| T0759 |
| ID: | 1398962297 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 109 (105) | ||
| Sequences: | 1821 (1126.2) | ||
| Seq/Len: | 17.343 | ||
| Nf(neff/√len): | 109.9 |
Jackhmmer Results: (2014_04_16)
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: 17.343).
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 |
| 70_K | 80_S | 2.005 | 1.00 |
| 23_S | 26_E | 1.904 | 1.00 |
| 57_N | 60_S | 1.882 | 1.00 |
| 49_E | 53_V | 1.807 | 1.00 |
| 34_D | 37_M | 1.789 | 1.00 |
| 94_K | 97_S | 1.636 | 1.00 |
| 57_N | 61_S | 1.570 | 1.00 |
| 26_E | 29_R | 1.539 | 1.00 |
| 58_G | 61_S | 1.538 | 1.00 |
| 24_P | 31_G | 1.532 | 1.00 |
| 13_V | 24_P | 1.530 | 1.00 |
| 18_P | 30_A | 1.506 | 1.00 |
| 24_P | 38_F | 1.488 | 1.00 |
| 65_D | 68_S | 1.484 | 1.00 |
| 96_M | 99_Q | 1.438 | 1.00 |
| 84_T | 87_H | 1.428 | 1.00 |
| 15_H | 18_P | 1.420 | 1.00 |
| 24_P | 27_A | 1.384 | 0.99 |
| 15_H | 30_A | 1.379 | 0.99 |
| 28_H | 38_F | 1.374 | 0.99 |
| 20_R | 30_A | 1.338 | 0.99 |
| 46_C | 51_I | 1.328 | 0.99 |
| 102_A | 105_V | 1.288 | 0.99 |
| 6_H | 9_S | 1.274 | 0.99 |
| 64_H | 69_G | 1.256 | 0.99 |
| 102_A | 107_G | 1.250 | 0.99 |
| 91_Y | 94_K | 1.233 | 0.98 |
| 95_D | 99_Q | 1.232 | 0.98 |
| 100_E | 105_V | 1.230 | 0.98 |
| 54_K | 57_N | 1.223 | 0.98 |
| 83_L | 89_D | 1.218 | 0.98 |
| 74_I | 95_D | 1.215 | 0.98 |
| 27_A | 32_L | 1.212 | 0.98 |
| 14_I | 21_E | 1.208 | 0.98 |
| 93_N | 96_M | 1.208 | 0.98 |
| 78_L | 88_Y | 1.204 | 0.98 |
| 48_W | 52_S | 1.193 | 0.98 |
| 49_E | 52_S | 1.190 | 0.98 |
| 46_C | 53_V | 1.190 | 0.98 |
| 76_E | 80_S | 1.179 | 0.98 |
| 92_V | 95_D | 1.163 | 0.97 |
| 56_P | 60_S | 1.155 | 0.97 |
| 22_L | 27_A | 1.139 | 0.97 |
| 35_W | 39_V | 1.139 | 0.97 |
| 30_A | 34_D | 1.113 | 0.96 |
| 16_P | 31_G | 1.109 | 0.96 |
| 46_C | 52_S | 1.105 | 0.96 |
| 56_P | 59_E | 1.095 | 0.96 |
| 47_D | 51_I | 1.082 | 0.96 |
| 62_V | 65_D | 1.077 | 0.95 |
| 31_G | 43_S | 1.073 | 0.95 |
| 88_Y | 98_I | 1.073 | 0.95 |
| 99_Q | 102_A | 1.071 | 0.95 |
| 31_G | 38_F | 1.069 | 0.95 |
| 53_V | 56_P | 1.053 | 0.95 |
| 52_S | 55_G | 1.049 | 0.94 |
| 99_Q | 103_V | 1.043 | 0.94 |
| 75_E | 88_Y | 1.037 | 0.94 |
| 39_V | 42_R | 1.027 | 0.94 |
| 38_F | 42_R | 1.006 | 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 | |
| 1lm7A | 2 | 0.8624 | 99.7 | 0.269 | Contact Map |
| 1lm5A | 2 | 0.945 | 99.7 | 0.275 | Contact Map |
| 3zwcA | 2 | 0.8899 | 17.2 | 0.879 | Contact Map |
| 4kpkA | 1 | 0.8716 | 13.5 | 0.884 | Contact Map |
| 1wdkA | 2 | 0.8899 | 12.3 | 0.886 | Contact Map |
| 2wtbA | 1 | 0.8899 | 12 | 0.887 | Contact Map |
| 2oy9A | 2 | 0.4954 | 11.9 | 0.887 | Contact Map |
| 3fduA | 6 | 0.8991 | 11.6 | 0.887 | Contact Map |
| 4og1A | 1 | 0.945 | 10.4 | 0.89 | Contact Map |
| 3m6nA | 3 | 0.9541 | 10.2 | 0.89 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)