| 3e86 |
| ID: | 1461694820 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 96 (89) | ||
| Sequences: | 5084 (3292.6) | ||
| Seq/Len: | 57.124 | ||
| Nf(neff/√len): | 349.0 |
HHblits Results: (2016_02)
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: 57.124).
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 |
| 31_R | 34_D | 3.100 | 1.00 |
| 55_T | 58_G | 2.811 | 1.00 |
| 25_S | 32_P | 2.332 | 1.00 |
| 34_D | 59_K | 2.111 | 1.00 |
| 44_T | 66_I | 2.019 | 1.00 |
| 37_Y | 50_N | 1.855 | 1.00 |
| 41_V | 66_I | 1.852 | 1.00 |
| 17_L | 21_T | 1.805 | 1.00 |
| 42_T | 48_D | 1.774 | 1.00 |
| 21_T | 32_P | 1.738 | 1.00 |
| 38_F | 62_T | 1.693 | 1.00 |
| 46_V | 66_I | 1.671 | 1.00 |
| 20_G | 65_Y | 1.581 | 1.00 |
| 41_V | 50_N | 1.479 | 1.00 |
| 79_K | 83_N | 1.464 | 1.00 |
| 33_I | 63_I | 1.444 | 1.00 |
| 27_V | 57_F | 1.423 | 1.00 |
| 23_F | 61_F | 1.412 | 1.00 |
| 24_Y | 27_V | 1.338 | 0.99 |
| 27_V | 58_G | 1.305 | 0.99 |
| 32_P | 36_L | 1.283 | 0.99 |
| 27_V | 61_F | 1.275 | 0.99 |
| 34_D | 51_F | 1.273 | 0.99 |
| 38_F | 50_N | 1.269 | 0.99 |
| 60_I | 64_L | 1.255 | 0.99 |
| 42_T | 66_I | 1.225 | 0.98 |
| 86_L | 89_I | 1.221 | 0.98 |
| 20_G | 35_A | 1.202 | 0.98 |
| 39_S | 65_Y | 1.199 | 0.98 |
| 56_D | 60_I | 1.159 | 0.97 |
| 30_L | 51_F | 1.139 | 0.97 |
| 19_S | 23_F | 1.126 | 0.97 |
| 37_Y | 62_T | 1.103 | 0.96 |
| 21_T | 25_S | 1.073 | 0.95 |
| 78_H | 81_A | 1.047 | 0.94 |
| 25_S | 29_G | 1.042 | 0.94 |
| 40_V | 63_I | 1.027 | 0.94 |
| 55_T | 59_K | 1.001 | 0.92 |
| 73_V | 77_I | 1.000 | 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 | |
| 2q67A | 2 | 0.8958 | 99.6 | 0.14 | Contact Map |
| 3oufA | 2 | 1 | 99.6 | 0.153 | Contact Map |
| 3vouA | 2 | 1 | 99.5 | 0.18 | Contact Map |
| 3pjsK | 4 | 1 | 99.5 | 0.18 | Contact Map |
| 1lnqA | 8 | 0.8021 | 99.5 | 0.188 | Contact Map |
| 4twkA | 2 | 0.9688 | 99.5 | 0.195 | Contact Map |
| 4bw5A | 4 | 0.9375 | 99.5 | 0.203 | Contact Map |
| 2k1eA | 4 | 0.9792 | 99.5 | 0.204 | Contact Map |
| 4h33A | 1 | 0.9271 | 99.5 | 0.205 | Contact Map |
| 4wfeA | 2 | 0.9062 | 99.5 | 0.214 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)