| d2z0ma2 |
| ID: | 1447475826 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 139 (132) | ||
| Sequences: | 29872 (14736.5) | ||
| Seq/Len: | 226.303 | ||
| Nf(neff/√len): | 1282.6 |
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: 226.303).
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 |
| 52_I | 75_Y | 3.178 | 1.00 |
| 45_V | 53_E | 2.793 | 1.00 |
| 31_V | 95_K | 2.692 | 1.00 |
| 38_R | 57_D | 2.532 | 1.00 |
| 42_A | 53_E | 2.469 | 1.00 |
| 52_I | 69_A | 2.375 | 1.00 |
| 35_V | 44_L | 2.323 | 1.00 |
| 45_V | 51_A | 2.181 | 1.00 |
| 69_A | 74_E | 2.159 | 1.00 |
| 52_I | 66_N | 2.157 | 1.00 |
| 18_S | 47_L | 2.131 | 1.00 |
| 68_D | 72_E | 2.087 | 1.00 |
| 95_K | 125_I | 2.021 | 1.00 |
| 65_R | 69_A | 1.948 | 1.00 |
| 45_V | 49_D | 1.892 | 1.00 |
| 112_I | 124_A | 1.883 | 1.00 |
| 35_V | 41_V | 1.870 | 1.00 |
| 35_V | 79_I | 1.823 | 1.00 |
| 29_K | 94_E | 1.729 | 1.00 |
| 8_K | 123_E | 1.699 | 1.00 |
| 50_N | 76_D | 1.673 | 1.00 |
| 98_N | 126_T | 1.637 | 1.00 |
| 41_V | 53_E | 1.610 | 1.00 |
| 6_E | 123_E | 1.562 | 1.00 |
| 41_V | 55_R | 1.555 | 1.00 |
| 44_L | 99_F | 1.545 | 1.00 |
| 66_N | 78_L | 1.529 | 1.00 |
| 84_A | 88_L | 1.525 | 1.00 |
| 40_R | 100_D | 1.500 | 1.00 |
| 69_A | 75_Y | 1.488 | 1.00 |
| 64_N | 68_D | 1.483 | 1.00 |
| 30_G | 92_L | 1.467 | 1.00 |
| 31_V | 77_M | 1.463 | 1.00 |
| 7_H | 108_Y | 1.462 | 1.00 |
| 80_T | 84_A | 1.456 | 1.00 |
| 102_P | 108_Y | 1.449 | 1.00 |
| 98_N | 112_I | 1.439 | 1.00 |
| 40_R | 43_K | 1.428 | 1.00 |
| 7_H | 112_I | 1.415 | 1.00 |
| 20_V | 97_I | 1.376 | 0.99 |
| 114_R | 117_R | 1.372 | 0.99 |
| 48_F | 79_I | 1.360 | 0.99 |
| 59_P | 62_V | 1.351 | 0.99 |
| 101_A | 126_T | 1.335 | 0.99 |
| 21_Q | 47_L | 1.330 | 0.99 |
| 96_V | 115_T | 1.322 | 0.99 |
| 30_G | 73_G | 1.319 | 0.99 |
| 55_R | 58_L | 1.287 | 0.99 |
| 37_T | 40_R | 1.269 | 0.99 |
| 58_L | 66_N | 1.247 | 0.99 |
| 36_R | 103_Q | 1.246 | 0.98 |
| 31_V | 97_I | 1.232 | 0.98 |
| 82_D | 111_R | 1.164 | 0.97 |
| 66_N | 75_Y | 1.161 | 0.97 |
| 21_Q | 25_E | 1.155 | 0.97 |
| 5_V | 116_G | 1.150 | 0.97 |
| 13_K | 16_W | 1.147 | 0.97 |
| 23_L | 125_I | 1.140 | 0.97 |
| 58_L | 62_V | 1.133 | 0.97 |
| 70_F | 93_V | 1.126 | 0.97 |
| 115_T | 122_G | 1.110 | 0.96 |
| 73_G | 76_D | 1.086 | 0.96 |
| 54_L | 83_V | 1.083 | 0.96 |
| 60_Q | 64_N | 1.074 | 0.95 |
| 66_N | 69_A | 1.073 | 0.95 |
| 4_N | 121_K | 1.068 | 0.95 |
| 33_V | 99_F | 1.065 | 0.95 |
| 45_V | 79_I | 1.062 | 0.95 |
| 95_K | 123_E | 1.062 | 0.95 |
| 23_L | 97_I | 1.061 | 0.95 |
| 104_D | 107_T | 1.038 | 0.94 |
| 113_G | 117_R | 1.038 | 0.94 |
| 62_V | 66_N | 1.027 | 0.94 |
| 54_L | 84_A | 1.021 | 0.93 |
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 | |
| 3i32A | 1 | 0.9496 | 99.9 | 0.205 | Contact Map |
| 4pxaA | 1 | 1 | 99.9 | 0.219 | Contact Map |
| 4crwB | 1 | 0.9856 | 99.9 | 0.224 | Contact Map |
| 3eaqA | 2 | 0.9856 | 99.9 | 0.224 | Contact Map |
| 2p6nA | 2 | 0.9712 | 99.9 | 0.229 | Contact Map |
| 1fukA | 1 | 0.9353 | 99.9 | 0.235 | Contact Map |
| 2jgnA | 3 | 1 | 99.9 | 0.235 | Contact Map |
| 2db3A | 4 | 1 | 99.9 | 0.237 | Contact Map |
| 1t5iA | 1 | 0.9784 | 99.9 | 0.237 | Contact Map |
| 4w7sA | 2 | 1 | 99.9 | 0.243 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)