| 1BE9_A PDZ -force run |
| ID: | 1415846233 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 119 (112) | ||
| Sequences: | 87 (56.9) | ||
| Seq/Len: | 0.777 | ||
| Nf(neff/√len): | 5.4 |
Jackhmmer Results: (2014_04_16)
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: 0.777).
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 |
| 57_L | 94_A | 2.499 | 0.99 |
| 18_I | 42_I | 2.472 | 0.99 |
| 22_R | 42_I | 2.282 | 0.97 |
| 47_A | 63_I | 2.100 | 0.95 |
| 40_I | 79_A | 1.947 | 0.92 |
| 98_P | 101_Y | 1.674 | 0.81 |
| 29_F | 76_H | 1.641 | 0.79 |
| 39_G | 86_A | 1.595 | 0.76 |
| 33_G | 73_N | 1.569 | 0.74 |
| 20_I | 57_L | 1.543 | 0.73 |
| 53_L | 63_I | 1.495 | 0.69 |
| 42_I | 85_N | 1.483 | 0.68 |
| 31_I | 60_G | 1.373 | 0.60 |
| 8_E | 45_I | 1.343 | 0.57 |
| 41_F | 62_Q | 1.325 | 0.56 |
| 48_G | 52_D | 1.300 | 0.53 |
| 42_I | 69_V | 1.278 | 0.51 |
| 26_G | 29_F | 1.277 | 0.51 |
| 75_S | 79_A | 1.272 | 0.51 |
| 49_G | 55_G | 1.251 | 0.49 |
| 22_R | 39_G | 1.243 | 0.48 |
| 14_E | 39_G | 1.237 | 0.48 |
| 34_G | 76_H | 1.235 | 0.48 |
| 58_R | 106_A | 1.226 | 0.47 |
| 71_L | 79_A | 1.224 | 0.47 |
| 71_L | 83_L | 1.212 | 0.46 |
| 22_R | 59_K | 1.209 | 0.46 |
| 96_Y | 101_Y | 1.193 | 0.44 |
| 93_I | 110_V | 1.182 | 0.43 |
| 29_F | 57_L | 1.153 | 0.41 |
| 17_R | 78_Q | 1.153 | 0.41 |
| 25_T | 92_I | 1.144 | 0.40 |
| 37_G | 80_A | 1.128 | 0.39 |
| 14_E | 52_D | 1.123 | 0.38 |
| 20_I | 88_Q | 1.123 | 0.38 |
| 43_S | 96_Y | 1.119 | 0.38 |
| 70_D | 73_N | 1.119 | 0.38 |
| 57_L | 75_S | 1.113 | 0.37 |
| 40_I | 83_L | 1.106 | 0.37 |
| 108_S | 111_N | 1.104 | 0.37 |
| 27_L | 83_L | 1.098 | 0.36 |
| 66_V | 72_R | 1.089 | 0.36 |
| 29_F | 75_S | 1.078 | 0.35 |
| 42_I | 88_Q | 1.073 | 0.34 |
| 41_F | 65_S | 1.071 | 0.34 |
| 74_A | 105_E | 1.065 | 0.34 |
| 8_E | 20_I | 1.062 | 0.33 |
| 31_I | 83_L | 1.051 | 0.33 |
| 16_R | 62_Q | 1.033 | 0.31 |
| 63_I | 100_E | 1.028 | 0.31 |
| 108_S | 112_S | 1.015 | 0.30 |
| 7_G | 45_I | 1.015 | 0.30 |
| 21_H | 63_I | 1.007 | 0.29 |
| 30_N | 46_L | 1.006 | 0.29 |
| 39_G | 62_Q | 1.005 | 0.29 |
| 66_V | 84_K | 1.000 | 0.29 |
| 32_I | 75_S | 1.000 | 0.29 |
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 | |
| 2xkxA | 2 | 1 | 99.8 | 0.458 | Contact Map |
| 1tp5A | 1 | 0.9664 | 99.7 | 0.512 | Contact Map |
| 1um7A | 1 | 0.9412 | 99.7 | 0.522 | Contact Map |
| 1i16A | 1 | 0.9244 | 99.7 | 0.537 | Contact Map |
| 2enoA | 1 | 0.9328 | 99.7 | 0.539 | Contact Map |
| 2bygA | 1 | 0.7731 | 99.7 | 0.54 | Contact Map |
| 2jikA | 2 | 0.7983 | 99.7 | 0.541 | Contact Map |
| 1z87A | 1 | 1 | 99.7 | 0.543 | Contact Map |
| 2fneA | 3 | 0.8403 | 99.7 | 0.544 | Contact Map |
| 3i4wA | 4 | 0.8151 | 99.7 | 0.549 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)