| HELLF2 |
| ID: | 1416837484 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 277 (165) | ||
| Sequences: | 361 (340.4) | ||
| Seq/Len: | 2.188 | ||
| Nf(neff/√len): | 26.5 |
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: 2.188).
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 |
| 2_D | 5_S | 7.557 | 1.00 |
| 27_L | 116_Y | 3.307 | 1.00 |
| 3_P | 7_T | 2.450 | 1.00 |
| 1_M | 6_V | 2.064 | 0.99 |
| 15_T | 19_Q | 1.867 | 0.98 |
| 37_S | 119_D | 1.805 | 0.98 |
| 2_D | 6_V | 1.802 | 0.98 |
| 6_V | 10_A | 1.755 | 0.97 |
| 1_M | 5_S | 1.722 | 0.97 |
| 12_A | 15_T | 1.713 | 0.97 |
| 45_L | 88_C | 1.682 | 0.97 |
| 9_S | 13_L | 1.640 | 0.96 |
| 133_Q | 138_M | 1.609 | 0.95 |
| 27_L | 91_F | 1.593 | 0.95 |
| 4_L | 7_T | 1.574 | 0.94 |
| 3_P | 6_V | 1.503 | 0.92 |
| 151_T | 155_I | 1.488 | 0.92 |
| 4_L | 9_S | 1.453 | 0.91 |
| 130_A | 133_Q | 1.423 | 0.89 |
| 33_D | 38_V | 1.395 | 0.88 |
| 44_L | 133_Q | 1.383 | 0.88 |
| 4_L | 16_A | 1.382 | 0.88 |
| 20_S | 129_L | 1.364 | 0.87 |
| 48_T | 84_T | 1.361 | 0.86 |
| 2_D | 7_T | 1.347 | 0.86 |
| 4_L | 13_L | 1.343 | 0.85 |
| 88_C | 111_D | 1.324 | 0.84 |
| 56_A | 60_E | 1.300 | 0.83 |
| 51_T | 132_C | 1.287 | 0.82 |
| 7_T | 13_L | 1.282 | 0.82 |
| 13_L | 24_L | 1.281 | 0.82 |
| 8_A | 13_L | 1.248 | 0.79 |
| 162_F | 165_Q | 1.214 | 0.76 |
| 17_A | 21_A | 1.211 | 0.76 |
| 5_S | 8_A | 1.193 | 0.75 |
| 20_S | 27_L | 1.184 | 0.74 |
| 44_L | 131_D | 1.183 | 0.74 |
| 77_L | 129_L | 1.175 | 0.73 |
| 153_G | 157_Q | 1.174 | 0.73 |
| 19_Q | 101_H | 1.171 | 0.73 |
| 80_V | 83_S | 1.141 | 0.70 |
| 157_Q | 160_T | 1.132 | 0.69 |
| 135_T | 139_V | 1.129 | 0.69 |
| 28_V | 31_L | 1.115 | 0.67 |
| 11_V | 32_A | 1.114 | 0.67 |
| 130_A | 134_R | 1.113 | 0.67 |
| 115_V | 126_N | 1.112 | 0.67 |
| 48_T | 51_T | 1.108 | 0.67 |
| 148_S | 155_I | 1.107 | 0.67 |
| 126_N | 136_I | 1.105 | 0.66 |
| 20_S | 91_F | 1.097 | 0.66 |
| 24_L | 91_F | 1.089 | 0.65 |
| 12_A | 19_Q | 1.087 | 0.65 |
| 11_V | 18_L | 1.072 | 0.63 |
| 30_G | 119_D | 1.065 | 0.62 |
| 41_S | 121_K | 1.053 | 0.61 |
| 44_L | 126_N | 1.052 | 0.61 |
| 6_V | 9_S | 1.046 | 0.60 |
| 12_A | 17_A | 1.042 | 0.60 |
| 2_D | 8_A | 1.034 | 0.59 |
| 4_L | 106_H | 1.032 | 0.59 |
| 152_S | 155_I | 1.023 | 0.58 |
| 30_G | 125_L | 1.022 | 0.57 |
| 13_L | 40_H | 1.020 | 0.57 |
| 155_I | 160_T | 1.016 | 0.57 |
| 160_T | 164_T | 1.000 | 0.55 |
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 | |
| 4btfA | 1 | 0.7148 | 93 | 0.916 | Contact Map |
| 2wvqA | 2 | 0.6462 | 70.2 | 0.937 | Contact Map |
| 3qflA | 1 | 0.3971 | 66.3 | 0.939 | Contact Map |
| 4egwA | 2 | 0.5126 | 42.6 | 0.947 | Contact Map |
| 4dndA | 1 | 0.343 | 38.8 | 0.948 | Contact Map |
| 2ljbA | 4 | 0.1083 | 36.6 | 0.949 | Contact Map |
| 3bkdA | 8 | 0.0866 | 31.1 | 0.951 | Contact Map |
| 2kihA | 4 | 0.13 | 20.7 | 0.955 | Contact Map |
| 1jthB | 2 | 0.2419 | 19.3 | 0.956 | Contact Map |
| 4m70A | 5 | 0.4116 | 19.3 | 0.956 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)