| Lem2_CTD |
| ID: | 1492620789 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 108 (103) | ||
| Sequences: | 320 (217.6) | ||
| Seq/Len: | 3.107 | ||
| Nf(neff/√len): | 21.4 |
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: 3.107).
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 |
| 28_V | 81_I | 2.282 | 1.00 |
| 75_A | 94_L | 1.887 | 0.99 |
| 24_I | 70_A | 1.799 | 0.99 |
| 84_E | 97_R | 1.576 | 0.97 |
| 63_M | 94_L | 1.554 | 0.97 |
| 17_M | 21_V | 1.522 | 0.96 |
| 13_E | 69_R | 1.499 | 0.96 |
| 5_Y | 8_R | 1.451 | 0.95 |
| 35_W | 39_M | 1.443 | 0.95 |
| 46_G | 49_H | 1.443 | 0.95 |
| 70_A | 74_L | 1.441 | 0.95 |
| 92_D | 97_R | 1.437 | 0.95 |
| 27_V | 97_R | 1.428 | 0.94 |
| 82_Q | 94_L | 1.365 | 0.92 |
| 86_H | 92_D | 1.345 | 0.92 |
| 31_H | 70_A | 1.299 | 0.90 |
| 21_V | 73_F | 1.295 | 0.89 |
| 63_M | 70_A | 1.291 | 0.89 |
| 51_R | 67_W | 1.271 | 0.88 |
| 3_L | 104_F | 1.260 | 0.88 |
| 50_V | 79_S | 1.228 | 0.86 |
| 4_K | 26_D | 1.217 | 0.85 |
| 30_D | 37_Q | 1.211 | 0.85 |
| 50_V | 94_L | 1.206 | 0.84 |
| 26_D | 30_D | 1.186 | 0.83 |
| 81_I | 96_W | 1.186 | 0.83 |
| 19_E | 37_Q | 1.179 | 0.82 |
| 73_F | 79_S | 1.176 | 0.82 |
| 86_H | 97_R | 1.172 | 0.82 |
| 63_M | 79_S | 1.149 | 0.80 |
| 55_I | 87_R | 1.148 | 0.80 |
| 19_E | 23_K | 1.144 | 0.80 |
| 82_Q | 96_W | 1.128 | 0.78 |
| 40_E | 72_E | 1.127 | 0.78 |
| 79_S | 98_W | 1.117 | 0.78 |
| 35_W | 38_D | 1.108 | 0.77 |
| 31_H | 74_L | 1.101 | 0.76 |
| 80_R | 87_R | 1.101 | 0.76 |
| 78_E | 93_M | 1.096 | 0.76 |
| 52_D | 77_N | 1.084 | 0.74 |
| 45_V | 49_H | 1.083 | 0.74 |
| 85_S | 92_D | 1.078 | 0.74 |
| 24_I | 48_L | 1.078 | 0.74 |
| 11_E | 101_P | 1.065 | 0.73 |
| 14_E | 69_R | 1.062 | 0.72 |
| 52_D | 55_I | 1.062 | 0.72 |
| 12_E | 17_M | 1.053 | 0.71 |
| 4_K | 25_I | 1.044 | 0.70 |
| 55_I | 77_N | 1.025 | 0.68 |
| 50_V | 77_N | 1.022 | 0.68 |
| 71_V | 96_W | 1.019 | 0.68 |
| 46_G | 95_V | 1.015 | 0.67 |
| 10_L | 33_V | 1.007 | 0.66 |
| 27_V | 56_P | 1.004 | 0.66 |
| 63_M | 73_F | 1.003 | 0.66 |
| 24_I | 57_P | 1.000 | 0.66 |
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 | |
| 2ch0A | 1 | 1 | 100 | 0.101 | Contact Map |
| 4gl6A | 2 | 0.3426 | 5.3 | 0.927 | Contact Map |
| 4waiA | 4 | 0.3611 | 4 | 0.931 | Contact Map |
| 2nppB | 2 | 0.5185 | 3.3 | 0.934 | Contact Map |
| 1hskA | 1 | 0.4259 | 3.2 | 0.934 | Contact Map |
| 4l5gA | 2 | 0.6759 | 3.1 | 0.934 | Contact Map |
| 3pvvA | 2 | 0.3056 | 2.8 | 0.936 | Contact Map |
| 1ozjA | 2 | 0.7407 | 2.7 | 0.936 | Contact Map |
| 4kbmB | 1 | 0.6019 | 2 | 0.941 | Contact Map |
| 4u3eA | 2 | 0.8611 | 1.9 | 0.941 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)