| d3lndc1 |
| ID: | 1450282122 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 96 (93) | ||
| Sequences: | 5858 (3996.9) | ||
| Seq/Len: | 62.989 | ||
| Nf(neff/√len): | 414.5 |
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: 62.989).
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 |
| 4_F | 19_G | 3.767 | 1.00 |
| 62_R | 66_P | 3.287 | 1.00 |
| 7_L | 94_H | 2.476 | 1.00 |
| 17_Y | 53_D | 2.420 | 1.00 |
| 32_L | 74_A | 2.373 | 1.00 |
| 33_K | 77_R | 2.191 | 1.00 |
| 37_S | 73_Q | 2.176 | 1.00 |
| 46_I | 55_Q | 2.158 | 1.00 |
| 48_N | 51_T | 2.023 | 1.00 |
| 20_K | 53_D | 1.989 | 1.00 |
| 73_Q | 84_E | 1.952 | 1.00 |
| 23_S | 34_Y | 1.947 | 1.00 |
| 9_E | 96_I | 1.813 | 1.00 |
| 5_F | 92_K | 1.768 | 1.00 |
| 65_K | 68_Y | 1.728 | 1.00 |
| 5_F | 94_H | 1.697 | 1.00 |
| 44_L | 58_K | 1.683 | 1.00 |
| 47_I | 54_I | 1.675 | 1.00 |
| 35_I | 75_V | 1.649 | 1.00 |
| 56_A | 60_L | 1.636 | 1.00 |
| 69_I | 88_E | 1.618 | 1.00 |
| 54_I | 89_F | 1.536 | 1.00 |
| 46_I | 57_T | 1.525 | 1.00 |
| 7_L | 96_I | 1.509 | 1.00 |
| 70_L | 89_F | 1.502 | 1.00 |
| 35_I | 73_Q | 1.498 | 1.00 |
| 78_R | 81_R | 1.473 | 1.00 |
| 67_V | 92_K | 1.462 | 1.00 |
| 75_V | 84_E | 1.445 | 1.00 |
| 10_Y | 56_A | 1.440 | 1.00 |
| 44_L | 68_Y | 1.420 | 1.00 |
| 31_S | 77_R | 1.355 | 0.99 |
| 33_K | 49_E | 1.351 | 0.99 |
| 71_R | 86_E | 1.302 | 0.99 |
| 72_A | 89_F | 1.269 | 0.99 |
| 31_S | 50_N | 1.267 | 0.99 |
| 71_R | 88_E | 1.256 | 0.99 |
| 10_Y | 16_Q | 1.209 | 0.98 |
| 69_I | 90_I | 1.186 | 0.98 |
| 73_Q | 86_E | 1.180 | 0.98 |
| 67_V | 90_I | 1.167 | 0.97 |
| 17_Y | 20_K | 1.149 | 0.97 |
| 8_E | 61_D | 1.140 | 0.97 |
| 8_E | 63_E | 1.122 | 0.97 |
| 21_L | 72_A | 1.099 | 0.96 |
| 45_F | 91_I | 1.084 | 0.96 |
| 62_R | 95_D | 1.081 | 0.95 |
| 17_Y | 55_Q | 1.081 | 0.95 |
| 45_F | 68_Y | 1.068 | 0.95 |
| 33_K | 50_N | 1.057 | 0.95 |
| 48_N | 55_Q | 1.018 | 0.93 |
| 63_E | 95_D | 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 | |
| 2omzB | 1 | 0.9688 | 99.6 | -0.017 | Contact Map |
| 1zxkA | 2 | 0.9583 | 99.6 | -0.005 | Contact Map |
| 1zvnA | 2 | 0.9896 | 99.6 | 0.003 | Contact Map |
| 3qrbA | 2 | 0.9792 | 99.5 | 0.048 | Contact Map |
| 3k6fA | 2 | 0.9479 | 99.5 | 0.078 | Contact Map |
| 3lndA | 4 | 1 | 99.5 | 0.085 | Contact Map |
| 3k6iA | 1 | 0.9479 | 99.5 | 0.085 | Contact Map |
| 2ystA | 1 | 0.9688 | 99.5 | 0.089 | Contact Map |
| 3q2wA | 1 | 0.9792 | 99.5 | 0.093 | Contact Map |
| 3q2vA | 2 | 0.9792 | 99.5 | 0.094 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)