| 1vfq |
| ID: | 1452700766 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 143 (134) | ||
| Sequences: | 2050 (1257.2) | ||
| Seq/Len: | 15.299 | ||
| Nf(neff/√len): | 108.6 |
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: 15.299).
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 |
| 9_E | 13_A | 2.260 | 1.00 |
| 56_D | 86_N | 2.236 | 1.00 |
| 57_V | 91_Q | 2.201 | 1.00 |
| 31_K | 39_P | 2.164 | 1.00 |
| 11_C | 30_F | 2.029 | 1.00 |
| 49_F | 61_A | 1.895 | 1.00 |
| 12_R | 105_V | 1.827 | 1.00 |
| 40_G | 52_Q | 1.745 | 1.00 |
| 12_R | 16_N | 1.738 | 1.00 |
| 109_F | 112_E | 1.694 | 1.00 |
| 8_K | 36_T | 1.686 | 1.00 |
| 32_Y | 60_F | 1.684 | 1.00 |
| 32_Y | 95_T | 1.674 | 1.00 |
| 79_L | 99_K | 1.597 | 1.00 |
| 45_E | 48_H | 1.590 | 1.00 |
| 88_S | 91_Q | 1.572 | 1.00 |
| 116_S | 120_E | 1.569 | 1.00 |
| 14_A | 17_L | 1.555 | 1.00 |
| 27_W | 61_A | 1.531 | 1.00 |
| 46_Y | 49_F | 1.517 | 1.00 |
| 66_T | 73_K | 1.516 | 1.00 |
| 80_I | 121_L | 1.507 | 1.00 |
| 32_Y | 98_D | 1.507 | 1.00 |
| 103_K | 112_E | 1.472 | 1.00 |
| 115_I | 121_L | 1.447 | 1.00 |
| 33_D | 38_V | 1.429 | 1.00 |
| 58_R | 87_V | 1.423 | 1.00 |
| 3_A | 6_I | 1.418 | 1.00 |
| 37_I | 98_D | 1.408 | 1.00 |
| 123_E | 127_K | 1.403 | 0.99 |
| 55_D | 118_R | 1.386 | 0.99 |
| 26_I | 45_E | 1.337 | 0.99 |
| 47_Q | 51_Q | 1.335 | 0.99 |
| 15_Y | 106_V | 1.318 | 0.99 |
| 13_A | 17_L | 1.276 | 0.99 |
| 99_K | 103_K | 1.274 | 0.99 |
| 93_A | 97_T | 1.270 | 0.99 |
| 65_F | 123_E | 1.249 | 0.99 |
| 17_L | 25_V | 1.243 | 0.98 |
| 81_T | 114_V | 1.198 | 0.98 |
| 39_P | 102_V | 1.195 | 0.98 |
| 10_A | 13_A | 1.181 | 0.98 |
| 80_I | 113_F | 1.169 | 0.97 |
| 18_V | 77_F | 1.161 | 0.97 |
| 17_L | 23_S | 1.159 | 0.97 |
| 99_K | 112_E | 1.151 | 0.97 |
| 82_W | 115_I | 1.150 | 0.97 |
| 124_D | 128_S | 1.147 | 0.97 |
| 46_Y | 126_I | 1.139 | 0.97 |
| 80_I | 126_I | 1.137 | 0.97 |
| 3_A | 101_L | 1.133 | 0.97 |
| 46_Y | 63_V | 1.132 | 0.97 |
| 89_G | 96_G | 1.115 | 0.96 |
| 54_T | 57_V | 1.096 | 0.96 |
| 47_Q | 123_E | 1.091 | 0.96 |
| 64_R | 77_F | 1.090 | 0.96 |
| 55_D | 86_N | 1.087 | 0.96 |
| 14_A | 18_V | 1.086 | 0.96 |
| 29_T | 61_A | 1.081 | 0.95 |
| 8_K | 38_V | 1.076 | 0.95 |
| 76_K | 110_A | 1.073 | 0.95 |
| 85_E | 116_S | 1.070 | 0.95 |
| 89_G | 92_R | 1.062 | 0.95 |
| 26_I | 63_V | 1.048 | 0.94 |
| 53_C | 61_A | 1.047 | 0.94 |
| 68_G | 73_K | 1.040 | 0.94 |
| 27_W | 52_Q | 1.031 | 0.94 |
| 101_L | 104_E | 1.030 | 0.94 |
| 98_D | 101_L | 1.030 | 0.94 |
| 30_F | 37_I | 1.030 | 0.94 |
| 90_L | 93_A | 1.028 | 0.94 |
| 90_L | 97_T | 1.027 | 0.94 |
| 42_Q | 45_E | 1.023 | 0.93 |
| 76_K | 122_E | 1.021 | 0.93 |
| 85_E | 92_R | 1.005 | 0.93 |
| 31_K | 59_L | 1.000 | 0.92 |
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 | |
| 1t3yA | 1 | 0.9161 | 100 | 0.07 | Contact Map |
| 4lizA | 1 | 0.9371 | 100 | 0.107 | Contact Map |
| 4kefA | 1 | 0.8951 | 100 | 0.132 | Contact Map |
| 2mp4A | 1 | 0.951 | 100 | 0.135 | Contact Map |
| 2i2qA | 1 | 0.8182 | 100 | 0.16 | Contact Map |
| 1f7sA | 1 | 0.8182 | 100 | 0.161 | Contact Map |
| 1x67A | 1 | 0.9441 | 100 | 0.162 | Contact Map |
| 2kvkA | 1 | 0.965 | 100 | 0.171 | Contact Map |
| 1hqz1 | 9 | 0.9301 | 100 | 0.177 | Contact Map |
| 2lj8A | 1 | 0.9161 | 100 | 0.182 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)