| d4bjhb1 |
| ID: | 1448374004 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 142 (139) | ||
| Sequences: | 3866 (1876) | ||
| Seq/Len: | 27.813 | ||
| Nf(neff/√len): | 159.1 |
HHblits Results: (2015_06)
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: 27.813).
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 |
| 56_A | 61_I | 3.045 | 1.00 |
| 23_K | 138_K | 2.988 | 1.00 |
| 80_F | 107_E | 2.968 | 1.00 |
| 36_S | 56_A | 2.940 | 1.00 |
| 87_E | 113_N | 2.923 | 1.00 |
| 37_A | 91_F | 2.841 | 1.00 |
| 26_K | 139_E | 2.758 | 1.00 |
| 6_S | 125_Q | 2.524 | 1.00 |
| 16_E | 138_K | 2.482 | 1.00 |
| 20_K | 138_K | 2.480 | 1.00 |
| 95_V | 119_A | 2.396 | 1.00 |
| 57_R | 62_E | 2.385 | 1.00 |
| 23_K | 135_F | 2.297 | 1.00 |
| 11_T | 14_E | 2.072 | 1.00 |
| 100_F | 103_F | 1.996 | 1.00 |
| 50_L | 86_F | 1.989 | 1.00 |
| 41_F | 103_F | 1.944 | 1.00 |
| 12_R | 16_E | 1.900 | 1.00 |
| 2_R | 14_E | 1.898 | 1.00 |
| 22_A | 135_F | 1.764 | 1.00 |
| 36_S | 93_Y | 1.701 | 1.00 |
| 83_L | 108_I | 1.660 | 1.00 |
| 19_L | 135_F | 1.617 | 1.00 |
| 98_V | 121_D | 1.605 | 1.00 |
| 102_F | 107_E | 1.596 | 1.00 |
| 46_T | 76_G | 1.590 | 1.00 |
| 46_T | 82_T | 1.574 | 1.00 |
| 36_S | 95_V | 1.544 | 1.00 |
| 46_T | 72_S | 1.533 | 1.00 |
| 52_F | 128_S | 1.523 | 1.00 |
| 24_E | 28_G | 1.518 | 1.00 |
| 87_E | 114_L | 1.481 | 1.00 |
| 21_Y | 24_E | 1.469 | 1.00 |
| 94_V | 108_I | 1.457 | 1.00 |
| 137_I | 141_F | 1.422 | 1.00 |
| 19_L | 23_K | 1.395 | 0.99 |
| 19_L | 138_K | 1.358 | 0.99 |
| 80_F | 111_S | 1.352 | 0.99 |
| 4_L | 131_L | 1.328 | 0.99 |
| 49_R | 53_E | 1.326 | 0.99 |
| 51_S | 128_S | 1.298 | 0.99 |
| 29_K | 58_E | 1.298 | 0.99 |
| 56_A | 63_T | 1.285 | 0.99 |
| 57_R | 63_T | 1.265 | 0.99 |
| 35_A | 58_E | 1.247 | 0.99 |
| 84_K | 111_S | 1.226 | 0.98 |
| 72_S | 75_K | 1.217 | 0.98 |
| 3_S | 109_V | 1.209 | 0.98 |
| 106_K | 110_K | 1.177 | 0.98 |
| 94_V | 114_L | 1.173 | 0.98 |
| 36_S | 61_I | 1.168 | 0.97 |
| 76_G | 82_T | 1.166 | 0.97 |
| 88_G | 140_H | 1.159 | 0.97 |
| 35_A | 62_E | 1.142 | 0.97 |
| 80_F | 84_K | 1.137 | 0.97 |
| 19_L | 22_A | 1.099 | 0.96 |
| 23_K | 139_E | 1.098 | 0.96 |
| 53_E | 65_L | 1.086 | 0.96 |
| 134_F | 137_I | 1.085 | 0.96 |
| 17_E | 21_Y | 1.073 | 0.95 |
| 52_F | 119_A | 1.071 | 0.95 |
| 26_K | 135_F | 1.048 | 0.94 |
| 96_F | 108_I | 1.046 | 0.94 |
| 20_K | 24_E | 1.023 | 0.93 |
| 107_E | 110_K | 1.018 | 0.93 |
| 23_K | 27_E | 1.016 | 0.93 |
| 7_S | 15_V | 1.012 | 0.93 |
| 3_S | 87_E | 1.001 | 0.92 |
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 | |
| 3r7fA | 3 | 0.9859 | 100 | -0.021 | Contact Map |
| 4iv5A | 6 | 0.9789 | 100 | -0.018 | Contact Map |
| 1ml4A | 1 | 0.9789 | 100 | -0.015 | Contact Map |
| 1pg5A | 1 | 0.9296 | 100 | -0.014 | Contact Map |
| 1pvvA | 1 | 0.9718 | 100 | -0.01 | Contact Map |
| 3tpfA | 6 | 0.9718 | 100 | -0.01 | Contact Map |
| 2i6uA | 3 | 0.9718 | 100 | -0.009 | Contact Map |
| 4nf2A | 3 | 0.9718 | 100 | -0.007 | Contact Map |
| 1duvG | 3 | 0.9718 | 100 | -0.006 | Contact Map |
| 1dxhA | 1 | 0.9718 | 100 | -0.006 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)