| Q9HYR3_1Z1S |
| ID: | 1404254727 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 141 (131) | ||
| Sequences: | 3408 (2665.7) | ||
| Seq/Len: | 26.015 | ||
| Nf(neff/√len): | 232.9 |
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: 26.015).
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 |
| 106_R | 114_L | 3.462 | 1.00 |
| 27_H | 113_L | 3.064 | 1.00 |
| 84_F | 101_Y | 2.948 | 1.00 |
| 28_P | 48_R | 2.926 | 1.00 |
| 18_D | 21_G | 2.423 | 1.00 |
| 108_R | 113_L | 2.383 | 1.00 |
| 23_C | 52_W | 2.307 | 1.00 |
| 4_K | 8_V | 2.192 | 1.00 |
| 8_V | 12_R | 2.065 | 1.00 |
| 30_G | 51_I | 1.923 | 1.00 |
| 71_F | 85_H | 1.821 | 1.00 |
| 6_I | 107_T | 1.813 | 1.00 |
| 81_I | 104_V | 1.733 | 1.00 |
| 85_H | 98_A | 1.696 | 1.00 |
| 103_S | 117_D | 1.680 | 1.00 |
| 87_D | 98_A | 1.641 | 1.00 |
| 31_V | 114_L | 1.609 | 1.00 |
| 79_L | 106_R | 1.597 | 1.00 |
| 83_E | 116_R | 1.594 | 1.00 |
| 4_K | 76_D | 1.591 | 1.00 |
| 84_F | 103_S | 1.586 | 1.00 |
| 12_R | 16_N | 1.584 | 1.00 |
| 20_R | 52_W | 1.570 | 1.00 |
| 26_F | 51_I | 1.570 | 1.00 |
| 33_E | 116_R | 1.568 | 1.00 |
| 33_E | 114_L | 1.566 | 1.00 |
| 5_E | 9_H | 1.565 | 1.00 |
| 47_G | 50_T | 1.546 | 1.00 |
| 83_E | 118_F | 1.540 | 1.00 |
| 19_A | 23_C | 1.537 | 1.00 |
| 72_Y | 83_E | 1.510 | 1.00 |
| 13_L | 18_D | 1.506 | 1.00 |
| 78_D | 108_R | 1.502 | 1.00 |
| 9_H | 25_L | 1.490 | 1.00 |
| 23_C | 48_R | 1.465 | 1.00 |
| 26_F | 30_G | 1.459 | 1.00 |
| 49_E | 52_W | 1.418 | 1.00 |
| 21_G | 24_D | 1.399 | 0.99 |
| 27_H | 109_D | 1.393 | 0.99 |
| 34_F | 117_D | 1.389 | 0.99 |
| 13_L | 21_G | 1.385 | 0.99 |
| 74_T | 81_I | 1.364 | 0.99 |
| 33_E | 44_R | 1.349 | 0.99 |
| 7_L | 80_A | 1.299 | 0.99 |
| 17_G | 59_P | 1.296 | 0.99 |
| 63_T | 89_V | 1.296 | 0.99 |
| 85_H | 100_D | 1.285 | 0.99 |
| 48_R | 111_Q | 1.281 | 0.99 |
| 52_W | 56_R | 1.271 | 0.99 |
| 53_A | 56_R | 1.267 | 0.99 |
| 49_E | 53_A | 1.265 | 0.99 |
| 106_R | 113_L | 1.251 | 0.99 |
| 3_A | 107_T | 1.241 | 0.98 |
| 9_H | 13_L | 1.229 | 0.98 |
| 87_D | 96_K | 1.224 | 0.98 |
| 72_Y | 79_L | 1.211 | 0.98 |
| 103_S | 115_Y | 1.190 | 0.98 |
| 78_D | 106_R | 1.176 | 0.98 |
| 31_V | 46_E | 1.155 | 0.97 |
| 122_L | 126_E | 1.135 | 0.97 |
| 67_T | 87_D | 1.131 | 0.97 |
| 20_R | 24_D | 1.122 | 0.97 |
| 28_P | 111_Q | 1.120 | 0.96 |
| 73_E | 82_G | 1.098 | 0.96 |
| 2_N | 5_E | 1.090 | 0.96 |
| 29_E | 108_R | 1.089 | 0.96 |
| 7_L | 105_L | 1.083 | 0.96 |
| 7_L | 107_T | 1.048 | 0.94 |
| 29_E | 113_L | 1.043 | 0.94 |
| 67_T | 71_F | 1.040 | 0.94 |
| 20_R | 23_C | 1.040 | 0.94 |
| 12_R | 15_E | 1.039 | 0.94 |
| 89_V | 96_K | 1.004 | 0.93 |
| 16_N | 21_G | 1.001 | 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
- 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 | |
| 1z1sA | 1 | 0.9007 | 99.9 | 0.171 | Contact Map |
| 1s5aA | 4 | 0.9574 | 99.9 | 0.248 | Contact Map |
| 3f9sA | 2 | 0.9078 | 99.8 | 0.266 | Contact Map |
| 3jumA | 2 | 0.9716 | 99.8 | 0.272 | Contact Map |
| 3fgyA | 2 | 0.922 | 99.8 | 0.273 | Contact Map |
| 3ff0A | 2 | 0.9716 | 99.8 | 0.279 | Contact Map |
| 3dm8A | 1 | 0.9078 | 99.8 | 0.28 | Contact Map |
| 4lgqA | 4 | 0.8723 | 99.8 | 0.285 | Contact Map |
| 3ec9A | 2 | 0.9007 | 99.8 | 0.288 | Contact Map |
| 1sjwA | 1 | 0.9291 | 99.8 | 0.295 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)