| 3ze3 |
| ID: | 1500381396 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 116 (115) | ||
| Sequences: | 2536 (1848.7) | ||
| Seq/Len: | 22.052 | ||
| Nf(neff/√len): | 172.4 |
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: 22.052).
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 | 3.379 | 1.00 |
| 14_K | 86_G | 3.072 | 1.00 |
| 20_W | 30_G | 2.981 | 1.00 |
| 19_A | 65_L | 2.909 | 1.00 |
| 63_V | 66_L | 2.425 | 1.00 |
| 58_M | 102_D | 2.288 | 1.00 |
| 33_V | 57_V | 2.286 | 1.00 |
| 17_R | 21_I | 2.111 | 1.00 |
| 76_R | 85_S | 1.940 | 1.00 |
| 16_L | 94_A | 1.885 | 1.00 |
| 73_V | 88_A | 1.834 | 1.00 |
| 63_V | 99_A | 1.812 | 1.00 |
| 62_I | 99_A | 1.811 | 1.00 |
| 40_A | 50_R | 1.785 | 1.00 |
| 45_V | 110_L | 1.781 | 1.00 |
| 72_A | 87_R | 1.723 | 1.00 |
| 108_A | 112_W | 1.607 | 1.00 |
| 20_W | 31_V | 1.570 | 1.00 |
| 60_V | 96_V | 1.562 | 1.00 |
| 46_D | 49_T | 1.522 | 1.00 |
| 68_S | 91_L | 1.493 | 1.00 |
| 59_L | 99_A | 1.488 | 1.00 |
| 49_T | 114_H | 1.485 | 1.00 |
| 26_F | 61_M | 1.472 | 1.00 |
| 48_V | 52_L | 1.450 | 1.00 |
| 18_A | 87_R | 1.449 | 1.00 |
| 44_D | 50_R | 1.448 | 1.00 |
| 65_L | 91_L | 1.378 | 0.99 |
| 65_L | 94_A | 1.373 | 0.99 |
| 22_N | 87_R | 1.358 | 0.99 |
| 26_F | 29_E | 1.340 | 0.99 |
| 73_V | 77_I | 1.328 | 0.99 |
| 19_A | 26_F | 1.313 | 0.99 |
| 52_L | 56_S | 1.285 | 0.99 |
| 19_A | 91_L | 1.285 | 0.99 |
| 63_V | 95_A | 1.281 | 0.99 |
| 54_I | 102_D | 1.259 | 0.99 |
| 11_Y | 14_K | 1.251 | 0.99 |
| 49_T | 110_L | 1.230 | 0.98 |
| 7_K | 10_G | 1.209 | 0.98 |
| 84_L | 88_A | 1.203 | 0.98 |
| 37_V | 57_V | 1.181 | 0.98 |
| 65_L | 98_I | 1.171 | 0.98 |
| 5_I | 24_A | 1.157 | 0.97 |
| 5_I | 28_Q | 1.154 | 0.97 |
| 12_S | 93_S | 1.148 | 0.97 |
| 5_I | 9_A | 1.126 | 0.97 |
| 60_V | 103_A | 1.107 | 0.96 |
| 38_V | 42_W | 1.104 | 0.96 |
| 55_S | 102_D | 1.089 | 0.96 |
| 23_E | 72_A | 1.083 | 0.96 |
| 29_E | 96_V | 1.063 | 0.95 |
| 45_V | 53_L | 1.059 | 0.95 |
| 47_A | 51_V | 1.021 | 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 | -0.003 | Contact Map |
| 4w252 | 1 | 0.4138 | 9.4 | 0.927 | Contact Map |
| 1rh5B | 1 | 0.3793 | 8.5 | 0.928 | Contact Map |
| 4b03D | 3 | 0.5603 | 3.9 | 0.939 | Contact Map |
| 3b8cA | 2 | 0.931 | 2.8 | 0.943 | Contact Map |
| 4k1cA | 2 | 0.9052 | 2.7 | 0.944 | Contact Map |
| 2lzrA | 1 | 0.2931 | 2.6 | 0.944 | Contact Map |
| 3mp7B | 1 | 0.4655 | 2.4 | 0.945 | Contact Map |
| 4od4A | 6 | 0.7845 | 2.2 | 0.946 | Contact Map |
| 1pi7A | 1 | 0.1638 | 1.9 | 0.948 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)