| d4f3wc_ |
| ID: | 1450931182 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 119 (118) | ||
| Sequences: | 2917 (1987.8) | ||
| Seq/Len: | 24.720 | ||
| Nf(neff/√len): | 183.0 |
HHblits Results: (2015_06)
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: 24.720).
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 |
| 50_L | 88_R | 4.410 | 1.00 |
| 33_D | 69_R | 3.169 | 1.00 |
| 61_A | 65_T | 3.072 | 1.00 |
| 59_V | 93_L | 2.529 | 1.00 |
| 61_A | 64_A | 2.432 | 1.00 |
| 31_L | 72_A | 2.431 | 1.00 |
| 9_K | 12_Q | 2.395 | 1.00 |
| 34_D | 67_G | 2.383 | 1.00 |
| 94_F | 119_P | 2.330 | 1.00 |
| 33_D | 71_V | 2.291 | 1.00 |
| 19_A | 25_P | 2.172 | 1.00 |
| 47_S | 50_L | 2.141 | 1.00 |
| 52_L | 60_C | 1.809 | 1.00 |
| 36_R | 67_G | 1.776 | 1.00 |
| 57_G | 60_C | 1.757 | 1.00 |
| 57_G | 61_A | 1.753 | 1.00 |
| 60_C | 92_L | 1.740 | 1.00 |
| 12_Q | 15_A | 1.732 | 1.00 |
| 52_L | 57_G | 1.725 | 1.00 |
| 5_Q | 9_K | 1.723 | 1.00 |
| 29_A | 37_V | 1.715 | 1.00 |
| 49_G | 88_R | 1.701 | 1.00 |
| 77_D | 83_L | 1.585 | 1.00 |
| 14_A | 78_G | 1.502 | 1.00 |
| 32_V | 38_V | 1.493 | 1.00 |
| 63_H | 96_H | 1.492 | 1.00 |
| 3_W | 109_P | 1.468 | 1.00 |
| 32_V | 67_G | 1.467 | 1.00 |
| 27_G | 41_C | 1.439 | 1.00 |
| 7_R | 74_A | 1.425 | 1.00 |
| 9_K | 39_T | 1.419 | 1.00 |
| 47_S | 88_R | 1.379 | 0.99 |
| 97_G | 101_L | 1.375 | 0.99 |
| 38_V | 67_G | 1.364 | 0.99 |
| 108_G | 118_E | 1.298 | 0.99 |
| 13_V | 27_G | 1.275 | 0.99 |
| 111_R | 114_D | 1.259 | 0.99 |
| 30_A | 70_L | 1.258 | 0.99 |
| 59_V | 92_L | 1.237 | 0.98 |
| 30_A | 58_V | 1.231 | 0.98 |
| 59_V | 70_L | 1.230 | 0.98 |
| 3_W | 72_A | 1.227 | 0.98 |
| 31_L | 71_V | 1.221 | 0.98 |
| 6_L | 29_A | 1.212 | 0.98 |
| 110_R | 114_D | 1.208 | 0.98 |
| 10_A | 29_A | 1.178 | 0.98 |
| 43_V | 63_H | 1.134 | 0.97 |
| 25_P | 78_G | 1.125 | 0.97 |
| 14_A | 76_V | 1.122 | 0.97 |
| 13_V | 41_C | 1.120 | 0.96 |
| 110_R | 118_E | 1.118 | 0.96 |
| 52_L | 56_C | 1.112 | 0.96 |
| 32_V | 36_R | 1.099 | 0.96 |
| 13_V | 39_T | 1.087 | 0.96 |
| 103_V | 109_P | 1.087 | 0.96 |
| 62_L | 70_L | 1.072 | 0.95 |
| 38_V | 65_T | 1.062 | 0.95 |
| 6_L | 10_A | 1.060 | 0.95 |
| 2_D | 5_Q | 1.053 | 0.95 |
| 14_A | 27_G | 1.022 | 0.93 |
| 21_Y | 48_Y | 1.015 | 0.93 |
| 32_V | 70_L | 1.012 | 0.93 |
| 11_T | 14_A | 1.011 | 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 | |
| 3dmoA | 4 | 1 | 100 | 0.01 | Contact Map |
| 2d30A | 2 | 1 | 100 | 0.013 | Contact Map |
| 1cttA | 1 | 0.9496 | 100 | 0.101 | Contact Map |
| 3b8fA | 4 | 0.9832 | 100 | 0.125 | Contact Map |
| 3mpzA | 4 | 1 | 100 | 0.184 | Contact Map |
| 4eg2A | 8 | 0.8992 | 100 | 0.206 | Contact Map |
| 2fr5A | 4 | 1 | 100 | 0.211 | Contact Map |
| 3r2nA | 4 | 0.9916 | 100 | 0.211 | Contact Map |
| 1uwzA | 2 | 1 | 100 | 0.224 | Contact Map |
| 1r5tA | 4 | 1 | 100 | 0.228 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)