| 1fmk |
| ID: | 1486855035 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 57 (56) | ||
| Sequences: | 10020 (5603.3) | ||
| Seq/Len: | 178.929 | ||
| Nf(neff/√len): | 748.8 |
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: 178.929).
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 |
| 11_S | 18_S | 3.304 | 1.00 |
| 37_L | 46_T | 2.890 | 1.00 |
| 8_D | 20_K | 2.620 | 1.00 |
| 38_A | 49_I | 2.459 | 1.00 |
| 5_A | 19_F | 2.392 | 1.00 |
| 29_N | 37_L | 2.285 | 1.00 |
| 23_E | 40_S | 2.247 | 1.00 |
| 40_S | 43_T | 2.154 | 1.00 |
| 26_Q | 39_H | 2.130 | 1.00 |
| 39_H | 46_T | 1.979 | 1.00 |
| 49_I | 54_V | 1.969 | 1.00 |
| 2_T | 24_R | 1.932 | 1.00 |
| 36_W | 51_S | 1.769 | 1.00 |
| 19_F | 25_L | 1.735 | 1.00 |
| 2_T | 26_Q | 1.610 | 1.00 |
| 6_L | 55_A | 1.602 | 1.00 |
| 4_V | 55_A | 1.563 | 1.00 |
| 3_F | 56_P | 1.491 | 1.00 |
| 40_S | 45_Q | 1.478 | 1.00 |
| 4_V | 24_R | 1.446 | 1.00 |
| 8_D | 21_K | 1.425 | 1.00 |
| 25_L | 38_A | 1.380 | 0.99 |
| 20_K | 23_E | 1.305 | 0.99 |
| 3_F | 54_V | 1.279 | 0.99 |
| 37_L | 48_Y | 1.266 | 0.99 |
| 3_F | 27_I | 1.235 | 0.98 |
| 10_E | 18_S | 1.049 | 0.94 |
| 9_Y | 12_R | 1.039 | 0.94 |
| 35_W | 38_A | 1.034 | 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 | |
| 4n78F | 1 | 0 | 98.7 | -0.262 | Contact Map |
| 2h8hA | 1 | 0.9825 | 98.6 | -0.24 | Contact Map |
| 3pvlA | 1 | 0.9474 | 98.5 | -0.231 | Contact Map |
| 1fmkA | 1 | 1 | 98.5 | -0.223 | Contact Map |
| 4mt7A | 1 | 0 | 98.5 | -0.221 | Contact Map |
| 4xi2A | 1 | 0.9825 | 98.5 | -0.22 | Contact Map |
| 2pz1A | 1 | 0.9649 | 98.5 | -0.217 | Contact Map |
| 2dvjA | 1 | 0.9825 | 98.5 | -0.217 | Contact Map |
| 1mv3A | 1 | 1 | 98.5 | -0.212 | Contact Map |
| 1k9aA | 6 | 0.9825 | 98.4 | -0.207 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)