| d4ntyc_ |
| ID: | 1447592893 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 118 (115) | ||
| Sequences: | 980 (596.9) | ||
| Seq/Len: | 8.522 | ||
| Nf(neff/√len): | 55.7 |
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: 8.522).
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 |
| 5_F | 97_A | 3.374 | 1.00 |
| 59_C | 86_C | 3.183 | 1.00 |
| 97_A | 101_I | 2.777 | 1.00 |
| 44_Q | 48_Q | 2.436 | 1.00 |
| 11_C | 70_C | 2.436 | 1.00 |
| 28_V | 47_K | 2.114 | 1.00 |
| 110_N | 113_I | 1.987 | 1.00 |
| 30_R | 47_K | 1.949 | 1.00 |
| 1_N | 4_Q | 1.856 | 1.00 |
| 5_F | 101_I | 1.756 | 1.00 |
| 95_R | 99_L | 1.752 | 1.00 |
| 42_C | 100_C | 1.730 | 1.00 |
| 88_N | 92_N | 1.645 | 1.00 |
| 42_C | 46_Q | 1.602 | 1.00 |
| 77_L | 99_L | 1.577 | 1.00 |
| 79_C | 91_C | 1.571 | 1.00 |
| 38_D | 104_A | 1.477 | 1.00 |
| 26_Y | 31_D | 1.448 | 0.99 |
| 53_A | 89_F | 1.444 | 0.99 |
| 26_Y | 47_K | 1.430 | 0.99 |
| 37_D | 40_D | 1.398 | 0.99 |
| 28_V | 42_C | 1.388 | 0.99 |
| 17_W | 21_V | 1.361 | 0.99 |
| 92_N | 96_T | 1.319 | 0.99 |
| 61_P | 90_V | 1.314 | 0.99 |
| 1_N | 65_F | 1.290 | 0.98 |
| 4_Q | 65_F | 1.262 | 0.98 |
| 22_D | 112_K | 1.257 | 0.98 |
| 28_V | 100_C | 1.245 | 0.98 |
| 23_Y | 37_D | 1.236 | 0.98 |
| 27_C | 37_D | 1.218 | 0.97 |
| 43_C | 49_C | 1.198 | 0.97 |
| 6_R | 17_W | 1.195 | 0.97 |
| 99_L | 103_T | 1.192 | 0.97 |
| 46_Q | 100_C | 1.184 | 0.97 |
| 27_C | 40_D | 1.181 | 0.97 |
| 77_L | 95_R | 1.170 | 0.97 |
| 47_K | 50_Y | 1.164 | 0.96 |
| 26_Y | 32_S | 1.147 | 0.96 |
| 3_N | 6_R | 1.145 | 0.96 |
| 39_L | 104_A | 1.130 | 0.96 |
| 6_R | 10_K | 1.110 | 0.95 |
| 64_M | 87_R | 1.101 | 0.95 |
| 22_D | 114_D | 1.101 | 0.95 |
| 81_G | 88_N | 1.093 | 0.94 |
| 46_Q | 50_Y | 1.087 | 0.94 |
| 24_G | 40_D | 1.078 | 0.94 |
| 112_K | 115_P | 1.070 | 0.93 |
| 13_N | 113_I | 1.066 | 0.93 |
| 20_F | 39_L | 1.065 | 0.93 |
| 31_D | 47_K | 1.056 | 0.93 |
| 42_C | 47_K | 1.051 | 0.93 |
| 57_H | 95_R | 1.050 | 0.93 |
| 25_C | 35_P | 1.029 | 0.92 |
| 25_C | 40_D | 1.027 | 0.92 |
| 9_I | 97_A | 1.018 | 0.91 |
| 51_D | 54_V | 1.018 | 0.91 |
| 24_G | 37_D | 1.009 | 0.91 |
| 50_Y | 100_C | 1.006 | 0.90 |
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 | |
| 1p7oA | 6 | 0.9831 | 100 | 0.029 | Contact Map |
| 4ntwC | 1 | 1 | 100 | 0.031 | Contact Map |
| 1g4iA | 1 | 0.9831 | 100 | 0.033 | Contact Map |
| 1gp7A | 3 | 0.9831 | 100 | 0.035 | Contact Map |
| 3jqlA | 1 | 0.9831 | 100 | 0.038 | Contact Map |
| 1le6A | 3 | 0.9746 | 100 | 0.038 | Contact Map |
| 1m8tA | 6 | 0.9831 | 100 | 0.04 | Contact Map |
| 1bunA | 1 | 0.9831 | 100 | 0.041 | Contact Map |
| 1g0zA | 2 | 0.9831 | 100 | 0.044 | Contact Map |
| 3vbzA | 2 | 0.9661 | 100 | 0.05 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)