| 2rt3_trim |
| ID: | 1397940353 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 84 (75) | ||
| Sequences: | 9049 (5774.3) | ||
| Seq/Len: | 120.653 | ||
| Nf(neff/√len): | 666.8 |
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: 120.653).
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 |
| 53_N | 56_A | 2.810 | 1.00 |
| 34_P | 52_L | 2.568 | 1.00 |
| 21_T | 24_E | 2.467 | 1.00 |
| 32_F | 63_E | 2.407 | 1.00 |
| 24_E | 71_S | 2.369 | 1.00 |
| 59_K | 63_E | 2.176 | 1.00 |
| 11_V | 61_V | 2.031 | 1.00 |
| 18_N | 73_R | 1.834 | 1.00 |
| 36_D | 52_L | 1.819 | 1.00 |
| 34_P | 56_A | 1.728 | 1.00 |
| 26_R | 30_E | 1.663 | 1.00 |
| 32_F | 64_L | 1.626 | 1.00 |
| 54_I | 58_I | 1.614 | 1.00 |
| 29_L | 49_V | 1.585 | 1.00 |
| 22_E | 26_R | 1.517 | 1.00 |
| 28_D | 68_P | 1.476 | 1.00 |
| 27_E | 30_E | 1.471 | 1.00 |
| 28_D | 64_L | 1.456 | 1.00 |
| 58_I | 62_Q | 1.423 | 1.00 |
| 19_G | 71_S | 1.416 | 1.00 |
| 36_D | 50_H | 1.403 | 0.99 |
| 10_N | 50_H | 1.399 | 0.99 |
| 41_V | 46_I | 1.373 | 0.99 |
| 17_P | 20_I | 1.346 | 0.99 |
| 52_L | 56_A | 1.343 | 0.99 |
| 25_I | 47_A | 1.300 | 0.99 |
| 13_L | 29_L | 1.269 | 0.99 |
| 69_K | 72_K | 1.261 | 0.99 |
| 10_N | 37_Q | 1.250 | 0.99 |
| 37_Q | 50_H | 1.188 | 0.98 |
| 11_V | 57_A | 1.166 | 0.97 |
| 18_N | 45_N | 1.145 | 0.97 |
| 14_G | 76_Y | 1.142 | 0.97 |
| 10_N | 39_K | 1.130 | 0.97 |
| 20_I | 70_W | 1.130 | 0.97 |
| 59_K | 62_Q | 1.122 | 0.97 |
| 9_R | 54_I | 1.110 | 0.96 |
| 66_L | 74_R | 1.108 | 0.96 |
| 64_L | 68_P | 1.054 | 0.95 |
| 17_P | 71_S | 1.037 | 0.94 |
| 9_R | 57_A | 1.027 | 0.94 |
| 22_E | 38_I | 1.026 | 0.94 |
| 51_F | 60_A | 1.021 | 0.93 |
| 55_A | 59_K | 1.020 | 0.93 |
| 35_I | 49_V | 1.014 | 0.93 |
| 28_D | 70_W | 1.008 | 0.93 |
| 20_I | 71_S | 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 | |
| 2l9wA | 1 | 0.9881 | 99.6 | 0.158 | Contact Map |
| 2rt3A | 1 | 1 | 99.6 | 0.187 | Contact Map |
| 3thtA | 4 | 0.9881 | 99.5 | 0.223 | Contact Map |
| 3pgwS | 2 | 0.9881 | 99.5 | 0.225 | Contact Map |
| 3pq1A | 2 | 0.7976 | 99.5 | 0.239 | Contact Map |
| 2mjnA | 1 | 0.9524 | 99.5 | 0.244 | Contact Map |
| 2m70A | 1 | 0.9762 | 99.5 | 0.252 | Contact Map |
| 3sdeA | 1 | 0.9881 | 99.5 | 0.255 | Contact Map |
| 2hzcA | 1 | 0.9048 | 99.5 | 0.256 | Contact Map |
| 2ad9A | 1 | 1 | 99.4 | 0.259 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)