| 3ze3 |
| ID: | 1500381969 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 116 (115) | ||
| Sequences: | 2493 (1811.6) | ||
| Seq/Len: | 21.678 | ||
| Nf(neff/√len): | 168.9 |
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: 21.678).
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 |
| 74_V | 85_S | 3.361 | 1.00 |
| 14_K | 86_G | 3.026 | 1.00 |
| 20_W | 30_G | 2.988 | 1.00 |
| 19_A | 65_L | 2.865 | 1.00 |
| 63_V | 66_L | 2.408 | 1.00 |
| 58_M | 102_D | 2.341 | 1.00 |
| 33_V | 57_V | 2.296 | 1.00 |
| 17_R | 21_I | 2.153 | 1.00 |
| 76_R | 85_S | 1.983 | 1.00 |
| 45_V | 110_L | 1.852 | 1.00 |
| 16_L | 94_A | 1.843 | 1.00 |
| 63_V | 99_A | 1.818 | 1.00 |
| 73_V | 88_A | 1.793 | 1.00 |
| 62_I | 99_A | 1.779 | 1.00 |
| 40_A | 50_R | 1.717 | 1.00 |
| 72_A | 87_R | 1.679 | 1.00 |
| 20_W | 31_V | 1.617 | 1.00 |
| 108_A | 112_W | 1.573 | 1.00 |
| 49_T | 114_H | 1.539 | 1.00 |
| 59_L | 99_A | 1.537 | 1.00 |
| 46_D | 49_T | 1.482 | 1.00 |
| 26_F | 61_M | 1.461 | 1.00 |
| 68_S | 91_L | 1.446 | 1.00 |
| 18_A | 87_R | 1.433 | 1.00 |
| 48_V | 52_L | 1.416 | 1.00 |
| 44_D | 50_R | 1.405 | 0.99 |
| 22_N | 87_R | 1.390 | 0.99 |
| 60_V | 96_V | 1.390 | 0.99 |
| 65_L | 94_A | 1.376 | 0.99 |
| 65_L | 91_L | 1.355 | 0.99 |
| 19_A | 26_F | 1.344 | 0.99 |
| 26_F | 29_E | 1.333 | 0.99 |
| 63_V | 95_A | 1.310 | 0.99 |
| 19_A | 91_L | 1.293 | 0.99 |
| 52_L | 56_S | 1.290 | 0.99 |
| 54_I | 102_D | 1.288 | 0.99 |
| 73_V | 77_I | 1.285 | 0.99 |
| 49_T | 110_L | 1.283 | 0.99 |
| 11_Y | 14_K | 1.259 | 0.99 |
| 84_L | 88_A | 1.218 | 0.98 |
| 7_K | 10_G | 1.198 | 0.98 |
| 65_L | 98_I | 1.190 | 0.98 |
| 37_V | 57_V | 1.189 | 0.98 |
| 12_S | 93_S | 1.172 | 0.98 |
| 60_V | 103_A | 1.171 | 0.98 |
| 5_I | 24_A | 1.167 | 0.97 |
| 5_I | 9_A | 1.150 | 0.97 |
| 5_I | 28_Q | 1.143 | 0.97 |
| 38_V | 42_W | 1.104 | 0.96 |
| 55_S | 102_D | 1.103 | 0.96 |
| 23_E | 72_A | 1.103 | 0.96 |
| 45_V | 53_L | 1.091 | 0.96 |
| 29_E | 96_V | 1.062 | 0.95 |
| 77_I | 85_S | 1.059 | 0.95 |
| 56_S | 106_T | 1.015 | 0.93 |
| 28_Q | 32_A | 1.007 | 0.93 |
| 25_A | 28_Q | 1.005 | 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 | |
| 3ze3A | 6 | 1 | 100 | 0.017 | Contact Map |
| 4w252 | 1 | 0.4138 | 7.8 | 0.932 | Contact Map |
| 1rh5B | 1 | 0.3362 | 5.6 | 0.937 | Contact Map |
| 3b8cA | 2 | 0.931 | 2.9 | 0.945 | Contact Map |
| 4b03D | 3 | 0.5603 | 2.7 | 0.946 | Contact Map |
| 4k1cA | 2 | 0.9052 | 2.7 | 0.946 | Contact Map |
| 2lzrA | 1 | 0.3276 | 2.5 | 0.947 | Contact Map |
| 3mp7B | 1 | 0.3707 | 2.1 | 0.949 | Contact Map |
| 3wajA | 1 | 0.7672 | 1.9 | 0.95 | Contact Map |
| 1pi7A | 1 | 0.1638 | 1.8 | 0.95 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)