| n |
| ID: | 1431668848 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 60 (60) | ||
| Sequences: | 73 (59.2) | ||
| Seq/Len: | 1.217 | ||
| Nf(neff/√len): | 7.6 |
Jackhmmer Results: (2015_01_07)
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: 1.217).
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 |
| 36_Q | 39_I | 2.785 | 1.00 |
| 34_K | 38_A | 1.620 | 0.88 |
| 50_A | 53_M | 1.591 | 0.86 |
| 38_A | 42_A | 1.389 | 0.74 |
| 33_Q | 37_G | 1.346 | 0.71 |
| 32_W | 37_G | 1.336 | 0.70 |
| 22_A | 56_T | 1.325 | 0.69 |
| 31_A | 35_E | 1.308 | 0.68 |
| 24_K | 27_E | 1.258 | 0.63 |
| 4_V | 9_Q | 1.253 | 0.63 |
| 26_G | 29_L | 1.218 | 0.60 |
| 15_M | 21_P | 1.211 | 0.59 |
| 25_T | 44_L | 1.209 | 0.59 |
| 26_G | 49_R | 1.201 | 0.58 |
| 22_A | 44_L | 1.176 | 0.56 |
| 44_L | 57_F | 1.158 | 0.54 |
| 42_A | 49_R | 1.148 | 0.53 |
| 11_L | 21_P | 1.137 | 0.52 |
| 27_E | 41_S | 1.130 | 0.51 |
| 42_A | 46_R | 1.125 | 0.51 |
| 28_E | 32_W | 1.121 | 0.50 |
| 41_S | 44_L | 1.116 | 0.50 |
| 44_L | 49_R | 1.110 | 0.49 |
| 27_E | 31_A | 1.104 | 0.49 |
| 8_M | 14_M | 1.104 | 0.49 |
| 11_L | 15_M | 1.103 | 0.48 |
| 40_R | 46_R | 1.099 | 0.48 |
| 3_N | 9_Q | 1.096 | 0.48 |
| 23_F | 37_G | 1.085 | 0.47 |
| 51_M | 55_R | 1.077 | 0.46 |
| 29_L | 32_W | 1.049 | 0.43 |
| 52_K | 55_R | 1.037 | 0.42 |
| 25_T | 50_A | 1.033 | 0.42 |
| 14_M | 18_H | 1.018 | 0.40 |
| 31_A | 57_F | 1.007 | 0.39 |
| 40_R | 43_A | 1.004 | 0.39 |
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 | |
| 4lmgA | 4 | 0.6 | 15.3 | 0.891 | Contact Map |
| 2ypaB | 1 | 0.85 | 10.7 | 0.898 | Contact Map |
| 1hloA | 2 | 0.85 | 10.1 | 0.9 | Contact Map |
| 2ke7A | 1 | 0.2167 | 9.9 | 0.9 | Contact Map |
| 2ypaA | 1 | 0.5833 | 8.7 | 0.902 | Contact Map |
| 2fi2A | 2 | 0.95 | 8.6 | 0.903 | Contact Map |
| 1y7qA | 2 | 0.9667 | 8.2 | 0.904 | Contact Map |
| 4e6sA | 1 | 0.8167 | 8.1 | 0.904 | Contact Map |
| 4x9tA | 1 | 0.7333 | 7.3 | 0.906 | Contact Map |
| 3lhrA | 2 | 0.95 | 6.8 | 0.907 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)