| T0808 300-418 -force run |
| ID: | 1404889125 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 119 (117) | ||
| Sequences: | 89 (78.1) | ||
| Seq/Len: | 0.761 | ||
| Nf(neff/√len): | 7.2 |
Jackhmmer Results: (2014_04_16)
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: 0.761).
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 |
| 6_F | 68_V | 2.178 | 0.96 |
| 54_T | 102_C | 2.160 | 0.96 |
| 64_A | 72_Y | 1.943 | 0.91 |
| 52_R | 102_C | 1.812 | 0.87 |
| 60_H | 96_M | 1.786 | 0.86 |
| 43_A | 107_K | 1.696 | 0.81 |
| 38_F | 84_L | 1.604 | 0.76 |
| 29_Q | 87_G | 1.592 | 0.75 |
| 38_F | 93_S | 1.571 | 0.74 |
| 63_T | 100_F | 1.468 | 0.67 |
| 15_Y | 18_P | 1.462 | 0.66 |
| 10_K | 87_G | 1.390 | 0.60 |
| 14_W | 66_A | 1.379 | 0.59 |
| 14_W | 63_T | 1.377 | 0.59 |
| 42_W | 50_W | 1.367 | 0.58 |
| 18_P | 53_L | 1.366 | 0.58 |
| 8_R | 74_G | 1.357 | 0.58 |
| 104_P | 107_K | 1.331 | 0.55 |
| 94_V | 103_K | 1.313 | 0.54 |
| 30_G | 71_D | 1.305 | 0.53 |
| 12_N | 19_H | 1.294 | 0.52 |
| 54_T | 106_G | 1.285 | 0.51 |
| 35_E | 78_K | 1.244 | 0.48 |
| 9_P | 89_F | 1.231 | 0.47 |
| 19_H | 113_W | 1.205 | 0.45 |
| 63_T | 89_F | 1.204 | 0.44 |
| 27_P | 84_L | 1.204 | 0.44 |
| 18_P | 36_V | 1.195 | 0.44 |
| 103_K | 108_E | 1.193 | 0.44 |
| 112_D | 115_A | 1.163 | 0.41 |
| 30_G | 89_F | 1.155 | 0.40 |
| 13_T | 17_R | 1.146 | 0.40 |
| 38_F | 45_S | 1.144 | 0.39 |
| 42_W | 109_P | 1.142 | 0.39 |
| 9_P | 71_D | 1.127 | 0.38 |
| 42_W | 54_T | 1.119 | 0.37 |
| 60_H | 73_Q | 1.113 | 0.37 |
| 71_D | 89_F | 1.112 | 0.37 |
| 3_I | 9_P | 1.102 | 0.36 |
| 86_M | 90_F | 1.102 | 0.36 |
| 45_S | 51_S | 1.092 | 0.35 |
| 28_E | 100_F | 1.091 | 0.35 |
| 55_D | 101_Y | 1.090 | 0.35 |
| 44_R | 108_E | 1.078 | 0.34 |
| 8_R | 90_F | 1.074 | 0.34 |
| 3_I | 41_Q | 1.074 | 0.34 |
| 19_H | 110_E | 1.064 | 0.33 |
| 34_R | 82_F | 1.061 | 0.33 |
| 15_Y | 62_A | 1.050 | 0.32 |
| 33_S | 85_K | 1.049 | 0.32 |
| 2_L | 57_T | 1.043 | 0.32 |
| 9_P | 30_G | 1.037 | 0.31 |
| 57_T | 65_S | 1.033 | 0.31 |
| 107_K | 112_D | 1.032 | 0.31 |
| 30_G | 69_R | 1.030 | 0.31 |
| 83_Y | 96_M | 1.029 | 0.30 |
| 105_T | 115_A | 1.020 | 0.30 |
| 8_R | 86_M | 1.011 | 0.29 |
| 74_G | 86_M | 1.005 | 0.29 |
| 22_L | 74_G | 1.001 | 0.28 |
| 41_Q | 56_A | 1.001 | 0.28 |
| 50_W | 54_T | 1.000 | 0.28 |
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 | |
| 2llzA | 1 | 0.7059 | 31.2 | 0.933 | Contact Map |
| 3owtC | 1 | 0.0924 | 6.8 | 0.951 | Contact Map |
| 3tg7A | 1 | 0.6975 | 5.5 | 0.953 | Contact Map |
| 4h62V | 1 | 0.0672 | 5 | 0.954 | Contact Map |
| 2fq3A | 1 | 0.2689 | 4.8 | 0.954 | Contact Map |
| 2ww6A | 3 | 0.2101 | 4.7 | 0.954 | Contact Map |
| 2vovA | 1 | 0.4622 | 4 | 0.956 | Contact Map |
| 3v7dA | 2 | 0.3109 | 3.5 | 0.957 | Contact Map |
| 2iqtA | 1 | 0.3361 | 3.4 | 0.957 | Contact Map |
| 2p1mA | 1 | 0.3529 | 3.1 | 0.958 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)