| T0833 -force run |
| ID: | 1403811137 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 136 (128) | ||
| Sequences: | 58 (44.7) | ||
| Seq/Len: | 0.453 | ||
| Nf(neff/√len): | 4.0 |
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: 0.453).
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 |
| 80_D | 87_V | 1.982 | 0.83 |
| 10_I | 83_N | 1.767 | 0.72 |
| 75_K | 117_F | 1.649 | 0.64 |
| 23_I | 27_S | 1.614 | 0.62 |
| 55_L | 110_W | 1.593 | 0.60 |
| 77_F | 80_D | 1.588 | 0.60 |
| 14_V | 66_N | 1.517 | 0.55 |
| 77_F | 117_F | 1.459 | 0.50 |
| 16_T | 29_K | 1.448 | 0.49 |
| 24_S | 94_Y | 1.439 | 0.49 |
| 44_S | 60_R | 1.394 | 0.45 |
| 21_L | 66_N | 1.384 | 0.45 |
| 70_K | 111_D | 1.383 | 0.45 |
| 2_K | 8_K | 1.378 | 0.44 |
| 115_K | 121_V | 1.359 | 0.43 |
| 21_L | 44_S | 1.338 | 0.41 |
| 5_V | 106_N | 1.304 | 0.39 |
| 78_R | 111_D | 1.242 | 0.34 |
| 11_L | 19_C | 1.235 | 0.34 |
| 63_F | 112_K | 1.224 | 0.33 |
| 6_W | 77_F | 1.217 | 0.33 |
| 76_A | 88_P | 1.216 | 0.33 |
| 57_K | 91_Q | 1.194 | 0.31 |
| 38_E | 92_I | 1.194 | 0.31 |
| 46_V | 49_L | 1.190 | 0.31 |
| 46_V | 63_F | 1.183 | 0.31 |
| 26_A | 38_E | 1.178 | 0.30 |
| 24_S | 31_Y | 1.171 | 0.30 |
| 30_D | 60_R | 1.167 | 0.30 |
| 59_V | 92_I | 1.158 | 0.29 |
| 74_K | 102_E | 1.156 | 0.29 |
| 60_R | 95_Q | 1.156 | 0.29 |
| 63_F | 89_F | 1.154 | 0.29 |
| 99_Q | 121_V | 1.150 | 0.28 |
| 4_S | 113_K | 1.139 | 0.28 |
| 66_N | 70_K | 1.129 | 0.27 |
| 32_L | 123_N | 1.125 | 0.27 |
| 36_K | 96_Y | 1.122 | 0.27 |
| 58_Q | 108_G | 1.121 | 0.27 |
| 77_F | 88_P | 1.121 | 0.27 |
| 39_N | 62_E | 1.115 | 0.26 |
| 43_I | 72_S | 1.115 | 0.26 |
| 72_S | 111_D | 1.115 | 0.26 |
| 49_L | 57_K | 1.100 | 0.26 |
| 98_D | 112_K | 1.095 | 0.25 |
| 34_D | 48_F | 1.094 | 0.25 |
| 103_I | 115_K | 1.082 | 0.25 |
| 36_K | 78_R | 1.077 | 0.24 |
| 23_I | 51_E | 1.076 | 0.24 |
| 8_K | 85_E | 1.074 | 0.24 |
| 51_E | 95_Q | 1.074 | 0.24 |
| 99_Q | 104_K | 1.067 | 0.24 |
| 3_T | 6_W | 1.066 | 0.24 |
| 18_M | 39_N | 1.063 | 0.23 |
| 20_S | 40_G | 1.061 | 0.23 |
| 2_K | 107_Y | 1.061 | 0.23 |
| 52_N | 94_Y | 1.057 | 0.23 |
| 35_T | 72_S | 1.051 | 0.23 |
| 99_Q | 111_D | 1.049 | 0.23 |
| 21_L | 87_V | 1.048 | 0.23 |
| 53_G | 71_V | 1.048 | 0.23 |
| 42_I | 119_L | 1.039 | 0.22 |
| 37_E | 83_N | 1.039 | 0.22 |
| 34_D | 78_R | 1.038 | 0.22 |
| 6_W | 32_L | 1.029 | 0.22 |
| 60_R | 94_Y | 1.027 | 0.22 |
| 16_T | 93_T | 1.027 | 0.22 |
| 93_T | 105_T | 1.023 | 0.21 |
| 19_C | 92_I | 1.021 | 0.21 |
| 36_K | 46_V | 1.014 | 0.21 |
| 34_D | 96_Y | 1.012 | 0.21 |
| 111_D | 118_S | 1.011 | 0.21 |
| 38_E | 54_L | 1.006 | 0.21 |
| 86_W | 124_M | 1.002 | 0.20 |
| 48_F | 93_T | 1.001 | 0.20 |
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 | |
| 4r03A | 1 | 0.8015 | 100 | 0.324 | Contact Map |
| 4r8oA | 2 | 0.7206 | 100 | 0.355 | Contact Map |
| 3mswA | 1 | 0.8088 | 100 | 0.378 | Contact Map |
| 4ghbA | 2 | 0.6691 | 41.9 | 0.934 | Contact Map |
| 4u6bA | 4 | 0.3603 | 10.1 | 0.951 | Contact Map |
| 2dckA | 1 | 0.7279 | 5.7 | 0.956 | Contact Map |
| 4x36A | 1 | 0 | 4.9 | 0.958 | Contact Map |
| 2m1jA | 1 | 0.2206 | 3.9 | 0.96 | Contact Map |
| 1z65A | 1 | 0.2206 | 3.9 | 0.96 | Contact Map |
| 1qleD | 1 | 0.1691 | 3.8 | 0.96 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)