| Protein2 |
| ID: | 1515742939 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 93 (83) | ||
| Sequences: | 998 (314.7) | ||
| Seq/Len: | 12.024 | ||
| Nf(neff/√len): | 34.5 |
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: 12.024).
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 |
| 83_Y | 87_H | 2.185 | 1.00 |
| 27_S | 79_V | 2.027 | 1.00 |
| 45_V | 49_N | 1.899 | 1.00 |
| 37_R | 46_V | 1.836 | 1.00 |
| 55_Y | 63_C | 1.706 | 1.00 |
| 83_Y | 89_H | 1.624 | 1.00 |
| 46_V | 54_S | 1.613 | 1.00 |
| 39_R | 43_Q | 1.537 | 1.00 |
| 56_Y | 66_R | 1.514 | 1.00 |
| 56_Y | 63_C | 1.496 | 1.00 |
| 55_Y | 58_C | 1.398 | 0.99 |
| 58_C | 63_C | 1.381 | 0.99 |
| 59_T | 66_R | 1.363 | 0.99 |
| 37_R | 49_N | 1.361 | 0.99 |
| 22_V | 48_G | 1.352 | 0.99 |
| 43_Q | 59_T | 1.283 | 0.99 |
| 75_D | 83_Y | 1.280 | 0.99 |
| 55_Y | 65_V | 1.268 | 0.99 |
| 72_A | 78_A | 1.249 | 0.99 |
| 48_G | 52_P | 1.201 | 0.98 |
| 14_K | 31_I | 1.190 | 0.98 |
| 25_T | 32_L | 1.186 | 0.98 |
| 57_K | 91_V | 1.162 | 0.97 |
| 75_D | 78_A | 1.122 | 0.97 |
| 37_R | 54_S | 1.113 | 0.96 |
| 35_G | 85_G | 1.103 | 0.96 |
| 61_I | 68_H | 1.095 | 0.96 |
| 55_Y | 59_T | 1.094 | 0.96 |
| 52_P | 65_V | 1.092 | 0.96 |
| 44_K | 47_K | 1.088 | 0.96 |
| 13_S | 16_V | 1.084 | 0.96 |
| 22_V | 28_D | 1.077 | 0.95 |
| 24_Q | 62_G | 1.071 | 0.95 |
| 36_Y | 91_V | 1.064 | 0.95 |
| 13_S | 93_A | 1.061 | 0.95 |
| 23_V | 48_G | 1.051 | 0.94 |
| 63_C | 69_V | 1.046 | 0.94 |
| 50_P | 60_T | 1.043 | 0.94 |
| 85_G | 89_H | 1.031 | 0.94 |
| 55_Y | 67_K | 1.031 | 0.94 |
| 34_D | 40_K | 1.022 | 0.93 |
| 72_A | 77_R | 1.010 | 0.93 |
| 13_S | 31_I | 1.004 | 0.93 |
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 | |
| 2aydA | 1 | 0.8065 | 100 | 0.17 | Contact Map |
| 1wj2A | 1 | 0.7634 | 100 | 0.194 | Contact Map |
| 2rprA | 1 | 0.7742 | 83.8 | 0.877 | Contact Map |
| 3ax1A | 1 | 0.9462 | 13.6 | 0.928 | Contact Map |
| 4nm6A | 1 | 0.6774 | 7.1 | 0.936 | Contact Map |
| 3i84A | 2 | 0.7527 | 6.1 | 0.938 | Contact Map |
| 4lmgA | 4 | 0.8495 | 5.9 | 0.939 | Contact Map |
| 2pbzA | 3 | 0.7419 | 4.3 | 0.943 | Contact Map |
| 4n1iA | 1 | 0.4624 | 3.9 | 0.944 | Contact Map |
| 4criA | 2 | 0.5806 | 3.7 | 0.944 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)