| Joana Pereira |
| ID: | 1497615008 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 99 (98) | ||
| Sequences: | 731 (730) | ||
| Seq/Len: | 7.459 | ||
| Nf(neff/√len): | 73.7 |
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: 7.459).
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 |
| 37_A | 62_I | 2.815 | 1.00 |
| 31_I | 65_N | 2.509 | 1.00 |
| 39_Y | 44_K | 2.076 | 1.00 |
| 3_R | 11_S | 1.987 | 1.00 |
| 32_V | 37_A | 1.824 | 1.00 |
| 12_I | 73_Y | 1.768 | 1.00 |
| 68_M | 74_H | 1.623 | 1.00 |
| 42_N | 45_R | 1.591 | 1.00 |
| 92_P | 95_H | 1.534 | 1.00 |
| 39_Y | 42_N | 1.466 | 0.99 |
| 12_I | 30_A | 1.420 | 0.99 |
| 10_L | 44_K | 1.400 | 0.99 |
| 65_N | 68_M | 1.385 | 0.99 |
| 93_K | 97_E | 1.376 | 0.99 |
| 91_L | 95_H | 1.369 | 0.99 |
| 17_E | 54_R | 1.347 | 0.98 |
| 7_S | 18_E | 1.342 | 0.98 |
| 3_R | 17_E | 1.323 | 0.98 |
| 32_V | 62_I | 1.315 | 0.98 |
| 27_E | 59_R | 1.303 | 0.98 |
| 84_T | 90_M | 1.278 | 0.98 |
| 34_V | 64_P | 1.261 | 0.97 |
| 95_H | 98_A | 1.224 | 0.97 |
| 3_R | 18_E | 1.219 | 0.97 |
| 90_M | 93_K | 1.190 | 0.96 |
| 29_H | 78_V | 1.177 | 0.96 |
| 10_L | 42_N | 1.171 | 0.96 |
| 48_V | 62_I | 1.170 | 0.95 |
| 33_P | 70_T | 1.167 | 0.95 |
| 20_A | 58_V | 1.146 | 0.95 |
| 30_A | 62_I | 1.133 | 0.94 |
| 13_L | 45_R | 1.121 | 0.94 |
| 90_M | 95_H | 1.081 | 0.92 |
| 32_V | 38_S | 1.080 | 0.92 |
| 45_R | 55_Q | 1.077 | 0.92 |
| 7_S | 15_L | 1.072 | 0.92 |
| 68_M | 71_P | 1.063 | 0.91 |
| 86_T | 93_K | 1.059 | 0.91 |
| 13_L | 47_A | 1.049 | 0.91 |
| 94_L | 97_E | 1.046 | 0.91 |
| 13_L | 41_L | 1.038 | 0.90 |
| 85_P | 92_P | 1.035 | 0.90 |
| 87_L | 95_H | 1.026 | 0.89 |
| 26_Q | 50_A | 1.019 | 0.89 |
| 93_K | 96_E | 1.013 | 0.89 |
| 85_P | 93_K | 1.010 | 0.88 |
| 37_A | 64_P | 1.007 | 0.88 |
| 85_P | 97_E | 1.006 | 0.88 |
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 | |
| 2bx2L | 1 | 1 | 99.5 | 0.288 | Contact Map |
| 2jvzA | 1 | 0.7475 | 37.4 | 0.843 | Contact Map |
| 2jzxA | 1 | 0.9798 | 33.3 | 0.847 | Contact Map |
| 2anrA | 1 | 0.9293 | 32.6 | 0.848 | Contact Map |
| 2hh2A | 1 | 0.7172 | 28.2 | 0.853 | Contact Map |
| 1j4wA | 1 | 0.7475 | 28.1 | 0.853 | Contact Map |
| 3n89A | 2 | 0.9192 | 24.8 | 0.857 | Contact Map |
| 3krmA | 3 | 0.7475 | 23.9 | 0.858 | Contact Map |
| 1dtjA | 4 | 0.7273 | 22.3 | 0.86 | Contact Map |
| 1ec6A | 2 | 0.7576 | 21.6 | 0.861 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)