| d2ig3b_ |
| ID: | 1447473570 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 124 (119) | ||
| Sequences: | 1962 (1300.3) | ||
| Seq/Len: | 16.487 | ||
| Nf(neff/√len): | 119.2 |
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: 16.487).
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 |
| 79_P | 82_F | 3.467 | 1.00 |
| 16_E | 47_K | 3.351 | 1.00 |
| 21_K | 96_I | 2.920 | 1.00 |
| 21_K | 92_E | 2.736 | 1.00 |
| 12_A | 51_G | 2.687 | 1.00 |
| 91_E | 111_Q | 2.279 | 1.00 |
| 25_D | 85_I | 2.259 | 1.00 |
| 17_I | 96_I | 2.104 | 1.00 |
| 91_E | 107_L | 2.093 | 1.00 |
| 8_Q | 55_A | 2.002 | 1.00 |
| 17_I | 21_K | 1.958 | 1.00 |
| 23_R | 43_W | 1.796 | 1.00 |
| 94_L | 103_K | 1.781 | 1.00 |
| 17_I | 20_E | 1.663 | 1.00 |
| 27_D | 85_I | 1.660 | 1.00 |
| 95_N | 107_L | 1.642 | 1.00 |
| 8_Q | 12_A | 1.637 | 1.00 |
| 20_E | 47_K | 1.636 | 1.00 |
| 12_A | 48_A | 1.574 | 1.00 |
| 15_M | 54_W | 1.499 | 1.00 |
| 13_K | 97_V | 1.496 | 1.00 |
| 36_I | 41_E | 1.495 | 1.00 |
| 67_Q | 70_K | 1.465 | 1.00 |
| 55_A | 63_D | 1.455 | 1.00 |
| 94_L | 107_L | 1.437 | 1.00 |
| 48_A | 52_N | 1.413 | 1.00 |
| 95_N | 103_K | 1.354 | 0.99 |
| 3_F | 6_I | 1.342 | 0.99 |
| 52_N | 63_D | 1.336 | 0.99 |
| 69_L | 120_M | 1.319 | 0.99 |
| 8_Q | 51_G | 1.275 | 0.99 |
| 85_I | 89_L | 1.259 | 0.99 |
| 23_R | 29_G | 1.258 | 0.99 |
| 28_L | 82_F | 1.229 | 0.98 |
| 46_H | 54_W | 1.202 | 0.98 |
| 119_N | 122_Y | 1.176 | 0.98 |
| 10_S | 13_K | 1.154 | 0.97 |
| 12_A | 16_E | 1.142 | 0.97 |
| 58_L | 106_I | 1.141 | 0.97 |
| 31_I | 82_F | 1.114 | 0.96 |
| 5_T | 105_V | 1.091 | 0.96 |
| 95_N | 100_E | 1.084 | 0.96 |
| 91_E | 95_N | 1.079 | 0.95 |
| 28_L | 86_W | 1.068 | 0.95 |
| 32_F | 46_H | 1.056 | 0.95 |
| 7_N | 10_S | 1.053 | 0.95 |
| 108_Q | 112_M | 1.047 | 0.94 |
| 27_D | 88_K | 1.030 | 0.94 |
| 27_D | 30_P | 1.028 | 0.94 |
| 69_L | 117_F | 1.022 | 0.93 |
| 27_D | 82_F | 1.011 | 0.93 |
| 27_D | 81_E | 1.007 | 0.93 |
| 47_K | 51_G | 1.002 | 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 | |
| 2ig3A | 2 | 0.9919 | 100 | 0.086 | Contact Map |
| 4c0nA | 1 | 0.9435 | 99.9 | 0.19 | Contact Map |
| 4nk2A | 2 | 0.9516 | 99.9 | 0.215 | Contact Map |
| 4uurA | 2 | 0 | 99.9 | 0.229 | Contact Map |
| 1dlyA | 1 | 0.9355 | 99.9 | 0.256 | Contact Map |
| 3aq9A | 2 | 0.9113 | 99.9 | 0.279 | Contact Map |
| 2kscA | 1 | 0.9113 | 99.9 | 0.279 | Contact Map |
| 1s69A | 1 | 0.9194 | 99.9 | 0.285 | Contact Map |
| 2xykA | 2 | 0.9435 | 99.9 | 0.286 | Contact Map |
| 1dlwA | 1 | 0.9113 | 99.9 | 0.29 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)