| 10006_1 |
| ID: | 1433410211 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 68 (66) | ||
| Sequences: | 124 (104.8) | ||
| Seq/Len: | 1.879 | ||
| Nf(neff/√len): | 12.9 |
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: 1.879).
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 |
| 9_P | 35_R | 2.566 | 1.00 |
| 45_E | 51_W | 2.291 | 1.00 |
| 19_E | 23_M | 2.110 | 0.99 |
| 36_E | 41_F | 2.020 | 0.99 |
| 41_F | 53_G | 1.715 | 0.96 |
| 13_L | 31_A | 1.703 | 0.96 |
| 10_P | 35_R | 1.680 | 0.95 |
| 15_R | 49_H | 1.531 | 0.91 |
| 49_H | 52_V | 1.473 | 0.89 |
| 39_F | 43_E | 1.467 | 0.89 |
| 24_S | 29_L | 1.434 | 0.87 |
| 2_L | 18_A | 1.394 | 0.85 |
| 13_L | 17_L | 1.357 | 0.83 |
| 6_D | 34_H | 1.339 | 0.82 |
| 28_V | 67_R | 1.335 | 0.82 |
| 16_I | 31_A | 1.303 | 0.79 |
| 42_P | 47_R | 1.235 | 0.74 |
| 2_L | 15_R | 1.234 | 0.74 |
| 24_S | 27_E | 1.179 | 0.69 |
| 36_E | 62_Y | 1.140 | 0.65 |
| 57_E | 61_T | 1.139 | 0.65 |
| 24_S | 51_W | 1.138 | 0.65 |
| 30_F | 65_M | 1.108 | 0.62 |
| 22_N | 58_T | 1.099 | 0.61 |
| 1_Y | 23_M | 1.097 | 0.61 |
| 11_E | 36_E | 1.080 | 0.59 |
| 23_M | 41_F | 1.067 | 0.58 |
| 25_A | 45_E | 1.047 | 0.56 |
| 7_M | 10_P | 1.031 | 0.54 |
| 54_N | 64_I | 1.002 | 0.51 |
| 63_R | 67_R | 1.002 | 0.51 |
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 | |
| 1pavA | 1 | 0.9853 | 98.6 | 0.538 | Contact Map |
| 1jdqA | 1 | 0.9853 | 98.6 | 0.543 | Contact Map |
| 3lvjC | 2 | 0.9853 | 98.6 | 0.548 | Contact Map |
| 3hz7A | 1 | 0.9853 | 98.6 | 0.552 | Contact Map |
| 1je3A | 1 | 0.9853 | 98.4 | 0.574 | Contact Map |
| 2lxrA | 1 | 0.9706 | 97 | 0.684 | Contact Map |
| 1okgA | 1 | 0.6618 | 93.7 | 0.751 | Contact Map |
| 3wx7A | 2 | 0.9853 | 20.5 | 0.87 | Contact Map |
| 2cc0A | 2 | 0.8382 | 18 | 0.874 | Contact Map |
| 2vkcA | 1 | 0.9412 | 17.3 | 0.875 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)