| 3MYM |
| ID: | 1453183535 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 67 (63) | ||
| Sequences: | 9815 (6564.2) | ||
| Seq/Len: | 155.794 | ||
| Nf(neff/√len): | 827.0 |
HHblits Results: (2015_06)
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: 155.794).
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 |
| 25_V | 41_A | 4.237 | 1.00 |
| 27_V | 35_C | 3.377 | 1.00 |
| 7_A | 12_C | 3.330 | 1.00 |
| 31_C | 34_A | 3.184 | 1.00 |
| 17_S | 23_R | 3.175 | 1.00 |
| 16_R | 27_V | 2.890 | 1.00 |
| 1_G | 4_V | 2.661 | 1.00 |
| 49_Q | 52_D | 2.463 | 1.00 |
| 16_R | 50_C | 2.452 | 1.00 |
| 28_R | 36_D | 2.070 | 1.00 |
| 16_R | 35_C | 1.946 | 1.00 |
| 29_E | 50_C | 1.840 | 1.00 |
| 9_C | 53_T | 1.839 | 1.00 |
| 8_C | 11_T | 1.766 | 1.00 |
| 10_D | 53_T | 1.694 | 1.00 |
| 15_T | 26_D | 1.646 | 1.00 |
| 37_K | 42_Y | 1.498 | 1.00 |
| 35_C | 48_C | 1.432 | 1.00 |
| 48_C | 51_Y | 1.389 | 0.99 |
| 18_Q | 48_C | 1.269 | 0.99 |
| 19_P | 23_R | 1.269 | 0.99 |
| 30_S | 36_D | 1.255 | 0.99 |
| 29_E | 35_C | 1.123 | 0.97 |
| 30_S | 34_A | 1.030 | 0.94 |
| 17_S | 24_C | 1.025 | 0.93 |
| 12_C | 15_T | 1.022 | 0.93 |
| 52_D | 62_H | 1.013 | 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 | |
| 4nzqA | 1 | 1 | 99.3 | -0.022 | Contact Map |
| 4durA | 2 | 1 | 99.3 | -0.021 | Contact Map |
| 3nxpA | 1 | 1 | 99.2 | -0.014 | Contact Map |
| 1hj8A | 1 | 1 | 99.2 | -0.011 | Contact Map |
| 1tonA | 1 | 0.9851 | 99.2 | -0.005 | Contact Map |
| 1spjA | 1 | 1 | 99.2 | 0.003 | Contact Map |
| 4i8hA | 1 | 1 | 99.2 | 0.004 | Contact Map |
| 2pkaA | 2 | 1 | 99.2 | 0.005 | Contact Map |
| 1gvzA | 1 | 1 | 99.2 | 0.006 | Contact Map |
| 1yc0A | 1 | 1 | 99.2 | 0.006 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)