| pengfei tian |
| ID: | 1447222132 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 56 (56) | ||
| Sequences: | 621 (621) | ||
| Seq/Len: | 11.089 | ||
| Nf(neff/√len): | 83.0 |
HHblits Results: (2015_06)
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: 11.089).
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 |
| 23_V | 53_W | 1.720 | 1.00 |
| 28_I | 34_Q | 1.545 | 1.00 |
| 2_A | 16_A | 1.536 | 1.00 |
| 7_W | 54_P | 1.488 | 1.00 |
| 38_T | 54_P | 1.438 | 1.00 |
| 17_Y | 53_W | 1.427 | 1.00 |
| 20_S | 54_P | 1.413 | 1.00 |
| 21_M | 50_S | 1.411 | 1.00 |
| 2_A | 17_Y | 1.406 | 0.99 |
| 30_F | 42_V | 1.399 | 0.99 |
| 23_V | 42_V | 1.347 | 0.99 |
| 37_K | 52_L | 1.347 | 0.99 |
| 27_D | 36_D | 1.336 | 0.99 |
| 33_I | 43_V | 1.296 | 0.99 |
| 16_A | 54_P | 1.291 | 0.99 |
| 30_F | 33_I | 1.222 | 0.98 |
| 4_V | 21_M | 1.208 | 0.98 |
| 20_S | 52_L | 1.193 | 0.98 |
| 18_E | 52_L | 1.180 | 0.98 |
| 2_A | 29_M | 1.139 | 0.97 |
| 6_N | 11_H | 1.132 | 0.97 |
| 24_G | 38_T | 1.131 | 0.97 |
| 4_V | 43_V | 1.106 | 0.96 |
| 48_L | 51_H | 1.100 | 0.96 |
| 5_T | 44_P | 1.094 | 0.96 |
| 32_N | 44_P | 1.093 | 0.96 |
| 23_V | 27_D | 1.072 | 0.95 |
| 4_V | 11_H | 1.052 | 0.95 |
| 29_M | 43_V | 1.043 | 0.94 |
| 2_A | 24_G | 1.026 | 0.94 |
| 6_N | 23_V | 1.009 | 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 | |
| 2jwsA | 1 | 1 | 97.2 | 0.243 | Contact Map |
| 2fs1A | 1 | 1 | 97 | 0.257 | Contact Map |
| 2j5yA | 2 | 0.9643 | 95.2 | 0.373 | Contact Map |
| 1gjsA | 1 | 0.9643 | 95 | 0.381 | Contact Map |
| 1pgxA | 1 | 1 | 30.3 | 0.671 | Contact Map |
| 1pn5A | 1 | 0 | 24.8 | 0.686 | Contact Map |
| 1igdA | 1 | 1 | 22 | 0.694 | Contact Map |
| 2rpvA | 1 | 1 | 20.4 | 0.698 | Contact Map |
| 2khuA | 1 | 0 | 16.8 | 0.71 | Contact Map |
| 1l1yA | 6 | 1 | 14.4 | 0.717 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)