| T0765 - R0046 -force run |
| ID: | 1399400767 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 128 (127) | ||
| Sequences: | 69 (44.5) | ||
| Seq/Len: | 0.543 | ||
| Nf(neff/√len): | 3.9 |
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: 0.543).
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 |
| 58_H | 67_F | 1.849 | 0.81 |
| 62_A | 81_F | 1.788 | 0.78 |
| 43_P | 56_V | 1.722 | 0.74 |
| 79_I | 119_R | 1.590 | 0.65 |
| 81_F | 84_T | 1.503 | 0.59 |
| 65_I | 68_K | 1.490 | 0.58 |
| 57_W | 67_F | 1.486 | 0.58 |
| 42_R | 62_A | 1.462 | 0.56 |
| 57_W | 80_K | 1.406 | 0.51 |
| 22_L | 45_G | 1.405 | 0.51 |
| 74_K | 80_K | 1.391 | 0.50 |
| 4_M | 8_S | 1.344 | 0.47 |
| 73_Q | 80_K | 1.338 | 0.46 |
| 14_W | 74_K | 1.327 | 0.45 |
| 42_R | 77_L | 1.319 | 0.45 |
| 87_G | 107_L | 1.311 | 0.44 |
| 39_L | 83_S | 1.290 | 0.42 |
| 22_L | 66_R | 1.288 | 0.42 |
| 43_P | 79_I | 1.270 | 0.41 |
| 11_Q | 14_W | 1.251 | 0.39 |
| 38_T | 78_L | 1.242 | 0.39 |
| 14_W | 30_L | 1.238 | 0.38 |
| 57_W | 84_T | 1.237 | 0.38 |
| 66_R | 92_E | 1.231 | 0.38 |
| 64_G | 86_Q | 1.220 | 0.37 |
| 86_Q | 94_L | 1.220 | 0.37 |
| 64_G | 94_L | 1.220 | 0.37 |
| 28_L | 66_R | 1.217 | 0.37 |
| 87_G | 97_A | 1.213 | 0.37 |
| 50_M | 58_H | 1.209 | 0.36 |
| 87_G | 106_L | 1.206 | 0.36 |
| 31_A | 79_I | 1.203 | 0.36 |
| 62_A | 79_I | 1.200 | 0.36 |
| 111_N | 119_R | 1.198 | 0.35 |
| 61_D | 66_R | 1.189 | 0.35 |
| 38_T | 59_H | 1.181 | 0.34 |
| 25_L | 119_R | 1.175 | 0.34 |
| 4_M | 18_G | 1.170 | 0.34 |
| 34_Q | 50_M | 1.170 | 0.34 |
| 40_A | 127_L | 1.168 | 0.33 |
| 39_L | 65_I | 1.159 | 0.33 |
| 38_T | 93_V | 1.153 | 0.32 |
| 87_G | 95_G | 1.153 | 0.32 |
| 104_I | 113_P | 1.149 | 0.32 |
| 63_N | 81_F | 1.147 | 0.32 |
| 4_M | 7_P | 1.134 | 0.31 |
| 79_I | 82_D | 1.128 | 0.31 |
| 63_N | 96_R | 1.126 | 0.30 |
| 39_L | 56_V | 1.119 | 0.30 |
| 92_E | 106_L | 1.104 | 0.29 |
| 59_H | 80_K | 1.099 | 0.29 |
| 20_L | 28_L | 1.089 | 0.28 |
| 40_A | 56_V | 1.083 | 0.28 |
| 72_P | 94_L | 1.073 | 0.27 |
| 64_G | 72_P | 1.073 | 0.27 |
| 72_P | 86_Q | 1.073 | 0.27 |
| 108_E | 127_L | 1.071 | 0.27 |
| 65_I | 75_D | 1.068 | 0.27 |
| 28_L | 103_I | 1.067 | 0.27 |
| 73_Q | 104_I | 1.065 | 0.27 |
| 79_I | 111_N | 1.065 | 0.27 |
| 75_D | 99_P | 1.046 | 0.25 |
| 68_K | 75_D | 1.041 | 0.25 |
| 80_K | 91_K | 1.037 | 0.25 |
| 4_M | 47_G | 1.030 | 0.24 |
| 19_S | 124_P | 1.029 | 0.24 |
| 16_L | 104_I | 1.016 | 0.24 |
| 58_H | 63_N | 1.009 | 0.23 |
| 32_V | 101_G | 1.008 | 0.23 |
| 81_F | 119_R | 1.006 | 0.23 |
| 95_G | 102_Y | 1.005 | 0.23 |
| 4_M | 114_T | 1.001 | 0.23 |
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 | |
| 4pwuA | 4 | 0.6172 | 99.9 | 0.518 | Contact Map |
| 3lqvP | 2 | 0.2812 | 33.7 | 0.939 | Contact Map |
| 2p4eP | 2 | 0.5312 | 28.5 | 0.941 | Contact Map |
| 2fhoA | 1 | 0.3438 | 26.4 | 0.942 | Contact Map |
| 2vrnA | 2 | 0.7344 | 16.6 | 0.947 | Contact Map |
| 4m1bA | 2 | 0.4844 | 14 | 0.949 | Contact Map |
| 2gqcA | 1 | 0.5469 | 13.6 | 0.949 | Contact Map |
| 2w3zA | 1 | 0.6406 | 12.3 | 0.95 | Contact Map |
| 3ucpA | 1 | 0.5859 | 11.1 | 0.951 | Contact Map |
| 2y9jY | 24 | 0.6562 | 10.3 | 0.952 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)