| X5DTE7_8iterations |
| ID: | 1447430026 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 129 (127) | ||
| Sequences: | 445 (177.4) | ||
| Seq/Len: | 3.504 | ||
| Nf(neff/√len): | 15.7 |
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: 3.504).
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 |
| 118_D | 125_N | 2.709 | 1.00 |
| 45_G | 57_T | 2.440 | 1.00 |
| 118_D | 121_D | 2.373 | 1.00 |
| 114_P | 117_D | 2.124 | 1.00 |
| 103_S | 107_P | 2.121 | 1.00 |
| 121_D | 125_N | 1.892 | 1.00 |
| 2_R | 18_Q | 1.804 | 0.99 |
| 118_D | 124_W | 1.746 | 0.99 |
| 15_E | 18_Q | 1.720 | 0.99 |
| 29_I | 46_H | 1.691 | 0.99 |
| 12_I | 16_H | 1.678 | 0.99 |
| 13_K | 16_H | 1.631 | 0.98 |
| 1_M | 4_S | 1.603 | 0.98 |
| 24_I | 41_I | 1.556 | 0.98 |
| 70_K | 75_Q | 1.442 | 0.96 |
| 8_Q | 14_Q | 1.387 | 0.94 |
| 13_K | 19_A | 1.377 | 0.94 |
| 23_A | 40_H | 1.360 | 0.94 |
| 16_H | 19_A | 1.347 | 0.93 |
| 1_M | 5_S | 1.336 | 0.93 |
| 54_H | 58_S | 1.330 | 0.93 |
| 11_S | 14_Q | 1.321 | 0.92 |
| 98_P | 107_P | 1.321 | 0.92 |
| 12_I | 17_R | 1.278 | 0.91 |
| 17_R | 107_P | 1.267 | 0.90 |
| 104_V | 115_S | 1.261 | 0.90 |
| 104_V | 107_P | 1.250 | 0.89 |
| 121_D | 124_W | 1.232 | 0.88 |
| 123_F | 126_D | 1.226 | 0.88 |
| 18_Q | 44_R | 1.225 | 0.88 |
| 8_Q | 107_P | 1.189 | 0.86 |
| 10_P | 14_Q | 1.177 | 0.85 |
| 27_R | 111_P | 1.170 | 0.85 |
| 8_Q | 12_I | 1.141 | 0.82 |
| 64_V | 103_S | 1.139 | 0.82 |
| 103_S | 106_S | 1.136 | 0.82 |
| 16_H | 20_K | 1.129 | 0.82 |
| 83_P | 89_S | 1.128 | 0.81 |
| 115_S | 118_D | 1.119 | 0.81 |
| 44_R | 112_E | 1.118 | 0.81 |
| 4_S | 7_S | 1.117 | 0.81 |
| 119_I | 125_N | 1.115 | 0.80 |
| 67_G | 108_Q | 1.112 | 0.80 |
| 46_H | 62_W | 1.106 | 0.80 |
| 120_D | 126_D | 1.090 | 0.78 |
| 96_V | 104_V | 1.087 | 0.78 |
| 13_K | 17_R | 1.085 | 0.78 |
| 3_S | 10_P | 1.085 | 0.78 |
| 39_F | 57_T | 1.076 | 0.77 |
| 86_Q | 93_S | 1.075 | 0.77 |
| 1_M | 7_S | 1.066 | 0.76 |
| 63_R | 66_L | 1.062 | 0.76 |
| 17_R | 23_A | 1.060 | 0.75 |
| 55_H | 71_S | 1.056 | 0.75 |
| 8_Q | 100_P | 1.054 | 0.75 |
| 56_C | 61_E | 1.051 | 0.75 |
| 109_V | 115_S | 1.046 | 0.74 |
| 84_I | 87_D | 1.043 | 0.74 |
| 71_S | 75_Q | 1.028 | 0.72 |
| 5_S | 126_D | 1.019 | 0.71 |
| 14_Q | 126_D | 1.015 | 0.71 |
| 90_I | 120_D | 1.013 | 0.71 |
| 86_Q | 91_P | 1.010 | 0.70 |
| 95_T | 98_P | 1.009 | 0.70 |
| 89_S | 95_T | 1.004 | 0.70 |
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 | |
| 2mbdA | 1 | 0.2093 | 21.6 | 0.953 | Contact Map |
| 4uz8A | 2 | 0.3643 | 18.7 | 0.954 | Contact Map |
| 2lpbB | 1 | 0.1938 | 16.2 | 0.955 | Contact Map |
| 1d1dA | 1 | 0.3411 | 13.2 | 0.957 | Contact Map |
| 3tirA | 1 | 0.4186 | 9.1 | 0.96 | Contact Map |
| 3n9uC | 2 | 0.1705 | 6.1 | 0.963 | Contact Map |
| 1em9A | 2 | 0.4419 | 5.8 | 0.964 | Contact Map |
| 3uitA | 4 | 0.5969 | 4.5 | 0.965 | Contact Map |
| 2p22C | 1 | 0.3023 | 4.1 | 0.966 | Contact Map |
| 1o7fA | 1 | 0.3411 | 3.9 | 0.966 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)