| PaHELLPc |
| ID: | 1492786548 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 180 (171) | ||
| Sequences: | 945 (766.4) | ||
| Seq/Len: | 5.526 | ||
| Nf(neff/√len): | 58.6 |
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: 5.526).
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 |
| 2_D | 5_S | 7.051 | 1.00 |
| 27_D | 114_I | 2.783 | 1.00 |
| 3_P | 7_T | 2.733 | 1.00 |
| 15_A | 19_H | 2.689 | 1.00 |
| 4_L | 9_G | 2.527 | 1.00 |
| 12_G | 15_A | 2.284 | 1.00 |
| 1_M | 5_S | 2.137 | 1.00 |
| 89_K | 93_D | 1.778 | 1.00 |
| 37_T | 117_Q | 1.728 | 1.00 |
| 44_N | 131_N | 1.685 | 1.00 |
| 56_G | 60_D | 1.583 | 0.99 |
| 131_N | 136_S | 1.578 | 0.99 |
| 81_C | 130_C | 1.563 | 0.99 |
| 2_D | 6_I | 1.496 | 0.99 |
| 44_N | 124_S | 1.489 | 0.99 |
| 4_L | 8_A | 1.470 | 0.99 |
| 74_S | 127_L | 1.441 | 0.98 |
| 4_L | 12_G | 1.419 | 0.98 |
| 165_T | 169_N | 1.407 | 0.98 |
| 161_S | 169_N | 1.382 | 0.98 |
| 3_P | 6_I | 1.365 | 0.97 |
| 154_E | 162_T | 1.345 | 0.97 |
| 153_A | 159_I | 1.334 | 0.97 |
| 136_S | 139_S | 1.332 | 0.97 |
| 51_A | 136_S | 1.304 | 0.96 |
| 163_K | 167_V | 1.303 | 0.96 |
| 166_A | 169_N | 1.298 | 0.96 |
| 82_K | 86_E | 1.295 | 0.96 |
| 11_V | 15_A | 1.294 | 0.96 |
| 135_T | 139_S | 1.293 | 0.96 |
| 88_F | 123_I | 1.289 | 0.96 |
| 45_L | 127_L | 1.266 | 0.95 |
| 6_I | 9_G | 1.238 | 0.95 |
| 5_S | 9_G | 1.237 | 0.95 |
| 157_K | 161_S | 1.227 | 0.94 |
| 152_A | 162_T | 1.211 | 0.94 |
| 154_E | 158_T | 1.184 | 0.93 |
| 52_L | 81_C | 1.171 | 0.92 |
| 77_T | 134_L | 1.170 | 0.92 |
| 81_C | 136_S | 1.168 | 0.92 |
| 20_C | 85_C | 1.161 | 0.92 |
| 79_A | 82_K | 1.160 | 0.92 |
| 153_A | 157_K | 1.159 | 0.92 |
| 157_K | 160_I | 1.143 | 0.91 |
| 164_E | 168_N | 1.137 | 0.91 |
| 159_I | 166_A | 1.130 | 0.90 |
| 162_T | 165_T | 1.125 | 0.90 |
| 77_T | 80_S | 1.124 | 0.90 |
| 157_K | 168_N | 1.112 | 0.89 |
| 152_A | 165_T | 1.105 | 0.89 |
| 168_N | 171_I | 1.104 | 0.89 |
| 8_A | 11_V | 1.095 | 0.89 |
| 158_T | 161_S | 1.094 | 0.88 |
| 158_T | 162_T | 1.083 | 0.88 |
| 158_T | 168_N | 1.082 | 0.88 |
| 20_C | 45_L | 1.080 | 0.88 |
| 165_T | 168_N | 1.076 | 0.87 |
| 5_S | 15_A | 1.076 | 0.87 |
| 85_C | 108_D | 1.075 | 0.87 |
| 152_A | 155_E | 1.072 | 0.87 |
| 149_Q | 152_A | 1.057 | 0.86 |
| 154_E | 165_T | 1.054 | 0.86 |
| 158_T | 169_N | 1.050 | 0.86 |
| 84_S | 87_R | 1.033 | 0.84 |
| 45_L | 102_G | 1.021 | 0.83 |
| 161_S | 168_N | 1.020 | 0.83 |
| 7_T | 13_I | 1.017 | 0.83 |
| 41_L | 119_H | 1.011 | 0.82 |
| 79_A | 89_K | 1.010 | 0.82 |
| 162_T | 171_I | 1.002 | 0.82 |
| 159_I | 162_T | 1.001 | 0.82 |
| 121_K | 125_K | 1.000 | 0.82 |
| 5_S | 8_A | 1.000 | 0.82 |
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 | |
| 4btfA | 1 | 0.7056 | 97.1 | 0.765 | Contact Map |
| 2msvA | 1 | 0.8111 | 93.6 | 0.818 | Contact Map |
| 2wvqA | 2 | 0.95 | 91.2 | 0.83 | Contact Map |
| 2kk1A | 1 | 0.4778 | 47.3 | 0.885 | Contact Map |
| 4q4gX | 1 | 0 | 45.9 | 0.886 | Contact Map |
| 3qflA | 1 | 0.6111 | 35.3 | 0.893 | Contact Map |
| 2ljbA | 4 | 0.1667 | 29.1 | 0.898 | Contact Map |
| 1zzpA | 1 | 0.4889 | 28.4 | 0.898 | Contact Map |
| 4dndA | 1 | 0.5167 | 26.9 | 0.899 | Contact Map |
| 4cgkA | 2 | 0.7333 | 24 | 0.901 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)