| test_jp |
| ID: | 1475105834 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 99 (99) | ||
| Sequences: | 1640 (238.2) | ||
| Seq/Len: | 16.566 | ||
| Nf(neff/√len): | 23.9 |
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: 16.566).
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 |
| 32_V | 47_I | 4.002 | 1.00 |
| 69_H | 89_L | 2.499 | 1.00 |
| 54_I | 82_V | 2.491 | 1.00 |
| 16_G | 63_L | 2.141 | 1.00 |
| 4_T | 7_Q | 2.087 | 1.00 |
| 25_D | 87_R | 1.962 | 1.00 |
| 48_G | 82_V | 1.623 | 1.00 |
| 10_L | 54_I | 1.594 | 1.00 |
| 12_T | 19_L | 1.567 | 1.00 |
| 54_I | 84_I | 1.502 | 1.00 |
| 24_L | 90_L | 1.489 | 1.00 |
| 9_P | 17_G | 1.470 | 1.00 |
| 25_D | 49_G | 1.446 | 1.00 |
| 6_W | 9_P | 1.437 | 1.00 |
| 33_L | 62_I | 1.393 | 0.99 |
| 46_M | 55_K | 1.354 | 0.99 |
| 51_G | 86_G | 1.353 | 0.99 |
| 36_M | 77_V | 1.332 | 0.99 |
| 25_D | 28_A | 1.330 | 0.99 |
| 73_G | 89_L | 1.320 | 0.99 |
| 86_G | 94_G | 1.317 | 0.99 |
| 71_A | 89_L | 1.304 | 0.99 |
| 22_A | 85_I | 1.217 | 0.98 |
| 15_I | 85_I | 1.197 | 0.98 |
| 30_D | 88_N | 1.173 | 0.98 |
| 24_L | 54_I | 1.172 | 0.98 |
| 84_I | 90_L | 1.165 | 0.97 |
| 27_G | 31_T | 1.159 | 0.97 |
| 63_L | 89_L | 1.156 | 0.97 |
| 57_R | 61_Q | 1.142 | 0.97 |
| 95_C | 99_F | 1.134 | 0.97 |
| 23_L | 26_T | 1.132 | 0.97 |
| 32_V | 77_V | 1.129 | 0.97 |
| 20_K | 36_M | 1.109 | 0.96 |
| 13_I | 33_L | 1.093 | 0.96 |
| 71_A | 93_I | 1.084 | 0.96 |
| 25_D | 29_D | 1.068 | 0.95 |
| 24_L | 30_D | 1.062 | 0.95 |
| 32_V | 54_I | 1.060 | 0.95 |
| 64_I | 89_L | 1.050 | 0.94 |
| 39_P | 42_W | 1.049 | 0.94 |
| 39_P | 72_I | 1.035 | 0.94 |
| 24_L | 80_T | 1.023 | 0.93 |
| 13_I | 93_I | 1.022 | 0.93 |
| 11_V | 15_I | 1.020 | 0.93 |
| 15_I | 68_G | 1.010 | 0.93 |
| 94_G | 97_L | 1.002 | 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 | |
| 3ec0A | 2 | 1 | 100 | 0.064 | Contact Map |
| 3sqfA | 2 | 0.8889 | 100 | 0.098 | Contact Map |
| 3liyA | 6 | 1 | 100 | 0.124 | Contact Map |
| 3ka2A | 1 | 0.9495 | 100 | 0.124 | Contact Map |
| 2rspA | 2 | 0.9293 | 100 | 0.125 | Contact Map |
| 2hs1A | 2 | 1 | 100 | 0.137 | Contact Map |
| 1fmbA | 1 | 0.9798 | 99.9 | 0.245 | Contact Map |
| 2hahA | 1 | 1 | 99.9 | 0.313 | Contact Map |
| 3slzA | 2 | 0.9697 | 99.9 | 0.356 | Contact Map |
| 2i1aA | 4 | 0.8889 | 98.8 | 0.662 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)