| lingyuan |
| ID: | 1421638415 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 143 (140) | ||
| Sequences: | 455 (363.6) | ||
| Seq/Len: | 3.250 | ||
| Nf(neff/√len): | 30.7 |
HHblits Results: (2013_03)
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: 3.250).
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 |
| 127_F | 130_M | 3.747 | 1.00 |
| 101_T | 109_H | 1.761 | 0.99 |
| 138_V | 141_Q | 1.698 | 0.99 |
| 20_F | 80_G | 1.681 | 0.98 |
| 110_R | 135_E | 1.668 | 0.98 |
| 16_S | 105_G | 1.539 | 0.97 |
| 113_L | 125_D | 1.525 | 0.97 |
| 112_R | 128_D | 1.511 | 0.96 |
| 102_A | 131_L | 1.465 | 0.96 |
| 98_A | 105_G | 1.454 | 0.95 |
| 46_E | 51_R | 1.453 | 0.95 |
| 54_P | 57_V | 1.421 | 0.95 |
| 46_E | 50_V | 1.409 | 0.94 |
| 131_L | 141_Q | 1.408 | 0.94 |
| 18_A | 78_L | 1.363 | 0.93 |
| 14_T | 89_L | 1.348 | 0.92 |
| 26_V | 92_L | 1.325 | 0.91 |
| 110_R | 132_A | 1.273 | 0.89 |
| 24_A | 77_G | 1.263 | 0.89 |
| 58_F | 88_M | 1.263 | 0.89 |
| 121_R | 125_D | 1.260 | 0.88 |
| 73_L | 141_Q | 1.249 | 0.88 |
| 81_G | 141_Q | 1.235 | 0.87 |
| 47_R | 51_R | 1.222 | 0.86 |
| 131_L | 138_V | 1.211 | 0.86 |
| 13_L | 74_L | 1.210 | 0.86 |
| 66_A | 138_V | 1.194 | 0.85 |
| 86_G | 128_D | 1.192 | 0.84 |
| 105_G | 141_Q | 1.189 | 0.84 |
| 75_V | 97_E | 1.187 | 0.84 |
| 83_F | 94_R | 1.160 | 0.82 |
| 107_L | 138_V | 1.158 | 0.82 |
| 10_R | 14_T | 1.156 | 0.82 |
| 32_V | 39_Q | 1.146 | 0.81 |
| 102_A | 111_I | 1.145 | 0.81 |
| 77_G | 140_E | 1.140 | 0.81 |
| 35_F | 66_A | 1.134 | 0.80 |
| 86_G | 125_D | 1.126 | 0.79 |
| 103_A | 126_A | 1.122 | 0.79 |
| 78_L | 102_A | 1.119 | 0.79 |
| 66_A | 120_Y | 1.118 | 0.79 |
| 36_L | 72_F | 1.117 | 0.79 |
| 14_T | 141_Q | 1.112 | 0.78 |
| 30_V | 79_V | 1.092 | 0.76 |
| 107_L | 131_L | 1.081 | 0.75 |
| 73_L | 77_G | 1.078 | 0.75 |
| 37_L | 41_W | 1.078 | 0.75 |
| 77_G | 80_G | 1.074 | 0.75 |
| 73_L | 138_V | 1.070 | 0.74 |
| 74_L | 98_A | 1.062 | 0.74 |
| 102_A | 123_L | 1.061 | 0.74 |
| 47_R | 57_V | 1.061 | 0.74 |
| 14_T | 17_Y | 1.052 | 0.73 |
| 50_V | 75_V | 1.051 | 0.73 |
| 121_R | 128_D | 1.051 | 0.73 |
| 12_K | 126_A | 1.050 | 0.72 |
| 68_W | 117_R | 1.046 | 0.72 |
| 66_A | 73_L | 1.046 | 0.72 |
| 15_L | 94_R | 1.042 | 0.72 |
| 113_L | 128_D | 1.040 | 0.71 |
| 99_T | 130_M | 1.039 | 0.71 |
| 105_G | 138_V | 1.037 | 0.71 |
| 21_L | 81_G | 1.035 | 0.71 |
| 82_W | 143_R | 1.034 | 0.71 |
| 45_N | 48_G | 1.032 | 0.71 |
| 11_L | 14_T | 1.026 | 0.70 |
| 7_L | 11_L | 1.024 | 0.70 |
| 87_R | 123_L | 1.021 | 0.69 |
| 118_D | 124_A | 1.018 | 0.69 |
| 107_L | 141_Q | 1.013 | 0.69 |
| 81_G | 128_D | 1.013 | 0.69 |
| 96_T | 133_R | 1.002 | 0.67 |
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 | |
| 2f95B | 1 | 0.3706 | 99.4 | 0.54 | Contact Map |
| 4gycB | 1 | 0.4266 | 99.4 | 0.546 | Contact Map |
| 4i5sA | 2 | 0.4476 | 99.2 | 0.599 | Contact Map |
| 4cq4A | 4 | 0.6643 | 99.1 | 0.611 | Contact Map |
| 4i3mA | 1 | 0.3986 | 98.9 | 0.647 | Contact Map |
| 4bixA | 2 | 0.1538 | 98.8 | 0.656 | Contact Map |
| 3zccA | 2 | 0.4056 | 98.7 | 0.668 | Contact Map |
| 3zx6A | 2 | 0.4056 | 98.5 | 0.687 | Contact Map |
| 4ctiA | 4 | 0.3986 | 98.4 | 0.692 | Contact Map |
| 2rm8A | 1 | 0.2867 | 97.2 | 0.768 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)