| z15-jck |
| ID: | 1487816352 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 127 (121) | ||
| Sequences: | 403 (273.7) | ||
| Seq/Len: | 3.331 | ||
| Nf(neff/√len): | 24.9 |
Jackhmmer Results: (2016_04)
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: 3.331).
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_M | 8_E | 2.615 | 1.00 |
| 12_A | 98_I | 2.105 | 1.00 |
| 99_D | 106_Q | 1.783 | 0.99 |
| 63_H | 93_D | 1.711 | 0.99 |
| 16_I | 71_V | 1.675 | 0.99 |
| 8_E | 69_D | 1.542 | 0.97 |
| 85_D | 98_I | 1.530 | 0.97 |
| 8_E | 91_P | 1.437 | 0.95 |
| 44_Y | 80_G | 1.431 | 0.95 |
| 47_H | 59_F | 1.372 | 0.93 |
| 9_I | 41_K | 1.371 | 0.93 |
| 61_C | 93_D | 1.346 | 0.93 |
| 47_H | 50_P | 1.342 | 0.92 |
| 56_G | 60_R | 1.330 | 0.92 |
| 111_G | 114_K | 1.330 | 0.92 |
| 65_G | 95_S | 1.302 | 0.91 |
| 16_I | 68_V | 1.292 | 0.90 |
| 5_M | 69_D | 1.255 | 0.89 |
| 64_I | 81_L | 1.254 | 0.89 |
| 16_I | 35_E | 1.246 | 0.88 |
| 63_H | 95_S | 1.242 | 0.88 |
| 57_S | 105_Y | 1.233 | 0.87 |
| 25_P | 35_E | 1.229 | 0.87 |
| 91_P | 105_Y | 1.225 | 0.87 |
| 65_G | 93_D | 1.225 | 0.87 |
| 49_Y | 55_K | 1.221 | 0.87 |
| 6_Q | 41_K | 1.211 | 0.86 |
| 26_R | 29_V | 1.204 | 0.86 |
| 32_F | 69_D | 1.202 | 0.86 |
| 99_D | 104_S | 1.195 | 0.85 |
| 97_W | 106_Q | 1.192 | 0.85 |
| 55_K | 58_G | 1.189 | 0.85 |
| 9_I | 13_L | 1.179 | 0.84 |
| 42_K | 45_E | 1.160 | 0.83 |
| 52_K | 55_K | 1.141 | 0.81 |
| 20_L | 89_N | 1.121 | 0.80 |
| 66_E | 96_V | 1.102 | 0.78 |
| 56_G | 97_W | 1.099 | 0.78 |
| 54_Y | 96_V | 1.096 | 0.77 |
| 59_F | 97_W | 1.094 | 0.77 |
| 92_Q | 96_V | 1.090 | 0.77 |
| 62_I | 101_F | 1.081 | 0.76 |
| 7_L | 11_V | 1.076 | 0.76 |
| 91_P | 109_E | 1.075 | 0.76 |
| 8_E | 86_V | 1.075 | 0.76 |
| 26_R | 82_D | 1.074 | 0.75 |
| 44_Y | 113_V | 1.066 | 0.75 |
| 47_H | 56_G | 1.065 | 0.75 |
| 16_I | 81_L | 1.055 | 0.74 |
| 43_K | 64_I | 1.055 | 0.74 |
| 58_G | 97_W | 1.052 | 0.73 |
| 26_R | 84_D | 1.052 | 0.73 |
| 10_Q | 14_N | 1.048 | 0.73 |
| 112_P | 115_V | 1.038 | 0.72 |
| 85_D | 90_L | 1.032 | 0.71 |
| 15_F | 44_Y | 1.030 | 0.71 |
| 28_R | 51_E | 1.029 | 0.71 |
| 41_K | 96_V | 1.028 | 0.71 |
| 57_S | 113_V | 1.024 | 0.70 |
| 12_A | 94_L | 1.020 | 0.70 |
| 113_V | 117_Y | 1.016 | 0.70 |
| 76_S | 114_K | 1.015 | 0.69 |
| 47_H | 69_D | 1.006 | 0.68 |
| 115_V | 119_D | 1.004 | 0.68 |
| 79_S | 83_I | 1.003 | 0.68 |
| 6_Q | 62_I | 1.003 | 0.68 |
| 25_P | 31_I | 1.002 | 0.68 |
| 74_Q | 78_E | 1.000 | 0.68 |
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 | |
| 2z15A | 4 | 0.9528 | 100 | 0.038 | Contact Map |
| 3e9vA | 1 | 0.9291 | 100 | 0.08 | Contact Map |
| 3shrA | 2 | 0.5433 | 31.1 | 0.926 | Contact Map |
| 2yskA | 1 | 0.7953 | 23.8 | 0.931 | Contact Map |
| 3iaiA | 4 | 0.4961 | 13.4 | 0.938 | Contact Map |
| 2p41A | 1 | 0.1102 | 11 | 0.94 | Contact Map |
| 3ky9A | 2 | 0.8661 | 10.9 | 0.941 | Contact Map |
| 3fw3A | 2 | 0.4803 | 10.7 | 0.941 | Contact Map |
| 1wymA | 1 | 0.9528 | 10.5 | 0.941 | Contact Map |
| 4aikA | 2 | 0.378 | 10.2 | 0.941 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)