| leafs_1ptf_fastRelax_13 |
| ID: | 1507536308 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 87 (87) | ||
| Sequences: | 487 (268.7) | ||
| Seq/Len: | 5.598 | ||
| Nf(neff/√len): | 28.8 |
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: 5.598).
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 |
| 15_D | 54_K | 3.935 | 1.00 |
| 8_P | 59_D | 3.437 | 1.00 |
| 5_T | 60_T | 2.064 | 1.00 |
| 30_V | 68_E | 2.055 | 1.00 |
| 2_L | 74_F | 2.001 | 1.00 |
| 36_D | 77_L | 1.908 | 1.00 |
| 10_A | 18_F | 1.680 | 1.00 |
| 33_I | 73_T | 1.645 | 1.00 |
| 22_L | 44_M | 1.627 | 0.99 |
| 52_S | 55_V | 1.592 | 0.99 |
| 5_T | 71_A | 1.562 | 0.99 |
| 8_P | 61_L | 1.549 | 0.99 |
| 46_V | 49_Q | 1.441 | 0.98 |
| 25_E | 38_K | 1.439 | 0.98 |
| 48_D | 52_S | 1.369 | 0.98 |
| 2_L | 71_A | 1.362 | 0.97 |
| 20_H | 47_K | 1.317 | 0.97 |
| 36_D | 41_I | 1.292 | 0.96 |
| 65_V | 74_F | 1.260 | 0.95 |
| 25_E | 76_R | 1.240 | 0.95 |
| 33_I | 44_M | 1.240 | 0.95 |
| 6_L | 48_D | 1.196 | 0.93 |
| 29_Y | 58_G | 1.193 | 0.93 |
| 55_V | 83_R | 1.111 | 0.90 |
| 59_D | 66_I | 1.110 | 0.90 |
| 73_T | 84_L | 1.091 | 0.89 |
| 60_T | 74_F | 1.080 | 0.88 |
| 79_L | 83_R | 1.080 | 0.88 |
| 49_Q | 68_E | 1.074 | 0.87 |
| 3_R | 12_N | 1.061 | 0.87 |
| 28_L | 51_A | 1.045 | 0.85 |
| 72_D | 75_R | 1.040 | 0.85 |
| 10_A | 35_L | 1.032 | 0.84 |
| 3_R | 7_V | 1.032 | 0.84 |
| 44_M | 66_I | 1.016 | 0.83 |
| 6_L | 22_L | 1.016 | 0.83 |
| 1_P | 41_I | 1.013 | 0.83 |
| 25_E | 75_R | 1.012 | 0.83 |
| 17_H | 55_V | 1.005 | 0.82 |
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 | |
| 3ccdA | 2 | 0.977 | 98.2 | 0.77 | Contact Map |
| 1kklH | 3 | 1 | 98.1 | 0.774 | Contact Map |
| 1ka5A | 1 | 0.9885 | 98 | 0.777 | Contact Map |
| 1ptfA | 1 | 1 | 98 | 0.779 | Contact Map |
| 3ihsA | 2 | 0.931 | 98 | 0.781 | Contact Map |
| 1pchA | 1 | 0.9885 | 97.9 | 0.784 | Contact Map |
| 1y51A | 3 | 0.9885 | 97.9 | 0.786 | Contact Map |
| 1sphA | 2 | 0.9885 | 97.9 | 0.786 | Contact Map |
| 3le1A | 2 | 0.977 | 97.7 | 0.793 | Contact Map |
| 3n6rA | 6 | 0.8966 | 8.9 | 0.936 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)