| SecondMerge_cdhit76_satedit2CORGLtop |
| ID: | 1509120676 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 152 (148) | ||
| Sequences: | 939 (745.7) | ||
| Seq/Len: | 6.345 | ||
| Nf(neff/√len): | 61.3 |
HHblits Results: (2016_02)
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: 6.345).
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 |
| 85_G | 117_F | 4.173 | 1.00 |
| 100_L | 108_I | 3.106 | 1.00 |
| 120_R | 136_E | 2.136 | 1.00 |
| 87_F | 119_L | 2.032 | 1.00 |
| 88_R | 120_R | 1.772 | 1.00 |
| 84_G | 115_L | 1.749 | 1.00 |
| 107_R | 110_D | 1.672 | 1.00 |
| 106_R | 131_F | 1.580 | 0.99 |
| 73_E | 99_L | 1.561 | 0.99 |
| 145_L | 148_A | 1.504 | 0.99 |
| 118_A | 121_G | 1.485 | 0.99 |
| 84_G | 117_F | 1.477 | 0.99 |
| 107_R | 115_L | 1.466 | 0.99 |
| 125_K | 131_F | 1.455 | 0.99 |
| 70_V | 86_A | 1.439 | 0.99 |
| 24_Y | 28_E | 1.422 | 0.99 |
| 95_F | 112_A | 1.403 | 0.98 |
| 73_E | 127_D | 1.393 | 0.98 |
| 53_P | 57_A | 1.381 | 0.98 |
| 65_Y | 86_A | 1.374 | 0.98 |
| 69_I | 132_A | 1.356 | 0.98 |
| 74_L | 96_D | 1.352 | 0.98 |
| 109_V | 132_A | 1.342 | 0.98 |
| 87_F | 115_L | 1.336 | 0.98 |
| 81_Q | 85_G | 1.328 | 0.98 |
| 75_H | 99_L | 1.302 | 0.97 |
| 1_M | 7_T | 1.292 | 0.97 |
| 53_P | 56_V | 1.270 | 0.97 |
| 86_A | 91_D | 1.265 | 0.97 |
| 95_F | 130_T | 1.229 | 0.96 |
| 109_V | 113_A | 1.228 | 0.96 |
| 76_S | 80_A | 1.224 | 0.96 |
| 98_S | 113_A | 1.224 | 0.96 |
| 74_L | 83_I | 1.216 | 0.95 |
| 106_R | 122_K | 1.204 | 0.95 |
| 84_G | 113_A | 1.199 | 0.95 |
| 12_G | 129_V | 1.185 | 0.94 |
| 84_G | 106_R | 1.181 | 0.94 |
| 54_A | 58_P | 1.164 | 0.94 |
| 33_G | 36_A | 1.162 | 0.94 |
| 57_A | 60_P | 1.155 | 0.93 |
| 97_M | 127_D | 1.155 | 0.93 |
| 56_V | 59_S | 1.155 | 0.93 |
| 8_K | 14_A | 1.151 | 0.93 |
| 126_I | 132_A | 1.145 | 0.93 |
| 105_A | 109_V | 1.143 | 0.93 |
| 92_A | 138_S | 1.133 | 0.93 |
| 107_R | 113_A | 1.119 | 0.92 |
| 52_A | 62_P | 1.114 | 0.92 |
| 6_K | 94_V | 1.110 | 0.91 |
| 4_L | 7_T | 1.106 | 0.91 |
| 53_P | 58_P | 1.105 | 0.91 |
| 78_E | 104_E | 1.104 | 0.91 |
| 105_A | 129_V | 1.104 | 0.91 |
| 81_Q | 107_R | 1.098 | 0.91 |
| 109_V | 134_V | 1.087 | 0.90 |
| 118_A | 133_V | 1.085 | 0.90 |
| 50_P | 53_P | 1.076 | 0.90 |
| 9_E | 14_A | 1.062 | 0.89 |
| 108_I | 127_D | 1.059 | 0.89 |
| 74_L | 95_F | 1.052 | 0.88 |
| 70_V | 91_D | 1.051 | 0.88 |
| 24_Y | 27_D | 1.051 | 0.88 |
| 92_A | 95_F | 1.049 | 0.88 |
| 94_V | 126_I | 1.043 | 0.88 |
| 127_D | 130_T | 1.041 | 0.88 |
| 88_R | 130_T | 1.040 | 0.88 |
| 79_D | 138_S | 1.026 | 0.87 |
| 94_V | 132_A | 1.024 | 0.86 |
| 112_A | 116_C | 1.021 | 0.86 |
| 96_D | 127_D | 1.018 | 0.86 |
| 8_K | 11_F | 1.015 | 0.86 |
| 73_E | 105_A | 1.012 | 0.86 |
| 84_G | 107_R | 1.008 | 0.85 |
| 83_I | 95_F | 1.008 | 0.85 |
| 11_F | 118_A | 1.006 | 0.85 |
| 123_M | 133_V | 1.000 | 0.85 |
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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 3zihA | 2 | 0.5263 | 100 | 0.353 | Contact Map |
| 3p04A | 2 | 0.5132 | 100 | 0.358 | Contact Map |
| 3zieA | 6 | 0.5461 | 99.9 | 0.411 | Contact Map |
| 3zigA | 2 | 0.5329 | 99.9 | 0.419 | Contact Map |
| 1k0wA | 6 | 0.3684 | 25.9 | 0.926 | Contact Map |
| 2opiA | 2 | 0.3618 | 16.1 | 0.933 | Contact Map |
| 4pj2A | 2 | 0.4211 | 14.6 | 0.934 | Contact Map |
| 2fk5A | 2 | 0.375 | 13.6 | 0.935 | Contact Map |
| 4m6rA | 4 | 0.375 | 13.3 | 0.935 | Contact Map |
| 1e4cP | 1 | 0.3684 | 8.9 | 0.94 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)