| 1BNI |
| ID: | 1429442344 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 110 (110) | ||
| Sequences: | 256 (164) | ||
| Seq/Len: | 2.327 | ||
| Nf(neff/√len): | 15.6 |
HHblits Results: (2013_03)
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: 2.327).
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 |
| 90_Y | 96_I | 2.037 | 0.99 |
| 77_N | 86_D | 1.948 | 0.99 |
| 71_W | 89_L | 1.861 | 0.99 |
| 60_E | 85_S | 1.741 | 0.98 |
| 73_E | 102_H | 1.664 | 0.97 |
| 4_I | 7_F | 1.654 | 0.97 |
| 92_S | 95_L | 1.599 | 0.96 |
| 50_S | 80_S | 1.596 | 0.95 |
| 51_I | 54_D | 1.567 | 0.95 |
| 69_R | 95_L | 1.487 | 0.93 |
| 3_V | 6_T | 1.409 | 0.90 |
| 2_Q | 6_T | 1.373 | 0.88 |
| 33_L | 46_A | 1.368 | 0.88 |
| 42_L | 53_G | 1.361 | 0.88 |
| 32_A | 66_K | 1.356 | 0.87 |
| 7_F | 98_K | 1.342 | 0.87 |
| 76_I | 98_K | 1.323 | 0.86 |
| 57_S | 105_T | 1.268 | 0.82 |
| 6_T | 9_G | 1.266 | 0.82 |
| 69_R | 93_D | 1.264 | 0.82 |
| 87_R | 103_Y | 1.263 | 0.82 |
| 61_G | 65_G | 1.260 | 0.82 |
| 20_L | 34_G | 1.254 | 0.81 |
| 83_R | 106_F | 1.246 | 0.81 |
| 70_T | 92_S | 1.243 | 0.80 |
| 3_V | 12_D | 1.212 | 0.78 |
| 90_Y | 107_T | 1.209 | 0.78 |
| 30_A | 94_W | 1.174 | 0.75 |
| 1_A | 80_S | 1.170 | 0.74 |
| 32_A | 67_S | 1.168 | 0.74 |
| 88_I | 109_I | 1.164 | 0.74 |
| 30_A | 43_A | 1.164 | 0.74 |
| 35_W | 42_L | 1.160 | 0.74 |
| 19_K | 22_D | 1.158 | 0.73 |
| 46_A | 76_I | 1.151 | 0.73 |
| 4_I | 98_K | 1.151 | 0.73 |
| 36_V | 84_N | 1.139 | 0.72 |
| 91_S | 95_L | 1.136 | 0.71 |
| 62_K | 85_S | 1.135 | 0.71 |
| 43_A | 80_S | 1.120 | 0.70 |
| 27_K | 30_A | 1.107 | 0.68 |
| 25_I | 51_I | 1.106 | 0.68 |
| 4_I | 9_G | 1.099 | 0.68 |
| 51_I | 81_G | 1.095 | 0.67 |
| 65_G | 104_Q | 1.090 | 0.67 |
| 26_T | 54_D | 1.085 | 0.66 |
| 30_A | 54_D | 1.083 | 0.66 |
| 25_I | 33_L | 1.078 | 0.65 |
| 1_A | 43_A | 1.076 | 0.65 |
| 41_N | 78_Y | 1.074 | 0.65 |
| 3_V | 14_L | 1.051 | 0.63 |
| 58_N | 63_L | 1.036 | 0.61 |
| 36_V | 39_K | 1.032 | 0.60 |
| 62_K | 104_Q | 1.032 | 0.60 |
| 69_R | 91_S | 1.029 | 0.60 |
| 27_K | 94_W | 1.025 | 0.60 |
| 8_D | 12_D | 1.022 | 0.59 |
| 78_Y | 81_G | 1.022 | 0.59 |
| 77_N | 81_G | 1.022 | 0.59 |
| 67_S | 104_Q | 1.021 | 0.59 |
| 55_I | 105_T | 1.021 | 0.59 |
| 4_I | 80_S | 1.020 | 0.59 |
| 58_N | 102_H | 1.004 | 0.57 |
| 58_N | 87_R | 1.001 | 0.57 |
| 60_E | 83_R | 1.001 | 0.57 |
| 25_I | 49_K | 1.001 | 0.57 |
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 | |
| 2c4bA | 2 | 0.9818 | 100 | 0.086 | Contact Map |
| 3q3fA | 1 | 1 | 100 | 0.223 | Contact Map |
| 1lniA | 2 | 0.8273 | 99.9 | 0.353 | Contact Map |
| 1pylA | 2 | 0.8364 | 99.9 | 0.361 | Contact Map |
| 3da7A | 4 | 0.6 | 99.9 | 0.475 | Contact Map |
| 1fusA | 1 | 0.7909 | 22.5 | 0.924 | Contact Map |
| 3whoA | 3 | 0.7273 | 15.8 | 0.93 | Contact Map |
| 1i0vA | 1 | 0.7909 | 14.2 | 0.931 | Contact Map |
| 2kaaA | 1 | 0.8909 | 10.1 | 0.936 | Contact Map |
| 1rdsA | 1 | 0.8364 | 10.1 | 0.936 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)