| SYNTH CC low coverage |
| ID: | 1425300256 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 182 (179) | ||
| Sequences: | 1309 (671.8) | ||
| Seq/Len: | 7.313 | ||
| Nf(neff/√len): | 50.2 |
HHblits Results: (2013_03)
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: 7.313).
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_D | 113_E | 3.670 | 1.00 |
| 54_I | 113_E | 3.094 | 1.00 |
| 57_S | 60_D | 3.053 | 1.00 |
| 8_I | 68_V | 2.974 | 1.00 |
| 151_R | 158_D | 2.851 | 1.00 |
| 22_F | 116_D | 2.664 | 1.00 |
| 11_R | 14_S | 2.609 | 1.00 |
| 20_R | 113_E | 2.540 | 1.00 |
| 40_I | 45_M | 2.507 | 1.00 |
| 18_P | 56_D | 2.244 | 1.00 |
| 3_L | 102_R | 2.176 | 1.00 |
| 145_R | 162_I | 2.103 | 1.00 |
| 68_V | 98_V | 2.061 | 1.00 |
| 1_V | 23_G | 2.047 | 1.00 |
| 4_V | 106_I | 1.733 | 1.00 |
| 53_V | 64_A | 1.726 | 1.00 |
| 55_V | 64_A | 1.720 | 1.00 |
| 10_A | 14_S | 1.681 | 1.00 |
| 59_E | 63_R | 1.659 | 1.00 |
| 9_A | 13_E | 1.658 | 1.00 |
| 48_I | 84_S | 1.613 | 1.00 |
| 11_R | 71_A | 1.590 | 1.00 |
| 160_H | 164_C | 1.578 | 1.00 |
| 138_C | 164_C | 1.569 | 1.00 |
| 60_D | 63_R | 1.563 | 1.00 |
| 138_C | 160_H | 1.553 | 1.00 |
| 113_E | 117_R | 1.540 | 1.00 |
| 64_A | 67_V | 1.530 | 0.99 |
| 159_V | 180_L | 1.496 | 0.99 |
| 2_A | 5_S | 1.464 | 0.99 |
| 33_R | 37_R | 1.453 | 0.99 |
| 56_D | 60_D | 1.432 | 0.99 |
| 35_L | 82_F | 1.404 | 0.99 |
| 69_H | 96_T | 1.369 | 0.99 |
| 74_S | 84_S | 1.351 | 0.98 |
| 134_F | 141_V | 1.345 | 0.98 |
| 92_R | 118_V | 1.326 | 0.98 |
| 80_K | 97_T | 1.301 | 0.98 |
| 137_C | 160_H | 1.299 | 0.98 |
| 137_C | 164_C | 1.292 | 0.98 |
| 78_R | 97_T | 1.278 | 0.98 |
| 62_Y | 69_H | 1.272 | 0.97 |
| 65_L | 69_H | 1.268 | 0.97 |
| 58_E | 70_R | 1.265 | 0.97 |
| 5_S | 9_A | 1.265 | 0.97 |
| 55_V | 60_D | 1.260 | 0.97 |
| 117_R | 121_E | 1.246 | 0.97 |
| 116_D | 120_E | 1.243 | 0.97 |
| 4_V | 51_F | 1.223 | 0.97 |
| 5_S | 51_F | 1.221 | 0.97 |
| 15_S | 64_A | 1.219 | 0.97 |
| 147_V | 167_L | 1.207 | 0.96 |
| 20_R | 35_L | 1.202 | 0.96 |
| 40_I | 166_K | 1.182 | 0.96 |
| 147_V | 177_W | 1.155 | 0.95 |
| 4_V | 72_W | 1.154 | 0.95 |
| 127_F | 137_C | 1.126 | 0.94 |
| 15_S | 67_V | 1.122 | 0.94 |
| 13_E | 19_A | 1.119 | 0.94 |
| 12_L | 64_A | 1.116 | 0.94 |
| 134_F | 159_V | 1.115 | 0.94 |
| 65_L | 87_K | 1.113 | 0.93 |
| 99_V | 103_G | 1.111 | 0.93 |
| 7_E | 72_W | 1.108 | 0.93 |
| 69_H | 79_F | 1.105 | 0.93 |
| 62_Y | 65_L | 1.097 | 0.93 |
| 40_I | 78_R | 1.096 | 0.93 |
| 6_Q | 10_A | 1.091 | 0.93 |
| 149_I | 176_L | 1.080 | 0.92 |
| 101_P | 106_I | 1.075 | 0.92 |
| 8_I | 181_N | 1.069 | 0.92 |
| 149_I | 170_Y | 1.066 | 0.91 |
| 127_F | 140_P | 1.055 | 0.91 |
| 12_L | 19_A | 1.048 | 0.90 |
| 8_I | 108_M | 1.042 | 0.90 |
| 19_A | 64_A | 1.039 | 0.90 |
| 135_A | 158_D | 1.015 | 0.88 |
| 5_S | 21_V | 1.014 | 0.88 |
| 13_E | 18_P | 1.000 | 0.87 |
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 | |
| 1vj7A | 2 | 0.7308 | 100 | 0.439 | Contact Map |
| 3l9dA | 2 | 0.8516 | 100 | 0.542 | Contact Map |
| 2be3A | 2 | 0.8571 | 100 | 0.567 | Contact Map |
| 1x5bA | 1 | 0.3736 | 20.5 | 0.965 | Contact Map |
| 4r3oF | 2 | 0.3571 | 18.1 | 0.966 | Contact Map |
| 1nthA | 1 | 0.3681 | 13.6 | 0.968 | Contact Map |
| 1evlA | 4 | 0.4615 | 10.3 | 0.97 | Contact Map |
| 4r3oC | 2 | 0.3462 | 10.2 | 0.97 | Contact Map |
| 3rh7A | 6 | 0.456 | 9.1 | 0.971 | Contact Map |
| 4driB | 1 | 0.1923 | 8.6 | 0.971 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)