| 3ze3 |
| ID: | 1501760511 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 116 (114) | ||
| Sequences: | 693 (692) | ||
| Seq/Len: | 6.079 | ||
| Nf(neff/√len): | 64.8 |
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: 6.079).
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 | 4.177 | 1.00 |
| 14_K | 86_G | 3.135 | 1.00 |
| 19_A | 65_L | 2.738 | 1.00 |
| 20_W | 30_G | 2.574 | 1.00 |
| 63_V | 66_L | 2.479 | 1.00 |
| 76_R | 85_S | 2.469 | 1.00 |
| 60_V | 96_V | 2.017 | 1.00 |
| 68_S | 91_L | 1.831 | 1.00 |
| 58_M | 102_D | 1.801 | 1.00 |
| 73_V | 88_A | 1.769 | 1.00 |
| 40_A | 50_R | 1.755 | 1.00 |
| 16_L | 94_A | 1.742 | 1.00 |
| 33_V | 57_V | 1.699 | 1.00 |
| 62_I | 99_A | 1.629 | 1.00 |
| 46_D | 49_T | 1.583 | 0.99 |
| 5_I | 28_Q | 1.548 | 0.99 |
| 17_R | 21_I | 1.519 | 0.99 |
| 107_W | 111_L | 1.452 | 0.99 |
| 63_V | 99_A | 1.438 | 0.99 |
| 84_L | 88_A | 1.424 | 0.99 |
| 40_A | 53_L | 1.375 | 0.98 |
| 8_A | 25_A | 1.372 | 0.98 |
| 25_A | 29_E | 1.367 | 0.98 |
| 73_V | 77_I | 1.354 | 0.98 |
| 25_A | 28_Q | 1.347 | 0.98 |
| 12_S | 93_S | 1.337 | 0.97 |
| 63_V | 95_A | 1.322 | 0.97 |
| 65_L | 91_L | 1.296 | 0.97 |
| 45_V | 110_L | 1.276 | 0.96 |
| 65_L | 94_A | 1.276 | 0.96 |
| 29_E | 96_V | 1.270 | 0.96 |
| 72_A | 87_R | 1.268 | 0.96 |
| 75_D | 89_K | 1.264 | 0.96 |
| 68_S | 72_A | 1.253 | 0.96 |
| 3_T | 7_K | 1.242 | 0.96 |
| 30_G | 61_M | 1.239 | 0.96 |
| 8_A | 12_S | 1.215 | 0.95 |
| 68_S | 87_R | 1.201 | 0.95 |
| 26_F | 29_E | 1.196 | 0.94 |
| 44_D | 50_R | 1.189 | 0.94 |
| 18_A | 87_R | 1.164 | 0.93 |
| 108_A | 112_W | 1.157 | 0.93 |
| 72_A | 91_L | 1.157 | 0.93 |
| 7_K | 10_G | 1.147 | 0.93 |
| 88_A | 92_G | 1.141 | 0.92 |
| 19_A | 26_F | 1.126 | 0.92 |
| 77_I | 85_S | 1.107 | 0.91 |
| 26_F | 61_M | 1.105 | 0.91 |
| 108_A | 111_L | 1.063 | 0.88 |
| 18_A | 91_L | 1.059 | 0.88 |
| 29_E | 100_I | 1.058 | 0.88 |
| 74_V | 88_A | 1.050 | 0.87 |
| 78_G | 85_S | 1.048 | 0.87 |
| 19_A | 91_L | 1.040 | 0.87 |
| 38_V | 42_W | 1.040 | 0.87 |
| 45_V | 50_R | 1.037 | 0.87 |
| 45_V | 53_L | 1.032 | 0.86 |
| 5_I | 9_A | 1.027 | 0.86 |
| 49_T | 110_L | 1.012 | 0.85 |
| 69_A | 88_A | 1.010 | 0.85 |
| 73_V | 85_S | 1.008 | 0.84 |
| 65_L | 98_I | 1.005 | 0.84 |
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 | Contact Map |
| 1rh5B | 1 | 0.3793 | 6.5 | 0.932 | Contact Map |
| 4w252 | 1 | 0.4138 | 5.2 | 0.935 | Contact Map |
| 4b03D | 3 | 0.5603 | 3.9 | 0.939 | Contact Map |
| 3b8cA | 2 | 0.931 | 3.9 | 0.939 | Contact Map |
| 4od4A | 6 | 0.7845 | 3 | 0.942 | Contact Map |
| 4k1cA | 2 | 0.8966 | 2.9 | 0.942 | Contact Map |
| 1pi7A | 1 | 0.1638 | 2 | 0.947 | Contact Map |
| 3nd0A | 2 | 0.2328 | 1.9 | 0.948 | Contact Map |
| 4cctD | 3 | 0.5517 | 1.8 | 0.948 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)