| 4bp2 |
| ID: | 1453737508 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 130 (127) | ||
| Sequences: | 942 (558.7) | ||
| Seq/Len: | 7.417 | ||
| Nf(neff/√len): | 49.6 |
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: 7.417).
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 |
| 12_F | 109_A | 3.432 | 1.00 |
| 68_C | 98_C | 3.186 | 1.00 |
| 109_A | 113_F | 2.885 | 1.00 |
| 18_C | 84_C | 2.558 | 1.00 |
| 53_Q | 57_N | 2.393 | 1.00 |
| 37_G | 56_D | 2.177 | 1.00 |
| 39_G | 56_D | 2.108 | 1.00 |
| 4_L | 7_R | 1.934 | 1.00 |
| 122_H | 125_L | 1.869 | 1.00 |
| 12_F | 113_F | 1.810 | 1.00 |
| 8_A | 11_Q | 1.753 | 1.00 |
| 51_C | 112_C | 1.738 | 1.00 |
| 3_G | 7_R | 1.588 | 1.00 |
| 35_Y | 56_D | 1.575 | 1.00 |
| 62_A | 101_F | 1.573 | 1.00 |
| 89_I | 111_I | 1.546 | 1.00 |
| 122_H | 130_C | 1.540 | 1.00 |
| 107_R | 111_I | 1.475 | 0.99 |
| 51_C | 55_H | 1.466 | 0.99 |
| 11_Q | 79_N | 1.458 | 0.99 |
| 26_L | 30_N | 1.456 | 0.99 |
| 37_G | 51_C | 1.446 | 0.99 |
| 75_P | 102_I | 1.426 | 0.99 |
| 46_D | 49_D | 1.424 | 0.99 |
| 100_A | 104_N | 1.398 | 0.99 |
| 47_D | 116_V | 1.396 | 0.99 |
| 89_I | 107_R | 1.382 | 0.99 |
| 126_D | 129_N | 1.358 | 0.99 |
| 35_Y | 40_G | 1.357 | 0.99 |
| 56_D | 59_Y | 1.332 | 0.98 |
| 111_I | 115_K | 1.304 | 0.98 |
| 36_C | 46_D | 1.298 | 0.98 |
| 3_G | 6_S | 1.279 | 0.98 |
| 55_H | 59_Y | 1.259 | 0.97 |
| 34_C | 44_P | 1.259 | 0.97 |
| 93_S | 100_A | 1.231 | 0.97 |
| 104_N | 108_N | 1.223 | 0.97 |
| 31_N | 124_N | 1.213 | 0.96 |
| 35_Y | 41_S | 1.211 | 0.96 |
| 36_C | 49_D | 1.190 | 0.96 |
| 37_G | 112_C | 1.148 | 0.95 |
| 51_C | 59_Y | 1.140 | 0.95 |
| 27_L | 30_N | 1.128 | 0.94 |
| 10_W | 13_N | 1.128 | 0.94 |
| 41_S | 45_V | 1.124 | 0.94 |
| 31_N | 126_D | 1.120 | 0.94 |
| 52_C | 58_C | 1.108 | 0.93 |
| 13_N | 26_L | 1.103 | 0.93 |
| 34_C | 46_D | 1.100 | 0.93 |
| 29_F | 48_L | 1.099 | 0.93 |
| 91_C | 103_C | 1.088 | 0.93 |
| 108_N | 111_I | 1.086 | 0.92 |
| 32_Y | 46_D | 1.085 | 0.92 |
| 33_G | 49_D | 1.078 | 0.92 |
| 55_H | 112_C | 1.076 | 0.92 |
| 33_G | 46_D | 1.075 | 0.92 |
| 59_Y | 112_C | 1.062 | 0.91 |
| 8_A | 79_N | 1.058 | 0.91 |
| 20_I | 23_S | 1.046 | 0.91 |
| 13_N | 17_K | 1.041 | 0.90 |
| 36_C | 52_C | 1.038 | 0.90 |
| 34_C | 49_D | 1.036 | 0.90 |
| 51_C | 56_D | 1.033 | 0.90 |
| 7_R | 130_C | 1.027 | 0.89 |
| 60_K | 63_K | 1.006 | 0.88 |
| 40_G | 56_D | 1.003 | 0.88 |
| 55_H | 58_C | 1.002 | 0.88 |
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 | |
| 1gp7A | 3 | 0.9462 | 100 | 0.081 | Contact Map |
| 1p7oA | 6 | 0.9462 | 100 | 0.086 | Contact Map |
| 1g4iA | 1 | 0.9462 | 100 | 0.088 | Contact Map |
| 1le6A | 3 | 0.8846 | 100 | 0.097 | Contact Map |
| 1bunA | 1 | 0.9077 | 100 | 0.097 | Contact Map |
| 1m8tA | 6 | 0.9077 | 100 | 0.098 | Contact Map |
| 3jqlA | 1 | 0.9 | 100 | 0.1 | Contact Map |
| 4ntwC | 1 | 0.8923 | 100 | 0.101 | Contact Map |
| 3u8iA | 2 | 0.8769 | 100 | 0.109 | Contact Map |
| 4e4cA | 1 | 0.9 | 100 | 0.11 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)