| 1CCZA |
| ID: | 1411603611 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 171 (165) | ||
| Sequences: | 12468 (8897.3) | ||
| Seq/Len: | 75.564 | ||
| Nf(neff/√len): | 692.7 |
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: 75.564).
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 |
| 7_G | 67_L | 3.924 | 1.00 |
| 112_C | 152_C | 3.740 | 1.00 |
| 17_V | 77_M | 3.456 | 1.00 |
| 125_Y | 153_K | 3.407 | 1.00 |
| 29_K | 78_E | 2.961 | 1.00 |
| 21_V | 24_K | 2.362 | 1.00 |
| 14_T | 63_T | 2.199 | 1.00 |
| 116_E | 120_V | 2.183 | 1.00 |
| 13_V | 90_L | 2.155 | 1.00 |
| 74_E | 89_F | 2.121 | 1.00 |
| 126_Q | 148_A | 2.090 | 1.00 |
| 8_V | 11_G | 2.086 | 1.00 |
| 12_N | 63_T | 2.032 | 1.00 |
| 52_R | 71_D | 1.987 | 1.00 |
| 12_N | 65_Y | 1.974 | 1.00 |
| 30_K | 75_Y | 1.969 | 1.00 |
| 76_E | 87_K | 1.946 | 1.00 |
| 74_E | 87_K | 1.927 | 1.00 |
| 114_V | 122_L | 1.919 | 1.00 |
| 155_V | 160_Q | 1.871 | 1.00 |
| 27_L | 78_E | 1.857 | 1.00 |
| 126_Q | 150_F | 1.856 | 1.00 |
| 16_H | 61_S | 1.837 | 1.00 |
| 30_K | 73_D | 1.800 | 1.00 |
| 109_T | 140_S | 1.769 | 1.00 |
| 14_T | 61_S | 1.768 | 1.00 |
| 81_N | 84_D | 1.721 | 1.00 |
| 28_W | 62_L | 1.669 | 1.00 |
| 125_Y | 151_K | 1.649 | 1.00 |
| 67_L | 92_V | 1.648 | 1.00 |
| 151_K | 164_M | 1.629 | 1.00 |
| 153_K | 162_S | 1.623 | 1.00 |
| 114_V | 154_A | 1.612 | 1.00 |
| 7_G | 13_V | 1.604 | 1.00 |
| 9_V | 69_S | 1.583 | 1.00 |
| 156_N | 159_S | 1.568 | 1.00 |
| 123_K | 153_K | 1.561 | 1.00 |
| 121_E | 155_V | 1.555 | 1.00 |
| 15_F | 90_L | 1.534 | 1.00 |
| 12_N | 66_N | 1.516 | 1.00 |
| 27_L | 80_P | 1.501 | 1.00 |
| 19_S | 79_S | 1.489 | 1.00 |
| 107_N | 142_Q | 1.487 | 1.00 |
| 151_K | 162_S | 1.484 | 1.00 |
| 31_Q | 76_E | 1.478 | 1.00 |
| 29_K | 34_K | 1.477 | 1.00 |
| 123_K | 155_V | 1.468 | 1.00 |
| 109_T | 138_T | 1.467 | 1.00 |
| 29_K | 76_E | 1.439 | 1.00 |
| 153_K | 160_Q | 1.429 | 1.00 |
| 110_L | 167_V | 1.374 | 0.99 |
| 110_L | 150_F | 1.364 | 0.99 |
| 17_V | 112_C | 1.358 | 0.99 |
| 123_K | 130_H | 1.348 | 0.99 |
| 125_Y | 130_H | 1.335 | 0.99 |
| 107_N | 143_W | 1.327 | 0.99 |
| 69_S | 94_E | 1.313 | 0.99 |
| 111_T | 138_T | 1.313 | 0.99 |
| 120_V | 156_N | 1.307 | 0.99 |
| 67_L | 90_L | 1.295 | 0.99 |
| 139_M | 143_W | 1.281 | 0.99 |
| 15_F | 28_W | 1.227 | 0.98 |
| 19_S | 26_V | 1.204 | 0.98 |
| 30_K | 71_D | 1.190 | 0.98 |
| 25_E | 80_P | 1.174 | 0.98 |
| 108_A | 141_Y | 1.155 | 0.97 |
| 9_V | 94_E | 1.136 | 0.97 |
| 72_E | 92_V | 1.133 | 0.97 |
| 122_L | 154_A | 1.123 | 0.97 |
| 117_G | 120_V | 1.119 | 0.96 |
| 78_E | 85_T | 1.117 | 0.96 |
| 16_H | 59_S | 1.109 | 0.96 |
| 76_E | 85_T | 1.099 | 0.96 |
| 107_N | 140_S | 1.094 | 0.96 |
| 26_V | 60_G | 1.072 | 0.95 |
| 6_Y | 91_Y | 1.063 | 0.95 |
| 110_L | 124_L | 1.051 | 0.94 |
| 27_L | 34_K | 1.049 | 0.94 |
| 149_P | 164_M | 1.046 | 0.94 |
| 6_Y | 93_L | 1.041 | 0.94 |
| 64_I | 71_D | 1.003 | 0.93 |
| 15_F | 88_F | 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 | |
| 1cczA | 1 | 1 | 99.9 | 0.101 | Contact Map |
| 1hngA | 2 | 0.9825 | 99.9 | 0.149 | Contact Map |
| 2druA | 1 | 0.9825 | 99.8 | 0.199 | Contact Map |
| 1hnfA | 1 | 0.9766 | 99.8 | 0.222 | Contact Map |
| 2yd9A | 1 | 0.924 | 99.8 | 0.233 | Contact Map |
| 2if7A | 4 | 0.9825 | 99.8 | 0.244 | Contact Map |
| 3b43A | 1 | 0.9415 | 99.8 | 0.249 | Contact Map |
| 3lafA | 1 | 0.9298 | 99.8 | 0.251 | Contact Map |
| 1e07A | 1 | 0.9181 | 99.8 | 0.253 | Contact Map |
| 3p3yA | 1 | 0.9181 | 99.8 | 0.253 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)