| T0842 |
| ID: | 1404412742 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 146 (140) | ||
| Sequences: | 204 (187.7) | ||
| Seq/Len: | 1.457 | ||
| Nf(neff/√len): | 15.9 |
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: 1.457).
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 |
| 95_K | 103_E | 2.804 | 1.00 |
| 48_V | 87_A | 2.088 | 0.99 |
| 32_P | 41_V | 2.077 | 0.98 |
| 41_V | 44_W | 2.007 | 0.98 |
| 44_W | 105_G | 2.005 | 0.98 |
| 40_E | 92_C | 1.942 | 0.97 |
| 134_E | 137_R | 1.665 | 0.92 |
| 99_R | 102_A | 1.624 | 0.91 |
| 49_Y | 57_E | 1.606 | 0.90 |
| 23_E | 127_I | 1.598 | 0.90 |
| 11_A | 142_S | 1.552 | 0.88 |
| 59_M | 112_A | 1.486 | 0.85 |
| 57_E | 96_T | 1.470 | 0.84 |
| 45_C | 55_L | 1.449 | 0.83 |
| 60_Q | 72_L | 1.419 | 0.81 |
| 24_I | 124_Q | 1.394 | 0.79 |
| 47_I | 87_A | 1.350 | 0.76 |
| 23_E | 52_S | 1.332 | 0.75 |
| 60_Q | 106_F | 1.309 | 0.73 |
| 84_H | 119_A | 1.308 | 0.73 |
| 23_E | 131_P | 1.300 | 0.72 |
| 127_I | 131_P | 1.279 | 0.71 |
| 7_H | 45_C | 1.268 | 0.70 |
| 128_K | 139_G | 1.267 | 0.70 |
| 62_V | 113_L | 1.251 | 0.68 |
| 57_E | 136_R | 1.248 | 0.68 |
| 79_N | 96_T | 1.245 | 0.68 |
| 10_V | 14_S | 1.233 | 0.67 |
| 31_N | 139_G | 1.221 | 0.65 |
| 28_M | 85_K | 1.197 | 0.63 |
| 21_R | 124_Q | 1.194 | 0.63 |
| 69_G | 120_V | 1.189 | 0.62 |
| 36_A | 40_E | 1.186 | 0.62 |
| 35_Q | 108_H | 1.172 | 0.61 |
| 42_M | 53_D | 1.168 | 0.60 |
| 72_L | 82_S | 1.166 | 0.60 |
| 97_N | 120_V | 1.136 | 0.57 |
| 28_M | 54_V | 1.135 | 0.57 |
| 44_W | 134_E | 1.132 | 0.57 |
| 62_V | 120_V | 1.128 | 0.56 |
| 14_S | 46_K | 1.120 | 0.56 |
| 24_I | 72_L | 1.118 | 0.55 |
| 38_Q | 41_V | 1.117 | 0.55 |
| 89_R | 92_C | 1.097 | 0.53 |
| 87_A | 102_A | 1.093 | 0.53 |
| 73_S | 110_C | 1.092 | 0.53 |
| 61_E | 64_Q | 1.091 | 0.53 |
| 106_F | 117_T | 1.088 | 0.52 |
| 41_V | 60_Q | 1.082 | 0.52 |
| 66_P | 110_C | 1.080 | 0.51 |
| 55_L | 61_E | 1.079 | 0.51 |
| 120_V | 127_I | 1.077 | 0.51 |
| 4_H | 7_H | 1.076 | 0.51 |
| 24_I | 96_T | 1.076 | 0.51 |
| 51_N | 93_G | 1.076 | 0.51 |
| 121_T | 124_Q | 1.065 | 0.50 |
| 10_V | 142_S | 1.063 | 0.50 |
| 75_Q | 132_Q | 1.060 | 0.49 |
| 48_V | 94_L | 1.050 | 0.48 |
| 34_V | 123_A | 1.047 | 0.48 |
| 22_E | 129_H | 1.040 | 0.47 |
| 27_R | 137_R | 1.039 | 0.47 |
| 56_K | 130_V | 1.039 | 0.47 |
| 19_L | 127_I | 1.038 | 0.47 |
| 69_G | 117_T | 1.035 | 0.47 |
| 19_L | 137_R | 1.031 | 0.46 |
| 10_V | 16_I | 1.025 | 0.46 |
| 52_S | 64_Q | 1.020 | 0.45 |
| 54_V | 81_T | 1.016 | 0.45 |
| 17_P | 22_E | 1.014 | 0.45 |
| 16_I | 142_S | 1.006 | 0.44 |
| 12_M | 46_K | 1.005 | 0.44 |
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 | |
| 2lnmA | 1 | 0.4041 | 27.3 | 0.933 | Contact Map |
| 3hwsA | 6 | 0.6438 | 15.2 | 0.94 | Contact Map |
| 2llvA | 1 | 0.4863 | 13.1 | 0.942 | Contact Map |
| 2zbcA | 8 | 0.5274 | 12.8 | 0.942 | Contact Map |
| 2djwA | 10 | 0.5205 | 10.3 | 0.945 | Contact Map |
| 2llwA | 1 | 0.4863 | 9.8 | 0.945 | Contact Map |
| 4o4fA | 1 | 0.9452 | 8.3 | 0.947 | Contact Map |
| 2f4mB | 1 | 0.411 | 8 | 0.947 | Contact Map |
| 4l8iA | 2 | 0.363 | 6.6 | 0.949 | Contact Map |
| 1um8A | 1 | 0.6301 | 6.3 | 0.95 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)