| smn_tudor_domain |
| ID: | 1405072118 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 59 (57) | ||
| Sequences: | 533 (366.9) | ||
| Seq/Len: | 9.351 | ||
| Nf(neff/√len): | 48.6 |
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: 9.351).
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 |
| 22_P | 41_G | 3.727 | 1.00 |
| 15_S | 46_E | 2.589 | 1.00 |
| 11_S | 56_P | 1.831 | 1.00 |
| 18_G | 52_D | 1.776 | 1.00 |
| 4_W | 10_C | 1.762 | 1.00 |
| 39_Y | 44_N | 1.717 | 1.00 |
| 13_I | 52_D | 1.666 | 1.00 |
| 49_N | 52_D | 1.648 | 1.00 |
| 22_P | 43_G | 1.470 | 1.00 |
| 9_K | 40_T | 1.443 | 1.00 |
| 22_P | 40_T | 1.409 | 0.99 |
| 24_T | 40_T | 1.340 | 0.99 |
| 26_A | 45_R | 1.321 | 0.99 |
| 26_A | 38_V | 1.320 | 0.99 |
| 6_V | 27_S | 1.294 | 0.99 |
| 29_D | 50_L | 1.257 | 0.98 |
| 37_V | 46_E | 1.207 | 0.98 |
| 21_Y | 44_N | 1.187 | 0.97 |
| 17_D | 21_Y | 1.117 | 0.96 |
| 14_W | 22_P | 1.105 | 0.96 |
| 11_S | 22_P | 1.104 | 0.96 |
| 35_C | 48_Q | 1.100 | 0.95 |
| 9_K | 24_T | 1.085 | 0.95 |
| 38_V | 45_R | 1.072 | 0.95 |
| 10_C | 51_S | 1.060 | 0.94 |
| 4_W | 8_D | 1.045 | 0.94 |
| 15_S | 53_L | 1.013 | 0.92 |
| 5_K | 8_D | 1.013 | 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 | |
| 1g5vA | 1 | 0.9492 | 99.7 | 0.102 | Contact Map |
| 1mhnA | 1 | 1 | 99.7 | 0.105 | Contact Map |
| 3pnwC | 8 | 0.9492 | 99.7 | 0.11 | Contact Map |
| 2d9tA | 1 | 1 | 99.7 | 0.115 | Contact Map |
| 4a4fA | 1 | 1 | 99.7 | 0.116 | Contact Map |
| 1vu2E | 7 | 0 | 99.7 | 0.118 | Contact Map |
| 2eqkA | 1 | 0.9831 | 99.6 | 0.13 | Contact Map |
| 3s6wA | 1 | 0.8814 | 99.6 | 0.155 | Contact Map |
| 2digA | 1 | 0.9831 | 99.6 | 0.157 | Contact Map |
| 4b9xA | 1 | 0.9661 | 99.6 | 0.17 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)