| 1PTF_natural |
| ID: | 1496056224 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 84 (84) | ||
| Sequences: | 515 (515) | ||
| Seq/Len: | 6.131 | ||
| Nf(neff/√len): | 56.2 |
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: 6.131).
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 |
| 5_S | 60_T | 2.854 | 1.00 |
| 31_A | 69_Q | 2.579 | 1.00 |
| 65_A | 74_L | 2.298 | 1.00 |
| 22_L | 77_F | 2.172 | 1.00 |
| 30_D | 68_I | 2.141 | 1.00 |
| 1_A | 70_A | 2.104 | 1.00 |
| 4_V | 78_S | 1.818 | 1.00 |
| 30_D | 69_Q | 1.801 | 1.00 |
| 26_L | 73_V | 1.675 | 1.00 |
| 34_L | 41_C | 1.595 | 0.99 |
| 6_W | 78_S | 1.585 | 0.99 |
| 22_L | 44_P | 1.555 | 0.99 |
| 3_S | 62_R | 1.549 | 0.99 |
| 32_E | 43_N | 1.529 | 0.99 |
| 29_F | 73_V | 1.477 | 0.99 |
| 79_Q | 83_Q | 1.424 | 0.99 |
| 71_E | 75_A | 1.420 | 0.98 |
| 12_N | 18_P | 1.392 | 0.98 |
| 41_C | 64_L | 1.385 | 0.98 |
| 2_K | 71_E | 1.380 | 0.98 |
| 36_E | 62_R | 1.358 | 0.98 |
| 4_V | 75_A | 1.334 | 0.97 |
| 7_L | 60_T | 1.333 | 0.97 |
| 78_S | 82_Q | 1.308 | 0.97 |
| 22_L | 35_L | 1.304 | 0.97 |
| 36_E | 39_G | 1.294 | 0.97 |
| 42_V | 48_N | 1.275 | 0.96 |
| 10_N | 80_L | 1.247 | 0.96 |
| 48_N | 51_A | 1.246 | 0.96 |
| 32_E | 66_S | 1.245 | 0.96 |
| 23_V | 47_L | 1.228 | 0.95 |
| 75_A | 79_Q | 1.216 | 0.95 |
| 25_T | 28_P | 1.215 | 0.95 |
| 37_K | 59_D | 1.211 | 0.95 |
| 36_E | 64_L | 1.199 | 0.95 |
| 42_V | 53_L | 1.188 | 0.94 |
| 14_L | 22_L | 1.187 | 0.94 |
| 5_S | 62_R | 1.185 | 0.94 |
| 31_A | 65_A | 1.180 | 0.94 |
| 8_V | 81_A | 1.178 | 0.94 |
| 29_F | 76_A | 1.166 | 0.93 |
| 66_S | 70_A | 1.159 | 0.93 |
| 9_Q | 84_H | 1.139 | 0.92 |
| 25_T | 76_A | 1.088 | 0.90 |
| 36_E | 41_C | 1.088 | 0.90 |
| 61_I | 81_A | 1.081 | 0.89 |
| 33_L | 73_V | 1.059 | 0.88 |
| 2_K | 74_L | 1.053 | 0.88 |
| 10_N | 84_H | 1.037 | 0.87 |
| 3_S | 64_L | 1.032 | 0.86 |
| 35_L | 50_L | 1.029 | 0.86 |
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 | |
| 1kklH | 3 | 1 | 100 | 0.077 | Contact Map |
| 3le1A | 2 | 1 | 100 | 0.078 | Contact Map |
| 1ka5A | 1 | 1 | 100 | 0.079 | Contact Map |
| 3ccdA | 2 | 1 | 99.9 | 0.081 | Contact Map |
| 1sphA | 2 | 0.9881 | 99.9 | 0.082 | Contact Map |
| 1ptfA | 1 | 1 | 99.9 | 0.082 | Contact Map |
| 1y51A | 3 | 0.9881 | 99.9 | 0.083 | Contact Map |
| 3ihsA | 2 | 0.9762 | 99.9 | 0.084 | Contact Map |
| 1pchA | 1 | 0.9881 | 99.9 | 0.107 | Contact Map |
| 2jpiA | 1 | 0.9048 | 68.8 | 0.856 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)