| 1u61 |
| ID: | 1452700700 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 138 (130) | ||
| Sequences: | 945 (706.1) | ||
| Seq/Len: | 7.269 | ||
| Nf(neff/√len): | 61.9 |
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: 7.269).
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 |
| 59_V | 76_L | 3.527 | 1.00 |
| 56_A | 98_H | 3.112 | 1.00 |
| 73_E | 77_R | 2.757 | 1.00 |
| 31_L | 46_G | 2.519 | 1.00 |
| 76_L | 101_A | 2.482 | 1.00 |
| 91_T | 95_T | 2.397 | 1.00 |
| 60_Y | 98_H | 2.312 | 1.00 |
| 14_A | 32_L | 2.094 | 1.00 |
| 74_A | 77_R | 2.089 | 1.00 |
| 87_V | 93_V | 2.002 | 1.00 |
| 68_L | 105_L | 2.001 | 1.00 |
| 30_H | 126_I | 1.982 | 1.00 |
| 26_Y | 122_V | 1.903 | 1.00 |
| 17_Y | 24_E | 1.741 | 1.00 |
| 12_S | 35_G | 1.721 | 1.00 |
| 58_V | 125_A | 1.675 | 1.00 |
| 38_R | 41_Q | 1.659 | 1.00 |
| 61_H | 128_V | 1.652 | 1.00 |
| 21_A | 24_E | 1.598 | 1.00 |
| 67_F | 124_K | 1.598 | 1.00 |
| 102_F | 106_I | 1.579 | 1.00 |
| 84_S | 97_R | 1.579 | 1.00 |
| 106_I | 121_I | 1.540 | 1.00 |
| 106_I | 122_V | 1.534 | 1.00 |
| 92_D | 95_T | 1.523 | 0.99 |
| 93_V | 97_R | 1.500 | 0.99 |
| 76_L | 105_L | 1.486 | 0.99 |
| 45_L | 48_S | 1.484 | 0.99 |
| 59_V | 101_A | 1.459 | 0.99 |
| 63_L | 73_E | 1.419 | 0.99 |
| 26_Y | 118_L | 1.417 | 0.99 |
| 118_L | 122_V | 1.403 | 0.99 |
| 76_L | 98_H | 1.401 | 0.99 |
| 22_V | 106_I | 1.394 | 0.99 |
| 23_Y | 108_Y | 1.390 | 0.99 |
| 29_Y | 110_H | 1.370 | 0.99 |
| 88_P | 91_T | 1.316 | 0.98 |
| 12_S | 75_V | 1.307 | 0.98 |
| 40_N | 44_R | 1.286 | 0.98 |
| 102_F | 125_A | 1.264 | 0.97 |
| 90_N | 95_T | 1.257 | 0.97 |
| 79_G | 82_A | 1.236 | 0.97 |
| 51_S | 91_T | 1.229 | 0.97 |
| 29_Y | 33_Q | 1.203 | 0.96 |
| 68_L | 76_L | 1.192 | 0.96 |
| 18_M | 110_H | 1.149 | 0.95 |
| 124_K | 127_A | 1.143 | 0.94 |
| 117_R | 120_E | 1.141 | 0.94 |
| 5_I | 9_Q | 1.130 | 0.94 |
| 59_V | 102_F | 1.099 | 0.93 |
| 86_T | 97_R | 1.086 | 0.92 |
| 23_Y | 49_F | 1.082 | 0.92 |
| 106_I | 118_L | 1.081 | 0.92 |
| 79_G | 104_A | 1.070 | 0.91 |
| 88_P | 92_D | 1.067 | 0.91 |
| 109_H | 114_N | 1.064 | 0.91 |
| 67_F | 121_I | 1.054 | 0.91 |
| 36_K | 43_H | 1.049 | 0.90 |
| 24_E | 28_R | 1.043 | 0.90 |
| 47_T | 88_P | 1.034 | 0.90 |
| 75_V | 104_A | 1.029 | 0.89 |
| 26_Y | 106_I | 1.022 | 0.89 |
| 61_H | 133_E | 1.015 | 0.88 |
| 51_S | 95_T | 1.005 | 0.88 |
| 100_T | 105_L | 1.003 | 0.88 |
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 | |
| 1u61A | 1 | 0.9203 | 100 | 0.429 | Contact Map |
| 2gslA | 6 | 0.9493 | 100 | 0.456 | Contact Map |
| 4ounA | 1 | 0.9058 | 99.9 | 0.461 | Contact Map |
| 3o2rA | 2 | 0.8478 | 99.5 | 0.674 | Contact Map |
| 2a11A | 1 | 0.913 | 99.5 | 0.69 | Contact Map |
| 3n3wA | 2 | 0.8551 | 99.4 | 0.708 | Contact Map |
| 2nugA | 2 | 0.8623 | 99.3 | 0.709 | Contact Map |
| 1vw49 | 1 | 0.8406 | 99.3 | 0.714 | Contact Map |
| 1o0wA | 2 | 0.913 | 99.3 | 0.715 | Contact Map |
| 3rv1A | 2 | 0.8623 | 99.2 | 0.727 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)