| cwet_573 |
| ID: | 1513358396 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 116 (116) | ||
| Sequences: | 389 (213.8) | ||
| Seq/Len: | 3.353 | ||
| Nf(neff/√len): | 19.9 |
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: 3.353).
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 |
| 1_C | 7_G | 2.404 | 1.00 |
| 3_E | 7_G | 2.255 | 1.00 |
| 60_S | 67_I | 2.255 | 1.00 |
| 2_W | 17_D | 2.136 | 1.00 |
| 2_W | 8_Q | 2.008 | 1.00 |
| 32_R | 53_S | 1.801 | 0.99 |
| 4_T | 8_Q | 1.722 | 0.99 |
| 73_I | 87_N | 1.607 | 0.98 |
| 76_G | 81_P | 1.604 | 0.98 |
| 2_W | 7_G | 1.582 | 0.98 |
| 70_Q | 74_W | 1.529 | 0.97 |
| 17_D | 90_R | 1.519 | 0.97 |
| 77_S | 92_H | 1.477 | 0.96 |
| 95_M | 98_Q | 1.476 | 0.96 |
| 10_F | 16_S | 1.453 | 0.96 |
| 76_G | 83_L | 1.426 | 0.95 |
| 64_L | 70_Q | 1.380 | 0.94 |
| 64_L | 74_W | 1.377 | 0.94 |
| 78_F | 115_A | 1.375 | 0.94 |
| 67_I | 113_F | 1.361 | 0.93 |
| 1_C | 8_Q | 1.333 | 0.92 |
| 89_L | 92_H | 1.330 | 0.92 |
| 6_V | 85_G | 1.308 | 0.91 |
| 33_A | 37_R | 1.292 | 0.90 |
| 102_V | 105_C | 1.286 | 0.90 |
| 8_Q | 17_D | 1.285 | 0.90 |
| 66_L | 91_L | 1.281 | 0.90 |
| 2_W | 9_E | 1.276 | 0.90 |
| 59_I | 103_M | 1.271 | 0.90 |
| 22_Y | 27_I | 1.260 | 0.89 |
| 16_S | 111_R | 1.250 | 0.88 |
| 29_D | 105_C | 1.241 | 0.88 |
| 86_I | 94_S | 1.219 | 0.87 |
| 57_F | 74_W | 1.209 | 0.86 |
| 57_F | 70_Q | 1.205 | 0.86 |
| 13_L | 17_D | 1.198 | 0.85 |
| 63_V | 84_P | 1.166 | 0.83 |
| 1_C | 9_E | 1.148 | 0.82 |
| 79_F | 111_R | 1.141 | 0.81 |
| 101_A | 112_V | 1.138 | 0.81 |
| 59_I | 91_L | 1.112 | 0.79 |
| 4_T | 114_K | 1.106 | 0.79 |
| 61_G | 105_C | 1.103 | 0.78 |
| 102_V | 111_R | 1.103 | 0.78 |
| 28_G | 31_L | 1.080 | 0.76 |
| 90_R | 94_S | 1.075 | 0.76 |
| 56_E | 111_R | 1.047 | 0.73 |
| 64_L | 84_P | 1.032 | 0.71 |
| 61_G | 65_A | 1.031 | 0.71 |
| 9_E | 12_R | 1.031 | 0.71 |
| 92_H | 115_A | 1.030 | 0.71 |
| 10_F | 111_R | 1.013 | 0.69 |
| 102_V | 114_K | 1.001 | 0.68 |
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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 4xxoA | 2 | 0 | 11 | 0.934 | Contact Map |
| 4wisA | 2 | 0.8966 | 7.1 | 0.939 | Contact Map |
| 4bkfC | 2 | 0.0862 | 2 | 0.954 | Contact Map |
| 1jb0M | 1 | 0.1034 | 1.4 | 0.958 | Contact Map |
| 2wscI | 1 | 0.2241 | 1.1 | 0.96 | Contact Map |
| 1tt5A | 2 | 0.3362 | 1.1 | 0.96 | Contact Map |
| 4xk8I | 2 | 0 | 1 | 0.962 | Contact Map |
| 1wijA | 1 | 0.2931 | 0.9 | 0.962 | Contact Map |
| 2vq5A | 2 | 0.3362 | 0.9 | 0.963 | Contact Map |
| 3pp4P | 1 | 0.1207 | 0.8 | 0.964 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)