| 2it6 |
| ID: | 1408343804 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 132 (128) | ||
| Sequences: | 5435 (4263.9) | ||
| Seq/Len: | 42.461 | ||
| Nf(neff/√len): | 376.9 |
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: 42.461).
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 |
| 104_C | 117_C | 4.696 | 1.00 |
| 29_I | 38_Q | 3.437 | 1.00 |
| 66_L | 105_A | 3.381 | 1.00 |
| 31_A | 123_W | 3.053 | 1.00 |
| 4_C | 15_C | 2.860 | 1.00 |
| 106_E | 113_N | 2.488 | 1.00 |
| 66_L | 77_W | 2.434 | 1.00 |
| 25_W | 78_V | 2.276 | 1.00 |
| 48_Q | 112_W | 2.189 | 1.00 |
| 14_N | 126_K | 2.156 | 1.00 |
| 45_A | 49_N | 2.153 | 1.00 |
| 23_R | 27_D | 2.137 | 1.00 |
| 68_D | 72_E | 2.029 | 1.00 |
| 102_E | 113_N | 2.020 | 1.00 |
| 106_E | 121_K | 1.928 | 1.00 |
| 11_F | 50_F | 1.812 | 1.00 |
| 24_N | 27_D | 1.767 | 1.00 |
| 42_I | 48_Q | 1.627 | 1.00 |
| 47_E | 126_K | 1.595 | 1.00 |
| 31_A | 35_V | 1.592 | 1.00 |
| 33_K | 38_Q | 1.525 | 1.00 |
| 44_S | 47_E | 1.511 | 1.00 |
| 17_F | 35_V | 1.500 | 1.00 |
| 23_R | 123_W | 1.472 | 1.00 |
| 72_E | 103_D | 1.468 | 1.00 |
| 115_D | 121_K | 1.447 | 1.00 |
| 29_I | 33_K | 1.437 | 1.00 |
| 75_W | 105_A | 1.412 | 1.00 |
| 40_V | 64_M | 1.407 | 0.99 |
| 23_R | 31_A | 1.386 | 0.99 |
| 42_I | 51_L | 1.385 | 0.99 |
| 28_S | 123_W | 1.351 | 0.99 |
| 5_P | 127_K | 1.345 | 0.99 |
| 8_W | 127_K | 1.337 | 0.99 |
| 16_Y | 40_V | 1.332 | 0.99 |
| 63_W | 115_D | 1.272 | 0.99 |
| 66_L | 83_L | 1.251 | 0.99 |
| 106_E | 115_D | 1.242 | 0.98 |
| 85_P | 88_K | 1.228 | 0.98 |
| 91_W | 96_P | 1.223 | 0.98 |
| 41_V | 79_D | 1.222 | 0.98 |
| 39_L | 123_W | 1.221 | 0.98 |
| 90_Y | 112_W | 1.213 | 0.98 |
| 97_N | 114_D | 1.189 | 0.98 |
| 8_W | 35_V | 1.177 | 0.98 |
| 19_S | 123_W | 1.166 | 0.97 |
| 25_W | 67_S | 1.157 | 0.97 |
| 102_E | 114_D | 1.141 | 0.97 |
| 28_S | 39_L | 1.139 | 0.97 |
| 5_P | 8_W | 1.138 | 0.97 |
| 68_D | 73_G | 1.129 | 0.97 |
| 68_D | 103_D | 1.128 | 0.97 |
| 18_M | 62_T | 1.128 | 0.97 |
| 43_K | 47_E | 1.127 | 0.97 |
| 64_M | 112_W | 1.118 | 0.96 |
| 48_Q | 90_Y | 1.116 | 0.96 |
| 40_V | 126_K | 1.089 | 0.96 |
| 27_D | 30_T | 1.078 | 0.95 |
| 48_Q | 52_Q | 1.076 | 0.95 |
| 96_P | 114_D | 1.060 | 0.95 |
| 95_E | 102_E | 1.057 | 0.95 |
| 92_N | 111_G | 1.052 | 0.95 |
| 41_V | 126_K | 1.050 | 0.94 |
| 43_K | 126_K | 1.049 | 0.94 |
| 41_V | 78_V | 1.049 | 0.94 |
| 117_C | 125_C | 1.045 | 0.94 |
| 16_Y | 126_K | 1.039 | 0.94 |
| 8_W | 37_A | 1.031 | 0.94 |
| 97_N | 102_E | 1.030 | 0.94 |
| 26_H | 69_L | 1.029 | 0.94 |
| 98_N | 103_D | 1.016 | 0.93 |
| 91_W | 95_E | 1.015 | 0.93 |
| 98_N | 114_D | 1.014 | 0.93 |
| 40_V | 51_L | 1.000 | 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
- 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 | |
| 1sl6A | 6 | 0.9924 | 100 | 0.069 | Contact Map |
| 2b6bD | 1 | 0.9697 | 100 | 0.085 | Contact Map |
| 2xr6A | 1 | 0.9848 | 100 | 0.086 | Contact Map |
| 3zhgA | 3 | 0.9924 | 99.9 | 0.105 | Contact Map |
| 3wh2A | 1 | 0.9545 | 99.9 | 0.118 | Contact Map |
| 3vppA | 2 | 0.9091 | 99.9 | 0.122 | Contact Map |
| 3t3aA | 2 | 0.9167 | 99.9 | 0.135 | Contact Map |
| 1qddA | 1 | 0.9545 | 99.9 | 0.139 | Contact Map |
| 3wbpA | 2 | 0.9394 | 99.9 | 0.139 | Contact Map |
| 1htnA | 1 | 0.9545 | 99.9 | 0.139 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)