| cb evalue 1000000 |
| ID: | 1494447095 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 129 (129) | ||
| Sequences: | 1148 (1073.1) | ||
| Seq/Len: | 8.899 | ||
| Nf(neff/√len): | 94.5 |
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: 8.899).
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 |
| 63_K | 66_P | 2.379 | 1.00 |
| 66_P | 69_N | 1.937 | 1.00 |
| 2_L | 5_V | 1.611 | 1.00 |
| 115_P | 118_Q | 1.525 | 1.00 |
| 20_I | 23_T | 1.503 | 1.00 |
| 100_Y | 103_S | 1.478 | 1.00 |
| 124_A | 127_R | 1.434 | 0.99 |
| 72_R | 75_L | 1.409 | 0.99 |
| 74_A | 77_S | 1.398 | 0.99 |
| 126_G | 129_D | 1.396 | 0.99 |
| 12_V | 15_P | 1.389 | 0.99 |
| 13_F | 16_S | 1.345 | 0.99 |
| 121_S | 124_A | 1.339 | 0.99 |
| 3_K | 8_P | 1.334 | 0.99 |
| 96_Q | 99_F | 1.326 | 0.99 |
| 4_N | 7_P | 1.325 | 0.99 |
| 85_F | 88_D | 1.323 | 0.99 |
| 22_H | 25_K | 1.322 | 0.99 |
| 9_E | 12_V | 1.311 | 0.99 |
| 1_D | 5_V | 1.277 | 0.98 |
| 119_I | 122_A | 1.258 | 0.98 |
| 4_N | 11_A | 1.253 | 0.98 |
| 102_L | 105_N | 1.246 | 0.98 |
| 16_S | 20_I | 1.236 | 0.98 |
| 86_W | 95_C | 1.234 | 0.98 |
| 125_W | 128_A | 1.219 | 0.98 |
| 89_P | 92_H | 1.215 | 0.98 |
| 10_V | 13_F | 1.213 | 0.98 |
| 25_K | 30_C | 1.198 | 0.97 |
| 75_L | 78_R | 1.195 | 0.97 |
| 117_T | 120_V | 1.183 | 0.97 |
| 118_Q | 122_A | 1.178 | 0.97 |
| 73_Y | 77_S | 1.176 | 0.97 |
| 72_R | 80_R | 1.169 | 0.97 |
| 99_F | 102_L | 1.155 | 0.96 |
| 77_S | 82_S | 1.149 | 0.96 |
| 19_E | 25_K | 1.149 | 0.96 |
| 13_F | 20_I | 1.149 | 0.96 |
| 111_D | 115_P | 1.147 | 0.96 |
| 76_S | 80_R | 1.145 | 0.96 |
| 59_P | 63_K | 1.141 | 0.96 |
| 17_E | 22_H | 1.113 | 0.95 |
| 116_V | 121_S | 1.113 | 0.95 |
| 118_Q | 128_A | 1.112 | 0.95 |
| 14_E | 21_S | 1.109 | 0.95 |
| 71_S | 76_S | 1.106 | 0.95 |
| 32_A | 45_W | 1.104 | 0.95 |
| 7_P | 10_V | 1.096 | 0.95 |
| 107_E | 113_A | 1.091 | 0.95 |
| 87_Q | 90_R | 1.089 | 0.95 |
| 71_S | 75_L | 1.075 | 0.94 |
| 8_P | 11_A | 1.069 | 0.94 |
| 88_D | 92_H | 1.065 | 0.94 |
| 24_Q | 27_T | 1.061 | 0.94 |
| 19_E | 22_H | 1.059 | 0.94 |
| 118_Q | 123_E | 1.058 | 0.94 |
| 26_A | 29_V | 1.049 | 0.93 |
| 30_C | 36_Y | 1.047 | 0.93 |
| 5_V | 10_V | 1.046 | 0.93 |
| 4_N | 22_H | 1.045 | 0.93 |
| 29_V | 34_G | 1.042 | 0.93 |
| 120_V | 123_E | 1.041 | 0.93 |
| 6_F | 11_A | 1.041 | 0.93 |
| 56_C | 59_P | 1.036 | 0.93 |
| 103_S | 111_D | 1.034 | 0.92 |
| 109_T | 112_R | 1.030 | 0.92 |
| 9_E | 13_F | 1.029 | 0.92 |
| 70_D | 73_Y | 1.027 | 0.92 |
| 36_Y | 41_E | 1.025 | 0.92 |
| 24_Q | 28_L | 1.022 | 0.92 |
| 83_A | 90_R | 1.019 | 0.92 |
| 105_N | 108_W | 1.012 | 0.91 |
| 103_S | 106_D | 1.012 | 0.91 |
| 115_P | 119_I | 1.012 | 0.91 |
| 81_V | 84_T | 1.009 | 0.91 |
| 73_Y | 76_S | 1.000 | 0.91 |
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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 4udtB | 1 | 0 | 98.7 | 0.583 | Contact Map |
| 4p2qE | 4 | 0 | 98.6 | 0.588 | Contact Map |
| 2bnuB | 1 | 0 | 98.6 | 0.59 | Contact Map |
| 3pl6D | 1 | 1 | 98.6 | 0.595 | Contact Map |
| 4mayD | 1 | 1 | 98.5 | 0.607 | Contact Map |
| 4jfhE | 1 | 1 | 98.5 | 0.611 | Contact Map |
| 3to4D | 1 | 1 | 98.4 | 0.616 | Contact Map |
| 4dzbB | 1 | 0.9922 | 98.4 | 0.617 | Contact Map |
| 1becA | 1 | 0.969 | 98.4 | 0.622 | Contact Map |
| 2wbjD | 2 | 0.9922 | 98.4 | 0.623 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)