| 1CEY |
| ID: | 1449143869 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 128 (123) | ||
| Sequences: | 108505 (80197.8) | ||
| Seq/Len: | 882.154 | ||
| Nf(neff/√len): | 7231.2 |
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: 882.154).
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 |
| 17_R | 34_E | 3.020 | 1.00 |
| 17_R | 36_E | 2.717 | 1.00 |
| 21_R | 34_E | 2.716 | 1.00 |
| 10_V | 41_A | 2.326 | 1.00 |
| 58_N | 88_E | 2.103 | 1.00 |
| 42_L | 70_T | 2.010 | 1.00 |
| 39_V | 61_N | 1.942 | 1.00 |
| 104_G | 118_K | 1.916 | 1.00 |
| 55_S | 67_L | 1.866 | 1.00 |
| 35_A | 44_K | 1.839 | 1.00 |
| 62_M | 70_T | 1.812 | 1.00 |
| 27_L | 116_E | 1.798 | 1.00 |
| 84_M | 102_A | 1.785 | 1.00 |
| 6_K | 32_V | 1.776 | 1.00 |
| 38_G | 62_M | 1.736 | 1.00 |
| 68_L | 82_V | 1.698 | 1.00 |
| 36_E | 40_D | 1.691 | 1.00 |
| 23_L | 112_A | 1.667 | 1.00 |
| 46_Q | 74_D | 1.662 | 1.00 |
| 37_D | 61_N | 1.627 | 1.00 |
| 32_V | 50_Y | 1.610 | 1.00 |
| 6_K | 30_N | 1.579 | 1.00 |
| 8_L | 35_A | 1.473 | 1.00 |
| 72_R | 103_S | 1.455 | 1.00 |
| 69_K | 100_A | 1.422 | 1.00 |
| 57_W | 65_L | 1.395 | 0.99 |
| 70_T | 74_D | 1.393 | 0.99 |
| 21_R | 25_K | 1.379 | 0.99 |
| 53_V | 80_L | 1.377 | 0.99 |
| 37_D | 40_D | 1.351 | 0.99 |
| 6_K | 51_G | 1.346 | 0.99 |
| 38_G | 67_L | 1.341 | 0.99 |
| 32_V | 44_K | 1.320 | 0.99 |
| 88_E | 93_N | 1.296 | 0.99 |
| 5_L | 123_F | 1.253 | 0.99 |
| 104_G | 121_K | 1.244 | 0.98 |
| 95_I | 99_Q | 1.219 | 0.98 |
| 62_M | 66_E | 1.214 | 0.98 |
| 118_K | 121_K | 1.203 | 0.98 |
| 63_D | 66_E | 1.200 | 0.98 |
| 44_K | 50_Y | 1.189 | 0.98 |
| 42_L | 67_L | 1.171 | 0.98 |
| 39_V | 62_M | 1.167 | 0.97 |
| 32_V | 48_G | 1.159 | 0.97 |
| 85_V | 110_F | 1.152 | 0.97 |
| 114_T | 118_K | 1.150 | 0.97 |
| 6_K | 48_G | 1.149 | 0.97 |
| 45_L | 71_I | 1.143 | 0.97 |
| 68_L | 84_M | 1.136 | 0.97 |
| 70_T | 73_A | 1.135 | 0.97 |
| 96_A | 100_A | 1.130 | 0.97 |
| 65_L | 97_A | 1.122 | 0.97 |
| 76_A | 80_L | 1.111 | 0.96 |
| 33_E | 50_Y | 1.097 | 0.96 |
| 116_E | 120_N | 1.095 | 0.96 |
| 91_K | 95_I | 1.086 | 0.96 |
| 5_L | 29_F | 1.085 | 0.96 |
| 44_K | 48_G | 1.081 | 0.95 |
| 84_M | 97_A | 1.079 | 0.95 |
| 103_S | 122_I | 1.073 | 0.95 |
| 90_K | 93_N | 1.057 | 0.95 |
| 8_L | 41_A | 1.056 | 0.95 |
| 18_R | 21_R | 1.052 | 0.95 |
| 41_A | 67_L | 1.046 | 0.94 |
| 65_L | 96_A | 1.042 | 0.94 |
| 14_S | 36_E | 1.028 | 0.94 |
| 9_V | 20_V | 1.027 | 0.94 |
| 12_D | 56_D | 1.025 | 0.93 |
| 8_L | 50_Y | 1.025 | 0.93 |
| 44_K | 47_A | 1.011 | 0.93 |
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 | |
| 3dzdA | 2 | 0.9453 | 99.5 | -0.16 | Contact Map |
| 3eq2A | 2 | 0.9609 | 99.5 | -0.16 | Contact Map |
| 4l4uA | 1 | 0.9766 | 99.5 | -0.157 | Contact Map |
| 1w25A | 2 | 0.9688 | 99.5 | -0.154 | Contact Map |
| 3r0jA | 2 | 0.9688 | 99.5 | -0.149 | Contact Map |
| 3rqiA | 1 | 0.9453 | 99.5 | -0.148 | Contact Map |
| 1jbeA | 1 | 0.9766 | 99.5 | -0.147 | Contact Map |
| 1ys7A | 2 | 0.9531 | 99.5 | -0.146 | Contact Map |
| 4g97A | 1 | 0.9609 | 99.5 | -0.142 | Contact Map |
| 2vycA | 10 | 0.9453 | 99.5 | -0.14 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)