| scpb |
| ID: | 1485873083 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 197 (176) | ||
| Sequences: | 2903 (1864.4) | ||
| Seq/Len: | 16.494 | ||
| Nf(neff/√len): | 140.5 |
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: 16.494).
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 |
| 136_V | 149_G | 5.112 | 1.00 |
| 9_K | 50_E | 4.534 | 1.00 |
| 14_A | 75_F | 3.273 | 1.00 |
| 9_K | 46_D | 3.196 | 1.00 |
| 11_I | 78_Y | 2.671 | 1.00 |
| 10_A | 75_F | 2.554 | 1.00 |
| 62_E | 161_K | 2.435 | 1.00 |
| 138_R | 146_I | 2.335 | 1.00 |
| 8_W | 43_I | 2.307 | 1.00 |
| 50_E | 56_R | 2.251 | 1.00 |
| 161_K | 165_E | 2.076 | 1.00 |
| 113_E | 120_S | 2.066 | 1.00 |
| 60_L | 69_L | 2.043 | 1.00 |
| 9_K | 43_I | 1.916 | 1.00 |
| 47_V | 51_Y | 1.913 | 1.00 |
| 150_T | 155_L | 1.857 | 1.00 |
| 59_E | 72_K | 1.857 | 1.00 |
| 135_E | 146_I | 1.849 | 1.00 |
| 29_L | 40_L | 1.764 | 1.00 |
| 12_V | 43_I | 1.757 | 1.00 |
| 91_S | 94_S | 1.729 | 1.00 |
| 28_Q | 31_T | 1.669 | 1.00 |
| 134_C | 149_G | 1.649 | 1.00 |
| 15_L | 24_L | 1.645 | 1.00 |
| 101_V | 133_L | 1.642 | 1.00 |
| 105_Q | 150_T | 1.641 | 1.00 |
| 111_E | 139_A | 1.634 | 1.00 |
| 128_V | 133_L | 1.628 | 1.00 |
| 36_E | 39_E | 1.618 | 1.00 |
| 142_P | 145_A | 1.613 | 1.00 |
| 107_I | 111_E | 1.607 | 1.00 |
| 100_I | 115_I | 1.586 | 1.00 |
| 131_A | 153_T | 1.579 | 1.00 |
| 25_T | 28_Q | 1.567 | 1.00 |
| 13_E | 51_Y | 1.559 | 1.00 |
| 26_K | 41_N | 1.555 | 1.00 |
| 68_M | 156_E | 1.530 | 1.00 |
| 103_Y | 167_P | 1.508 | 1.00 |
| 27_K | 37_E | 1.507 | 1.00 |
| 101_V | 124_L | 1.470 | 1.00 |
| 16_L | 69_L | 1.470 | 1.00 |
| 45_A | 48_A | 1.466 | 1.00 |
| 26_K | 40_L | 1.461 | 1.00 |
| 112_I | 124_L | 1.458 | 1.00 |
| 44_M | 60_L | 1.432 | 1.00 |
| 61_I | 70_S | 1.397 | 0.99 |
| 162_T | 165_E | 1.395 | 0.99 |
| 48_A | 60_L | 1.381 | 0.99 |
| 102_S | 154_F | 1.376 | 0.99 |
| 62_E | 67_Y | 1.367 | 0.99 |
| 13_E | 56_R | 1.343 | 0.99 |
| 23_G | 66_T | 1.340 | 0.99 |
| 14_A | 79_L | 1.330 | 0.99 |
| 21_D | 28_Q | 1.321 | 0.99 |
| 62_E | 65_D | 1.305 | 0.99 |
| 30_L | 40_L | 1.303 | 0.99 |
| 153_T | 156_E | 1.300 | 0.99 |
| 26_K | 67_Y | 1.279 | 0.99 |
| 105_Q | 163_L | 1.275 | 0.99 |
| 100_I | 107_I | 1.274 | 0.99 |
| 49_D | 52_R | 1.225 | 0.98 |
| 45_A | 49_D | 1.224 | 0.98 |
| 8_W | 35_I | 1.222 | 0.98 |
| 168_P | 171_E | 1.217 | 0.98 |
| 33_L | 40_L | 1.198 | 0.98 |
| 42_T | 45_A | 1.198 | 0.98 |
| 41_N | 62_E | 1.192 | 0.98 |
| 63_Y | 66_T | 1.185 | 0.98 |
| 140_D | 144_R | 1.164 | 0.97 |
| 43_I | 46_D | 1.156 | 0.97 |
| 137_G | 147_L | 1.133 | 0.97 |
| 34_E | 81_K | 1.127 | 0.97 |
| 48_A | 62_E | 1.103 | 0.96 |
| 17_Y | 71_T | 1.089 | 0.96 |
| 141_G | 145_A | 1.082 | 0.96 |
| 50_E | 54_D | 1.080 | 0.95 |
| 17_Y | 69_L | 1.077 | 0.95 |
| 97_V | 120_S | 1.071 | 0.95 |
| 30_L | 37_E | 1.061 | 0.95 |
| 126_S | 130_K | 1.061 | 0.95 |
| 10_A | 57_G | 1.047 | 0.94 |
| 168_P | 172_N | 1.044 | 0.94 |
| 35_I | 39_E | 1.042 | 0.94 |
| 15_L | 29_L | 1.036 | 0.94 |
| 17_Y | 58_I | 1.021 | 0.93 |
| 167_P | 170_P | 1.012 | 0.93 |
| 104_K | 111_E | 1.006 | 0.93 |
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 | |
| 3w6jB | 4 | 0.8528 | 100 | 0.1 | Contact Map |
| 4i98B | 2 | 0.8325 | 100 | 0.113 | Contact Map |
| 2z99A | 1 | 0.802 | 100 | 0.133 | Contact Map |
| 1t6sA | 2 | 0.8071 | 100 | 0.174 | Contact Map |
| 3w6kB | 4 | 0.4467 | 99.7 | 0.691 | Contact Map |
| 1p4xA | 1 | 0.8832 | 96.6 | 0.883 | Contact Map |
| 2bv6A | 1 | 0.6701 | 95.2 | 0.897 | Contact Map |
| 1z91A | 1 | 0.6751 | 94.8 | 0.899 | Contact Map |
| 3bddA | 4 | 0.6701 | 94.7 | 0.9 | Contact Map |
| 3hsrA | 4 | 0.6497 | 94.6 | 0.9 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)