| jul1B2M |
| ID: | 1478125394 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 104 (103) | ||
| Sequences: | 323 (243.3) | ||
| Seq/Len: | 3.136 | ||
| Nf(neff/√len): | 24.0 |
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: 3.136).
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 |
| 52_V | 87_A | 3.242 | 1.00 |
| 24_Y | 84_N | 2.840 | 1.00 |
| 23_G | 80_F | 2.645 | 1.00 |
| 42_Y | 45_Y | 2.530 | 1.00 |
| 5_T | 8_S | 2.292 | 1.00 |
| 100_F | 103_C | 2.013 | 1.00 |
| 79_V | 90_I | 1.998 | 1.00 |
| 36_N | 44_N | 1.738 | 0.99 |
| 4_Y | 86_L | 1.663 | 0.98 |
| 26_L | 31_E | 1.603 | 0.98 |
| 33_V | 36_N | 1.602 | 0.98 |
| 2_C | 10_C | 1.602 | 0.98 |
| 76_D | 91_T | 1.529 | 0.97 |
| 4_Y | 89_V | 1.526 | 0.96 |
| 22_A | 25_Q | 1.484 | 0.96 |
| 11_Y | 76_D | 1.475 | 0.96 |
| 19_A | 78_V | 1.464 | 0.95 |
| 91_T | 94_G | 1.461 | 0.95 |
| 50_F | 90_I | 1.434 | 0.95 |
| 52_V | 81_N | 1.424 | 0.94 |
| 58_E | 92_H | 1.422 | 0.94 |
| 20_Q | 80_F | 1.420 | 0.94 |
| 4_Y | 102_E | 1.414 | 0.94 |
| 26_L | 33_V | 1.337 | 0.91 |
| 52_V | 56_Y | 1.332 | 0.91 |
| 13_S | 17_S | 1.318 | 0.91 |
| 61_I | 89_V | 1.310 | 0.90 |
| 12_S | 15_D | 1.298 | 0.90 |
| 81_N | 87_A | 1.261 | 0.88 |
| 95_A | 101_V | 1.212 | 0.85 |
| 48_F | 90_I | 1.181 | 0.83 |
| 80_F | 84_N | 1.174 | 0.82 |
| 3_D | 12_S | 1.170 | 0.82 |
| 17_S | 21_A | 1.152 | 0.81 |
| 91_T | 95_A | 1.145 | 0.80 |
| 80_F | 87_A | 1.145 | 0.80 |
| 15_D | 65_G | 1.131 | 0.79 |
| 2_C | 86_L | 1.103 | 0.77 |
| 25_Q | 66_D | 1.099 | 0.76 |
| 18_T | 21_A | 1.086 | 0.75 |
| 86_L | 102_E | 1.086 | 0.75 |
| 44_N | 88_G | 1.062 | 0.73 |
| 93_T | 101_V | 1.060 | 0.72 |
| 81_N | 84_N | 1.059 | 0.72 |
| 86_L | 89_V | 1.053 | 0.72 |
| 12_S | 65_G | 1.030 | 0.69 |
| 84_N | 87_A | 1.004 | 0.66 |
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 | |
| 1i0vA | 1 | 1 | 100 | 0.07 | Contact Map |
| 1fusA | 1 | 0.9808 | 100 | 0.076 | Contact Map |
| 1rdsA | 1 | 0.9808 | 100 | 0.091 | Contact Map |
| 3agnA | 1 | 0.9808 | 100 | 0.126 | Contact Map |
| 3wr2A | 6 | 0.9231 | 100 | 0.155 | Contact Map |
| 2kaaA | 1 | 0.9712 | 100 | 0.258 | Contact Map |
| 1aqzA | 2 | 0.9519 | 99.9 | 0.348 | Contact Map |
| 1pylA | 2 | 0.8654 | 47.7 | 0.901 | Contact Map |
| 1lniA | 2 | 0.8654 | 42.8 | 0.904 | Contact Map |
| 2c4bA | 2 | 0.8942 | 37.7 | 0.907 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)