| lys |
| ID: | 1452532556 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 129 (128) | ||
| Sequences: | 543 (330.4) | ||
| Seq/Len: | 4.242 | ||
| Nf(neff/√len): | 29.2 |
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: 4.242).
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 |
| 85_S | 91_S | 3.287 | 1.00 |
| 85_S | 90_A | 2.804 | 1.00 |
| 78_I | 83_L | 2.459 | 1.00 |
| 53_Y | 84_L | 2.307 | 1.00 |
| 15_H | 92_V | 2.112 | 1.00 |
| 3_F | 8_L | 2.102 | 1.00 |
| 82_A | 85_S | 1.965 | 1.00 |
| 13_K | 22_G | 1.846 | 1.00 |
| 8_L | 88_I | 1.814 | 1.00 |
| 2_V | 39_N | 1.808 | 1.00 |
| 32_A | 55_I | 1.790 | 1.00 |
| 5_R | 33_K | 1.774 | 1.00 |
| 32_A | 38_F | 1.760 | 0.99 |
| 48_D | 61_R | 1.739 | 0.99 |
| 35_E | 52_D | 1.678 | 0.99 |
| 39_N | 42_A | 1.664 | 0.99 |
| 27_N | 31_A | 1.643 | 0.99 |
| 23_Y | 105_M | 1.611 | 0.99 |
| 24_S | 99_V | 1.595 | 0.99 |
| 53_Y | 60_S | 1.559 | 0.98 |
| 52_D | 59_N | 1.480 | 0.98 |
| 78_I | 91_S | 1.413 | 0.97 |
| 8_L | 32_A | 1.409 | 0.97 |
| 27_N | 111_W | 1.409 | 0.97 |
| 99_V | 105_M | 1.383 | 0.96 |
| 33_K | 37_N | 1.367 | 0.96 |
| 5_R | 112_R | 1.348 | 0.95 |
| 11_A | 92_V | 1.327 | 0.95 |
| 75_L | 101_D | 1.326 | 0.95 |
| 63_W | 107_A | 1.305 | 0.94 |
| 35_E | 50_S | 1.305 | 0.94 |
| 14_R | 87_D | 1.301 | 0.94 |
| 70_P | 123_W | 1.290 | 0.94 |
| 4_G | 7_E | 1.282 | 0.93 |
| 44_N | 52_D | 1.281 | 0.93 |
| 78_I | 90_A | 1.277 | 0.93 |
| 111_W | 117_G | 1.252 | 0.92 |
| 103_N | 107_A | 1.250 | 0.92 |
| 98_I | 108_W | 1.214 | 0.91 |
| 9_A | 13_K | 1.203 | 0.90 |
| 34_F | 114_R | 1.190 | 0.89 |
| 32_A | 88_I | 1.189 | 0.89 |
| 43_T | 51_T | 1.187 | 0.89 |
| 34_F | 110_A | 1.180 | 0.89 |
| 50_S | 59_N | 1.173 | 0.88 |
| 12_M | 29_V | 1.129 | 0.86 |
| 79_P | 82_A | 1.124 | 0.85 |
| 52_D | 62_W | 1.117 | 0.85 |
| 78_I | 82_A | 1.117 | 0.85 |
| 18_D | 24_S | 1.113 | 0.85 |
| 12_M | 56_L | 1.112 | 0.85 |
| 45_R | 51_T | 1.103 | 0.84 |
| 35_E | 59_N | 1.102 | 0.84 |
| 97_K | 101_D | 1.096 | 0.83 |
| 74_N | 79_P | 1.095 | 0.83 |
| 47_T | 52_D | 1.094 | 0.83 |
| 9_A | 32_A | 1.090 | 0.83 |
| 93_N | 100_S | 1.078 | 0.82 |
| 21_R | 100_S | 1.072 | 0.81 |
| 31_A | 105_M | 1.066 | 0.81 |
| 34_F | 38_F | 1.050 | 0.80 |
| 43_T | 84_L | 1.047 | 0.79 |
| 52_D | 109_V | 1.044 | 0.79 |
| 97_K | 102_G | 1.033 | 0.78 |
| 46_N | 51_T | 1.024 | 0.77 |
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 | |
| 2nwdX | 1 | 1 | 100 | 0.132 | Contact Map |
| 4yf2A | 3 | 0.9922 | 100 | 0.138 | Contact Map |
| 1lmqA | 1 | 1 | 100 | 0.143 | Contact Map |
| 2gv0A | 1 | 1 | 100 | 0.143 | Contact Map |
| 2z2fA | 1 | 0.9922 | 100 | 0.151 | Contact Map |
| 1qqyA | 1 | 0.9922 | 100 | 0.157 | Contact Map |
| 2vb1A | 1 | 1 | 100 | 0.179 | Contact Map |
| 1yroA | 2 | 0.9457 | 100 | 0.196 | Contact Map |
| 1b9oA | 1 | 0.9457 | 100 | 0.2 | Contact Map |
| 1jugA | 1 | 0.969 | 100 | 0.206 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)