| Pab1_RRM2 |
| ID: | 1504000843 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 75 (74) | ||
| Sequences: | 31678 (19271.2) | ||
| Seq/Len: | 428.081 | ||
| Nf(neff/√len): | 2240.2 |
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: 428.081).
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 |
| 50_E | 53_A | 2.305 | 1.00 |
| 26_D | 49_E | 2.295 | 1.00 |
| 28_L | 49_E | 2.285 | 1.00 |
| 13_D | 16_A | 2.171 | 1.00 |
| 16_A | 67_N | 2.144 | 1.00 |
| 24_F | 60_A | 2.122 | 1.00 |
| 2_N | 47_H | 1.839 | 1.00 |
| 56_E | 60_A | 1.755 | 1.00 |
| 51_E | 55_K | 1.680 | 1.00 |
| 24_F | 61_L | 1.652 | 1.00 |
| 6_K | 72_Y | 1.607 | 1.00 |
| 65_L | 70_E | 1.598 | 1.00 |
| 10_P | 69_Q | 1.595 | 1.00 |
| 33_A | 43_F | 1.580 | 1.00 |
| 14_N | 18_Y | 1.570 | 1.00 |
| 29_S | 47_H | 1.467 | 1.00 |
| 20_T | 64_M | 1.448 | 1.00 |
| 26_D | 53_A | 1.437 | 1.00 |
| 3_I | 58_I | 1.429 | 1.00 |
| 63_G | 70_E | 1.414 | 1.00 |
| 9_H | 12_I | 1.398 | 0.99 |
| 61_L | 64_M | 1.376 | 0.99 |
| 18_Y | 22_S | 1.356 | 0.99 |
| 66_L | 71_I | 1.352 | 0.99 |
| 3_I | 54_A | 1.299 | 0.99 |
| 49_E | 53_A | 1.288 | 0.99 |
| 48_F | 57_A | 1.265 | 0.99 |
| 21_F | 46_V | 1.262 | 0.99 |
| 19_D | 22_S | 1.260 | 0.99 |
| 20_T | 61_L | 1.222 | 0.98 |
| 28_L | 47_H | 1.206 | 0.98 |
| 5_I | 21_F | 1.188 | 0.98 |
| 65_L | 68_G | 1.185 | 0.98 |
| 55_K | 59_D | 1.149 | 0.97 |
| 10_P | 39_K | 1.145 | 0.97 |
| 32_I | 40_S | 1.142 | 0.97 |
| 33_A | 45_F | 1.137 | 0.97 |
| 11_D | 67_N | 1.119 | 0.96 |
| 12_I | 66_L | 1.090 | 0.96 |
| 52_G | 56_E | 1.084 | 0.96 |
| 20_T | 66_L | 1.082 | 0.96 |
| 15_K | 19_D | 1.076 | 0.95 |
| 7_N | 72_Y | 1.076 | 0.95 |
| 12_I | 16_A | 1.030 | 0.94 |
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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 3pgwS | 2 | 1 | 98.9 | -0.216 | Contact Map |
| 4wikA | 2 | 1 | 98.8 | -0.199 | Contact Map |
| 3q2sC | 2 | 1 | 98.8 | -0.197 | Contact Map |
| 3n9uC | 2 | 1 | 98.8 | -0.18 | Contact Map |
| 2f3jA | 1 | 1 | 98.8 | -0.172 | Contact Map |
| 2hglA | 1 | 0.9867 | 98.7 | -0.163 | Contact Map |
| 2qfjA | 2 | 1 | 98.7 | -0.161 | Contact Map |
| 2fy1A | 1 | 1 | 98.7 | -0.161 | Contact Map |
| 1rk8A | 1 | 1 | 98.7 | -0.161 | Contact Map |
| 2m70A | 1 | 0.9867 | 98.7 | -0.156 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)