| ParD3 |
| ID: | 1448146924 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 99 (98) | ||
| Sequences: | 3860 (3200.7) | ||
| Seq/Len: | 39.388 | ||
| Nf(neff/√len): | 323.3 |
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: 39.388).
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 |
| 14_D | 87_A | 2.962 | 1.00 |
| 7_W | 42_T | 2.897 | 1.00 |
| 44_K | 51_L | 2.535 | 1.00 |
| 55_D | 64_R | 2.496 | 1.00 |
| 6_E | 82_Q | 2.286 | 1.00 |
| 27_S | 30_D | 2.043 | 1.00 |
| 50_R | 76_V | 1.973 | 1.00 |
| 77_D | 84_R | 1.925 | 1.00 |
| 5_V | 46_A | 1.880 | 1.00 |
| 12_I | 16_T | 1.824 | 1.00 |
| 52_Y | 65_I | 1.821 | 1.00 |
| 53_E | 64_R | 1.770 | 1.00 |
| 37_R | 68_V | 1.756 | 1.00 |
| 19_F | 32_R | 1.716 | 1.00 |
| 75_E | 86_L | 1.702 | 1.00 |
| 15_V | 35_T | 1.668 | 1.00 |
| 3_Y | 76_V | 1.654 | 1.00 |
| 94_N | 97_S | 1.507 | 1.00 |
| 62_V | 86_L | 1.417 | 1.00 |
| 41_A | 65_I | 1.414 | 1.00 |
| 52_Y | 74_Y | 1.411 | 1.00 |
| 22_I | 30_D | 1.399 | 0.99 |
| 64_R | 73_L | 1.392 | 0.99 |
| 22_I | 26_S | 1.381 | 0.99 |
| 73_L | 95_P | 1.378 | 0.99 |
| 89_V | 93_Q | 1.369 | 0.99 |
| 17_A | 93_Q | 1.364 | 0.99 |
| 18_L | 88_V | 1.361 | 0.99 |
| 30_D | 33_D | 1.326 | 0.99 |
| 42_T | 72_V | 1.312 | 0.99 |
| 39_L | 43_D | 1.310 | 0.99 |
| 7_W | 11_A | 1.304 | 0.99 |
| 4_D | 82_Q | 1.291 | 0.99 |
| 30_D | 34_V | 1.285 | 0.99 |
| 22_I | 34_V | 1.276 | 0.99 |
| 41_A | 44_K | 1.263 | 0.99 |
| 45_L | 65_I | 1.253 | 0.99 |
| 19_F | 31_A | 1.231 | 0.98 |
| 6_E | 84_R | 1.225 | 0.98 |
| 22_I | 71_H | 1.212 | 0.98 |
| 29_W | 33_D | 1.204 | 0.98 |
| 26_S | 30_D | 1.182 | 0.98 |
| 90_G | 93_Q | 1.179 | 0.98 |
| 48_F | 51_L | 1.178 | 0.98 |
| 15_V | 88_V | 1.137 | 0.97 |
| 19_F | 35_T | 1.135 | 0.97 |
| 8_K | 86_L | 1.124 | 0.97 |
| 37_R | 69_G | 1.123 | 0.97 |
| 23_A | 31_A | 1.108 | 0.96 |
| 62_V | 73_L | 1.100 | 0.96 |
| 15_V | 38_I | 1.096 | 0.96 |
| 55_D | 62_V | 1.092 | 0.96 |
| 35_T | 39_L | 1.083 | 0.96 |
| 73_L | 89_V | 1.080 | 0.95 |
| 55_D | 73_L | 1.064 | 0.95 |
| 75_E | 84_R | 1.045 | 0.94 |
| 16_T | 20_D | 1.031 | 0.94 |
| 89_V | 95_P | 1.023 | 0.93 |
| 34_V | 38_I | 1.007 | 0.93 |
| 14_D | 17_A | 1.000 | 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 | |
| 3kxeA | 2 | 0.9495 | 99.7 | 0.125 | Contact Map |
| 4fxiA | 3 | 0.8485 | 98.5 | 0.507 | Contact Map |
| 2kheA | 1 | 0.8788 | 98.5 | 0.509 | Contact Map |
| 1wmiA | 2 | 0.8283 | 98.3 | 0.528 | Contact Map |
| 3g5oB | 2 | 0.8182 | 98.1 | 0.555 | Contact Map |
| 3bpqB | 2 | 0.8081 | 97.6 | 0.607 | Contact Map |
| 2a6sA | 4 | 0.798 | 97.3 | 0.622 | Contact Map |
| 4ml2A | 1 | 0.8384 | 97.3 | 0.627 | Contact Map |
| 4lttA | 1 | 0.8586 | 97.1 | 0.638 | Contact Map |
| 4nrnA | 2 | 0.8485 | 97 | 0.641 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)