99 |
| 79_I | 84_G | 1.372 | 0.99 |
| 72_D | 81_D | 1.356 | 0.99 |
| 62_L | 87_F | 1.339 | 0.99 |
| 57_L | 70_H | 1.315 | 0.99 |
| 3_D | 55_E | 1.308 | 0.99 |
| 54_Q | 57_L | 1.307 | 0.99 |
| 1_M | 5_E | 1.293 | 0.99 |
| 71_F | 85_E | 1.285 | 0.99 |
| 9_L | 73_L | 1.252 | 0.98 |
| 36_G | 53_R | 1.230 | 0.98 |
| 69_Y | 90_L | 1.225 | 0.98 |
| 73_L | 76_D | 1.217 | 0.98 |
| 63_A | 68_G | 1.211 | 0.98 |
| 69_Y | 80_C | 1.210 | 0.98 |
| 71_F | 90_L | 1.203 | 0.98 |
| 39_L | 82_R | 1.188 | 0.97 |
| 93_Q | 97_Q | 1.179 | 0.97 |
| 33_E | 55_E | 1.172 | 0.97 |
| 7_H | 55_E | 1.171 | 0.97 |
| 44_E | 47_S | 1.146 | 0.97 |
| 38_V | 48_K | 1.134 | 0.96 |
| 13_L | 91_L | 1.127 | 0.96 |
| 21_L | 24_W | 1.114 | 0.96 |
| 47_S | 68_G | 1.105 | 0.95 |
| 95_A | 105_F | 1.105 | 0.95 |
| 96_T | 103_V | 1.099 | 0.95 |
| 92_E | 105_F | 1.098 | 0.95 |
| 86_T | 89_D | 1.079 | 0.95 |
| 49_I | 94_A | 1.065 | 0.94 |
| 65_K | 68_G | 1.059 | 0.94 |
| 38_V | 52_N | 1.057 | 0.94 |
| 69_Y | 83_S | 1.055 | 0.94 |
| 49_I | 65_K | 1.037 | 0.93 |
| 54_Q | 68_G | 1.034 | 0.93 |
| 47_S | 65_K | 1.020 | 0.92 |
| 40_T | 50_I | 1.010 | 0.92 |
| 5_E | 29_D | 1.008 | 0.92 |
| 39_L | 42_T | 1.006 | 0.92 |
| 95_A | 99_A | 1.005 | 0.92 |
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 | |
| 1ew4A | 1 | 1 | 100 | -0.029 | Contact Map |
| 4jpdA | 1 | 1 | 100 | -0.017 | Contact Map |
| 3t3lA | 1 | 1 | 100 | -0.002 | Contact Map |
| 4hs5A | 2 | 0.9811 | 100 | 0.004 | Contact Map |
| 3oeqA | 1 | 0.9528 | 100 | 0.045 | Contact Map |
| 4da2A | 2 | 0.8962 | 30 | 0.903 | Contact Map |
| 1xkpB | 1 | 0.8491 | 18.6 | 0.912 | Contact Map |
| 4ydzA | 4 | 0 | 9.8 | 0.923 | Contact Map |
| 4qnlA | 1 | 0 | 7.5 | 0.927 | Contact Map |
| 1vcdA | 2 | 0.5472 | 6.8 | 0.928 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)