| sub11 |
| ID: | 1404142062 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 95 (94) | ||
| Sequences: | 1887 (1107.3) | ||
| Seq/Len: | 20.074 | ||
| Nf(neff/√len): | 114.2 |
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: 20.074).
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_G | 30_S | 5.598 | 1.00 |
| 84_S | 89_D | 2.348 | 1.00 |
| 78_I | 90_L | 2.283 | 1.00 |
| 39_N | 60_V | 2.178 | 1.00 |
| 5_L | 9_L | 2.019 | 1.00 |
| 23_T | 85_T | 2.003 | 1.00 |
| 77_A | 80_R | 1.966 | 1.00 |
| 11_F | 37_A | 1.905 | 1.00 |
| 16_Y | 20_T | 1.890 | 1.00 |
| 11_F | 34_M | 1.883 | 1.00 |
| 27_V | 87_V | 1.699 | 1.00 |
| 4_L | 8_A | 1.617 | 1.00 |
| 18_V | 30_S | 1.565 | 1.00 |
| 28_F | 75_I | 1.558 | 1.00 |
| 86_A | 89_D | 1.551 | 1.00 |
| 32_E | 68_V | 1.468 | 1.00 |
| 41_S | 45_F | 1.425 | 1.00 |
| 7_S | 37_A | 1.414 | 1.00 |
| 59_M | 62_A | 1.376 | 0.99 |
| 35_L | 67_E | 1.371 | 0.99 |
| 14_G | 34_M | 1.366 | 0.99 |
| 60_V | 64_A | 1.330 | 0.99 |
| 28_F | 41_S | 1.327 | 0.99 |
| 28_F | 71_G | 1.318 | 0.99 |
| 9_L | 13_L | 1.309 | 0.99 |
| 42_L | 56_A | 1.308 | 0.99 |
| 32_E | 67_E | 1.288 | 0.99 |
| 53_G | 60_V | 1.269 | 0.99 |
| 35_L | 63_V | 1.265 | 0.99 |
| 82_R | 92_E | 1.223 | 0.98 |
| 39_N | 57_A | 1.189 | 0.98 |
| 14_G | 30_S | 1.173 | 0.98 |
| 38_A | 41_S | 1.167 | 0.97 |
| 8_A | 12_A | 1.143 | 0.97 |
| 17_G | 21_R | 1.108 | 0.96 |
| 15_V | 34_M | 1.098 | 0.96 |
| 5_L | 8_A | 1.096 | 0.96 |
| 3_Y | 44_G | 1.096 | 0.96 |
| 22_R | 88_D | 1.084 | 0.96 |
| 35_L | 64_A | 1.083 | 0.96 |
| 7_S | 44_G | 1.074 | 0.95 |
| 7_S | 41_S | 1.064 | 0.95 |
| 4_L | 41_S | 1.046 | 0.94 |
| 6_T | 10_L | 1.030 | 0.94 |
| 12_A | 16_Y | 1.029 | 0.94 |
| 32_E | 36_N | 1.026 | 0.94 |
| 15_V | 18_V | 1.020 | 0.93 |
| 21_R | 26_L | 1.010 | 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 | |
| 4he8K | 2 | 1 | 99.9 | 0.224 | Contact Map |
| 3rkoK | 2 | 1 | 99.8 | 0.257 | Contact Map |
| 3rkoN | 2 | 0.9684 | 61.3 | 0.859 | Contact Map |
| 4he8M | 2 | 0.9684 | 54.1 | 0.865 | Contact Map |
| 3rkoL | 2 | 0.9789 | 46.3 | 0.871 | Contact Map |
| 4he8L | 2 | 0.9789 | 45.3 | 0.872 | Contact Map |
| 3rkoM | 2 | 0.9895 | 36.7 | 0.878 | Contact Map |
| 4he8N | 2 | 0.9579 | 21.6 | 0.891 | Contact Map |
| 2l2tA | 2 | 0.4632 | 5.9 | 0.916 | Contact Map |
| 2kluA | 1 | 0.4842 | 3.9 | 0.923 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)