| d2qe7c1 |
| ID: | 1448598730 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 68 (68) | ||
| Sequences: | 1531 (627.5) | ||
| Seq/Len: | 22.515 | ||
| Nf(neff/√len): | 76.1 |
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: 22.515).
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 |
| 15_V | 47_V | 4.577 | 1.00 |
| 1_E | 64_R | 3.543 | 1.00 |
| 21_V | 37_A | 3.492 | 1.00 |
| 5_V | 56_I | 3.338 | 1.00 |
| 27_L | 47_V | 2.784 | 1.00 |
| 27_L | 62_V | 2.643 | 1.00 |
| 28_E | 63_K | 2.464 | 1.00 |
| 21_V | 27_L | 2.114 | 1.00 |
| 1_E | 20_K | 1.929 | 1.00 |
| 29_F | 35_G | 1.876 | 1.00 |
| 14_R | 44_N | 1.861 | 1.00 |
| 13_A | 29_F | 1.709 | 1.00 |
| 33_V | 51_G | 1.486 | 1.00 |
| 26_L | 65_T | 1.424 | 1.00 |
| 7_Q | 14_R | 1.406 | 0.99 |
| 30_E | 60_T | 1.395 | 0.99 |
| 52_P | 55_E | 1.362 | 0.99 |
| 14_R | 41_E | 1.260 | 0.99 |
| 57_R | 60_T | 1.217 | 0.98 |
| 6_I | 44_N | 1.196 | 0.98 |
| 33_V | 55_E | 1.159 | 0.97 |
| 24_G | 48_V | 1.158 | 0.97 |
| 8_V | 53_Y | 1.153 | 0.97 |
| 28_E | 34_M | 1.146 | 0.97 |
| 10_D | 58_E | 1.143 | 0.97 |
| 9_G | 13_A | 1.140 | 0.97 |
| 31_N | 55_E | 1.137 | 0.97 |
| 34_M | 67_R | 1.104 | 0.96 |
| 24_G | 36_M | 1.093 | 0.96 |
| 16_H | 44_N | 1.076 | 0.95 |
| 6_I | 16_H | 1.047 | 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
- 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 | |
| 2ck3A | 3 | 1 | 99.5 | 0.303 | Contact Map |
| 1fx0A | 1 | 1 | 99.5 | 0.306 | Contact Map |
| 2qe7A | 3 | 1 | 99.4 | 0.331 | Contact Map |
| 3oaaA | 12 | 1 | 99.4 | 0.346 | Contact Map |
| 2r9vA | 1 | 1 | 99.4 | 0.346 | Contact Map |
| 3mfyA | 1 | 0.1618 | 98.9 | 0.473 | Contact Map |
| 3gqbB | 2 | 1 | 98.9 | 0.48 | Contact Map |
| 2c61A | 2 | 0.6912 | 98.8 | 0.483 | Contact Map |
| 3vr4D | 3 | 1 | 98.8 | 0.484 | Contact Map |
| 3j9tA | 3 | 0 | 98.7 | 0.503 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)