| CDR1 |
| ID: | 1502823404 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 62 (62) | ||
| Sequences: | 1655 (1154.4) | ||
| Seq/Len: | 26.694 | ||
| Nf(neff/√len): | 146.6 |
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: 26.694).
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 |
| 51_A | 57_Y | 3.444 | 1.00 |
| 38_V | 48_N | 3.276 | 1.00 |
| 6_H | 47_T | 3.142 | 1.00 |
| 58_N | 61_K | 3.139 | 1.00 |
| 45_S | 48_N | 3.016 | 1.00 |
| 9_E | 45_S | 2.731 | 1.00 |
| 6_H | 58_N | 2.695 | 1.00 |
| 2_V | 50_L | 2.478 | 1.00 |
| 2_V | 61_K | 1.952 | 1.00 |
| 15_Y | 30_Q | 1.811 | 1.00 |
| 38_V | 41_N | 1.690 | 1.00 |
| 9_E | 43_M | 1.628 | 1.00 |
| 31_V | 39_P | 1.552 | 1.00 |
| 2_V | 58_N | 1.523 | 1.00 |
| 1_M | 50_L | 1.465 | 1.00 |
| 57_Y | 60_H | 1.368 | 0.99 |
| 48_N | 51_A | 1.362 | 0.99 |
| 35_V | 53_A | 1.359 | 0.99 |
| 33_T | 37_S | 1.311 | 0.99 |
| 10_F | 34_A | 1.257 | 0.99 |
| 35_V | 52_G | 1.196 | 0.98 |
| 49_Y | 54_Y | 1.174 | 0.98 |
| 19_G | 22_Y | 1.166 | 0.97 |
| 48_N | 52_G | 1.147 | 0.97 |
| 19_G | 23_E | 1.044 | 0.94 |
| 21_G | 25_I | 1.008 | 0.93 |
| 2_V | 57_Y | 1.003 | 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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 2p2vA | 1 | 0.7258 | 4.6 | 0.892 | Contact Map |
| 2qsfA | 1 | 0.7742 | 4.5 | 0.893 | Contact Map |
| 1zkoA | 2 | 0.2742 | 4 | 0.896 | Contact Map |
| 3rg0A | 1 | 0.2903 | 3.7 | 0.897 | Contact Map |
| 3powA | 1 | 0.3226 | 3.4 | 0.899 | Contact Map |
| 3tzuA | 4 | 0.2097 | 2.9 | 0.902 | Contact Map |
| 2yorA | 2 | 0.3387 | 2.3 | 0.907 | Contact Map |
| 4bhwA | 2 | 0.8226 | 2.1 | 0.909 | Contact Map |
| 2wqqA | 1 | 0.5323 | 2 | 0.91 | Contact Map |
| 1ua4A | 1 | 0.9032 | 2 | 0.911 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)