| 1BE9_A PDZ |
| ID: | 1415842459 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 119 (108) | ||
| Sequences: | 3445 (2283.9) | ||
| Seq/Len: | 31.898 | ||
| Nf(neff/√len): | 219.8 |
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: 31.898).
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 | 3.725 | 1.00 |
| 16_R | 96_Y | 2.885 | 1.00 |
| 48_G | 52_D | 2.546 | 1.00 |
| 65_S | 93_I | 2.493 | 1.00 |
| 40_I | 79_A | 2.311 | 1.00 |
| 76_H | 80_A | 2.117 | 1.00 |
| 33_G | 76_H | 1.986 | 1.00 |
| 19_V | 91_T | 1.941 | 1.00 |
| 19_V | 89_T | 1.858 | 1.00 |
| 17_R | 93_I | 1.833 | 1.00 |
| 32_I | 43_S | 1.798 | 1.00 |
| 62_Q | 95_Q | 1.712 | 1.00 |
| 71_L | 79_A | 1.648 | 1.00 |
| 75_S | 78_Q | 1.608 | 1.00 |
| 105_E | 108_S | 1.538 | 1.00 |
| 58_R | 96_Y | 1.484 | 1.00 |
| 34_G | 76_H | 1.478 | 1.00 |
| 25_T | 53_L | 1.382 | 0.99 |
| 47_A | 52_D | 1.369 | 0.99 |
| 43_S | 59_K | 1.341 | 0.99 |
| 71_L | 74_A | 1.339 | 0.99 |
| 74_A | 78_Q | 1.307 | 0.99 |
| 74_A | 79_A | 1.306 | 0.99 |
| 39_G | 62_Q | 1.288 | 0.99 |
| 61_D | 96_Y | 1.286 | 0.99 |
| 104_F | 108_S | 1.282 | 0.99 |
| 41_F | 62_Q | 1.247 | 0.99 |
| 21_H | 89_T | 1.228 | 0.98 |
| 107_N | 111_N | 1.222 | 0.98 |
| 17_R | 91_T | 1.210 | 0.98 |
| 43_S | 46_L | 1.181 | 0.98 |
| 65_S | 68_G | 1.146 | 0.97 |
| 7_G | 10_D | 1.136 | 0.97 |
| 42_I | 57_L | 1.135 | 0.97 |
| 44_F | 59_K | 1.135 | 0.97 |
| 31_I | 80_A | 1.129 | 0.97 |
| 26_G | 50_P | 1.124 | 0.97 |
| 46_L | 59_K | 1.114 | 0.96 |
| 21_H | 88_Q | 1.113 | 0.96 |
| 26_G | 29_F | 1.110 | 0.96 |
| 27_L | 83_L | 1.109 | 0.96 |
| 100_E | 103_R | 1.107 | 0.96 |
| 40_I | 76_H | 1.105 | 0.96 |
| 32_I | 83_L | 1.104 | 0.96 |
| 81_I | 85_N | 1.101 | 0.96 |
| 70_D | 74_A | 1.088 | 0.96 |
| 107_N | 110_V | 1.081 | 0.95 |
| 34_G | 40_I | 1.075 | 0.95 |
| 69_V | 82_A | 1.062 | 0.95 |
| 103_R | 106_A | 1.053 | 0.95 |
| 18_I | 94_A | 1.052 | 0.95 |
| 65_S | 70_D | 1.019 | 0.93 |
| 74_A | 82_A | 1.015 | 0.93 |
| 81_I | 84_K | 1.005 | 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 | |
| 2xkxA | 2 | 1 | 99.6 | 0.343 | Contact Map |
| 2jikA | 2 | 0.7983 | 99.5 | 0.373 | Contact Map |
| 1um7A | 1 | 0.9412 | 99.5 | 0.377 | Contact Map |
| 1i16A | 1 | 0.9244 | 99.5 | 0.38 | Contact Map |
| 1tp5A | 1 | 0.9664 | 99.5 | 0.382 | Contact Map |
| 2bygA | 1 | 0.7731 | 99.5 | 0.382 | Contact Map |
| 3b76A | 2 | 0.8151 | 99.5 | 0.383 | Contact Map |
| 2enoA | 1 | 0.9328 | 99.5 | 0.39 | Contact Map |
| 1whaA | 1 | 0.8235 | 99.5 | 0.39 | Contact Map |
| 1z87A | 1 | 1 | 99.5 | 0.391 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)