| d3gc2a1 |
| ID: | 1450012435 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 101 (99) | ||
| Sequences: | 4115 (2784) | ||
| Seq/Len: | 41.566 | ||
| Nf(neff/√len): | 279.8 |
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: 41.566).
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 |
| 7_Q | 35_C | 3.761 | 1.00 |
| 35_C | 42_E | 3.154 | 1.00 |
| 12_Q | 28_T | 3.027 | 1.00 |
| 41_R | 96_L | 2.833 | 1.00 |
| 90_S | 94_A | 2.745 | 1.00 |
| 9_Y | 35_C | 2.589 | 1.00 |
| 75_G | 78_G | 2.094 | 1.00 |
| 95_E | 99_V | 2.062 | 1.00 |
| 10_R | 30_D | 2.037 | 1.00 |
| 47_I | 88_G | 1.971 | 1.00 |
| 41_R | 100_L | 1.968 | 1.00 |
| 35_C | 44_W | 1.905 | 1.00 |
| 20_V | 25_R | 1.887 | 1.00 |
| 37_R | 96_L | 1.875 | 1.00 |
| 2_A | 38_D | 1.834 | 1.00 |
| 37_R | 41_R | 1.826 | 1.00 |
| 12_Q | 30_D | 1.819 | 1.00 |
| 6_A | 36_L | 1.815 | 1.00 |
| 34_V | 88_G | 1.761 | 1.00 |
| 43_G | 92_A | 1.751 | 1.00 |
| 6_A | 69_V | 1.641 | 1.00 |
| 4_R | 38_D | 1.588 | 1.00 |
| 18_G | 25_R | 1.475 | 1.00 |
| 36_L | 93_L | 1.467 | 1.00 |
| 43_G | 95_E | 1.394 | 0.99 |
| 11_W | 31_G | 1.343 | 0.99 |
| 49_P | 84_S | 1.327 | 0.99 |
| 11_W | 33_Y | 1.299 | 0.99 |
| 5_S | 69_V | 1.280 | 0.99 |
| 39_G | 100_L | 1.262 | 0.99 |
| 33_Y | 44_W | 1.254 | 0.99 |
| 62_Q | 66_L | 1.237 | 0.98 |
| 9_Y | 44_W | 1.228 | 0.98 |
| 41_R | 99_V | 1.210 | 0.98 |
| 32_L | 62_Q | 1.188 | 0.98 |
| 45_G | 88_G | 1.149 | 0.97 |
| 45_G | 92_A | 1.149 | 0.97 |
| 26_L | 50_L | 1.096 | 0.96 |
| 47_I | 61_A | 1.090 | 0.96 |
| 87_F | 91_C | 1.087 | 0.96 |
| 65_L | 89_A | 1.083 | 0.96 |
| 81_E | 86_A | 1.080 | 0.95 |
| 8_V | 65_L | 1.064 | 0.95 |
| 31_G | 48_S | 1.043 | 0.94 |
| 82_M | 86_A | 1.040 | 0.94 |
| 60_E | 64_A | 1.030 | 0.94 |
| 29_R | 50_L | 1.028 | 0.94 |
| 15_M | 19_V | 1.007 | 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 | |
| 1r6wA | 1 | 0.9802 | 99.7 | 0.139 | Contact Map |
| 2p8bA | 1 | 1 | 99.7 | 0.143 | Contact Map |
| 1sjdA | 4 | 1 | 99.7 | 0.143 | Contact Map |
| 1tkkA | 8 | 1 | 99.7 | 0.148 | Contact Map |
| 3jvaA | 8 | 1 | 99.7 | 0.148 | Contact Map |
| 3ik4A | 4 | 1 | 99.7 | 0.148 | Contact Map |
| 3dg3A | 1 | 0.8911 | 99.7 | 0.151 | Contact Map |
| 3s5sA | 2 | 1 | 99.7 | 0.156 | Contact Map |
| 3q45A | 9 | 1 | 99.7 | 0.156 | Contact Map |
| 1nu5A | 1 | 1 | 99.7 | 0.156 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)