| 1CZ9A |
| ID: | 1411606623 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 139 (132) | ||
| Sequences: | 7836 (4895.7) | ||
| Seq/Len: | 59.364 | ||
| Nf(neff/√len): | 426.1 |
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: 59.364).
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 |
| 88_I | 94_G | 3.275 | 1.00 |
| 21_V | 102_N | 3.050 | 1.00 |
| 100_R | 103_R | 2.470 | 1.00 |
| 62_T | 84_H | 2.323 | 1.00 |
| 87_G | 95_Q | 2.297 | 1.00 |
| 25_T | 97_M | 2.185 | 1.00 |
| 61_K | 85_T | 2.126 | 1.00 |
| 30_I | 101_A | 2.012 | 1.00 |
| 64_N | 86_T | 2.004 | 1.00 |
| 100_R | 104_L | 1.894 | 1.00 |
| 4_Q | 25_T | 1.892 | 1.00 |
| 5_T | 62_T | 1.881 | 1.00 |
| 103_R | 107_D | 1.879 | 1.00 |
| 48_A | 76_W | 1.858 | 1.00 |
| 77_L | 82_I | 1.850 | 1.00 |
| 8_T | 106_K | 1.846 | 1.00 |
| 32_V | 135_M | 1.843 | 1.00 |
| 74_R | 84_H | 1.787 | 1.00 |
| 4_Q | 98_V | 1.761 | 1.00 |
| 98_V | 102_N | 1.755 | 1.00 |
| 76_W | 80_W | 1.740 | 1.00 |
| 64_N | 89_P | 1.637 | 1.00 |
| 38_V | 67_C | 1.595 | 1.00 |
| 40_S | 44_Q | 1.587 | 1.00 |
| 39_T | 42_A | 1.586 | 1.00 |
| 21_V | 98_V | 1.544 | 1.00 |
| 77_L | 84_H | 1.532 | 1.00 |
| 87_G | 94_G | 1.506 | 1.00 |
| 37_R | 42_A | 1.471 | 1.00 |
| 20_A | 68_F | 1.428 | 1.00 |
| 23_V | 98_V | 1.407 | 0.99 |
| 59_A | 85_T | 1.395 | 0.99 |
| 69_T | 86_T | 1.371 | 0.99 |
| 95_Q | 98_V | 1.323 | 0.99 |
| 28_S | 97_M | 1.316 | 0.99 |
| 88_I | 91_N | 1.310 | 0.99 |
| 5_T | 60_I | 1.296 | 0.99 |
| 23_V | 28_S | 1.285 | 0.99 |
| 91_N | 94_G | 1.281 | 0.99 |
| 5_T | 68_F | 1.274 | 0.99 |
| 31_V | 53_V | 1.248 | 0.99 |
| 65_G | 68_F | 1.246 | 0.98 |
| 75_E | 79_R | 1.244 | 0.98 |
| 128_G | 132_A | 1.238 | 0.98 |
| 12_R | 15_P | 1.218 | 0.98 |
| 75_E | 78_A | 1.207 | 0.98 |
| 7_F | 67_C | 1.200 | 0.98 |
| 61_K | 94_G | 1.197 | 0.98 |
| 3_W | 50_A | 1.194 | 0.98 |
| 4_Q | 95_Q | 1.141 | 0.97 |
| 67_C | 70_S | 1.128 | 0.97 |
| 23_V | 97_M | 1.126 | 0.97 |
| 63_D | 99_E | 1.118 | 0.96 |
| 33_T | 49_T | 1.109 | 0.96 |
| 8_T | 102_N | 1.105 | 0.96 |
| 51_I | 82_I | 1.096 | 0.96 |
| 20_A | 46_H | 1.092 | 0.96 |
| 16_R | 128_G | 1.077 | 0.95 |
| 2_I | 25_T | 1.070 | 0.95 |
| 135_M | 139_N | 1.064 | 0.95 |
| 74_R | 78_A | 1.060 | 0.95 |
| 19_L | 105_L | 1.046 | 0.94 |
| 73_T | 77_L | 1.038 | 0.94 |
| 40_S | 72_S | 1.011 | 0.93 |
| 109_I | 131_L | 1.006 | 0.93 |
| 66_S | 70_S | 1.003 | 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 | |
| 4fw2A | 2 | 0.9496 | 99.9 | 0.137 | Contact Map |
| 4fw1A | 2 | 1 | 99.9 | 0.143 | Contact Map |
| 1cxqA | 1 | 0.9712 | 99.9 | 0.15 | Contact Map |
| 3oymA | 2 | 0.9424 | 99.9 | 0.159 | Contact Map |
| 2x78A | 3 | 0.9137 | 99.9 | 0.187 | Contact Map |
| 3kksA | 2 | 0.9065 | 99.9 | 0.206 | Contact Map |
| 1c6vA | 4 | 0.8345 | 99.9 | 0.213 | Contact Map |
| 3hphA | 4 | 0.9065 | 99.9 | 0.217 | Contact Map |
| 3l3uA | 2 | 0.9065 | 99.9 | 0.22 | Contact Map |
| 1k6yA | 4 | 0.8417 | 99.9 | 0.233 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)