| hrd3_84-224 |
| ID: | 1472084441 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 141 (126) | ||
| Sequences: | 14546 (11137.5) | ||
| Seq/Len: | 115.444 | ||
| Nf(neff/√len): | 992.2 |
HHblits Results: (2016_02)
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: 115.444).
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 |
| 63_I | 94_Y | 2.160 | 1.00 |
| 67_A | 95_Y | 2.076 | 1.00 |
| 23_T | 47_Y | 2.068 | 1.00 |
| 107_K | 130_L | 2.018 | 1.00 |
| 107_K | 137_Q | 1.930 | 1.00 |
| 111_A | 131_Y | 1.889 | 1.00 |
| 23_T | 57_F | 1.875 | 1.00 |
| 63_I | 101_L | 1.867 | 1.00 |
| 27_S | 48_L | 1.832 | 1.00 |
| 126_K | 129_V | 1.805 | 1.00 |
| 115_Y | 131_Y | 1.799 | 1.00 |
| 43_L | 46_K | 1.687 | 1.00 |
| 90_K | 93_L | 1.680 | 1.00 |
| 96_Q | 100_Q | 1.552 | 1.00 |
| 71_A | 95_Y | 1.540 | 1.00 |
| 26_L | 30_H | 1.538 | 1.00 |
| 92_L | 120_V | 1.519 | 1.00 |
| 9_L | 13_S | 1.503 | 1.00 |
| 23_T | 53_D | 1.497 | 1.00 |
| 31_L | 48_L | 1.492 | 1.00 |
| 24_Y | 59_N | 1.491 | 1.00 |
| 64_F | 106_A | 1.487 | 1.00 |
| 64_F | 103_N | 1.486 | 1.00 |
| 128_L | 132_R | 1.436 | 1.00 |
| 132_R | 136_E | 1.432 | 1.00 |
| 45_H | 84_I | 1.426 | 1.00 |
| 45_H | 66_L | 1.416 | 1.00 |
| 54_L | 62_A | 1.410 | 1.00 |
| 55_T | 63_I | 1.406 | 0.99 |
| 13_S | 22_A | 1.400 | 0.99 |
| 63_I | 97_R | 1.395 | 0.99 |
| 49_E | 56_H | 1.385 | 0.99 |
| 92_L | 96_Q | 1.383 | 0.99 |
| 24_Y | 62_A | 1.376 | 0.99 |
| 99_A | 107_K | 1.360 | 0.99 |
| 98_A | 106_A | 1.344 | 0.99 |
| 10_L | 25_T | 1.331 | 0.99 |
| 107_K | 133_D | 1.329 | 0.99 |
| 14_S | 23_T | 1.316 | 0.99 |
| 11_V | 16_Q | 1.315 | 0.99 |
| 110_L | 114_Y | 1.298 | 0.99 |
| 66_L | 70_Y | 1.288 | 0.99 |
| 71_A | 91_A | 1.270 | 0.99 |
| 45_H | 49_E | 1.266 | 0.99 |
| 127_S | 131_Y | 1.263 | 0.99 |
| 88_S | 118_F | 1.243 | 0.98 |
| 24_Y | 65_D | 1.236 | 0.98 |
| 5_H | 8_E | 1.198 | 0.98 |
| 92_L | 110_L | 1.191 | 0.98 |
| 93_L | 97_R | 1.189 | 0.98 |
| 44_A | 48_L | 1.175 | 0.98 |
| 40_N | 43_L | 1.174 | 0.98 |
| 6_I | 10_L | 1.169 | 0.97 |
| 13_S | 19_N | 1.167 | 0.97 |
| 9_L | 12_Q | 1.165 | 0.97 |
| 7_Y | 26_L | 1.163 | 0.97 |
| 64_F | 109_V | 1.155 | 0.97 |
| 7_Y | 11_V | 1.155 | 0.97 |
| 7_Y | 37_F | 1.147 | 0.97 |
| 45_H | 69_M | 1.141 | 0.97 |
| 91_A | 95_Y | 1.135 | 0.97 |
| 130_L | 133_D | 1.120 | 0.96 |
| 87_D | 90_K | 1.095 | 0.96 |
| 123_N | 126_K | 1.092 | 0.96 |
| 94_Y | 97_R | 1.074 | 0.95 |
| 31_L | 44_A | 1.072 | 0.95 |
| 129_V | 133_D | 1.061 | 0.95 |
| 41_M | 74_G | 1.046 | 0.94 |
| 76_A | 84_I | 1.045 | 0.94 |
| 48_L | 65_D | 1.044 | 0.94 |
| 108_Q | 139_R | 1.042 | 0.94 |
| 92_L | 113_K | 1.025 | 0.93 |
| 117_G | 122_R | 1.024 | 0.93 |
| 114_Y | 126_K | 1.021 | 0.93 |
| 46_K | 53_D | 1.008 | 0.93 |
| 112_Y | 131_Y | 1.004 | 0.93 |
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 | |
| 4bwrA | 1 | 0.9078 | 99.8 | 0.123 | Contact Map |
| 1ouvA | 1 | 0.9078 | 99.7 | 0.175 | Contact Map |
| 1klxA | 1 | 0.8652 | 99.6 | 0.244 | Contact Map |
| 3e4bA | 4 | 0.9007 | 99.4 | 0.35 | Contact Map |
| 3rjvA | 1 | 0.9007 | 98.9 | 0.476 | Contact Map |
| 1hh8A | 1 | 0.8298 | 97.6 | 0.632 | Contact Map |
| 2pziA | 2 | 0.8298 | 97.4 | 0.649 | Contact Map |
| 2vsyA | 2 | 0.7234 | 97.3 | 0.654 | Contact Map |
| 4gywA | 2 | 0.8369 | 97.2 | 0.656 | Contact Map |
| 4ui9C | 2 | 0 | 97.2 | 0.659 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)