| SP13737C |
| ID: | 1381183389 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 189 (182) | ||
| Sequences: | 1210 (977.4) | ||
| Seq/Len: | 6.648 | ||
| Nf(neff/√len): | 72.4 |
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: 6.648).
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 |
| 42_E | 170_D | 4.254 | 1.00 |
| 25_A | 161_S | 3.567 | 1.00 |
| 65_Y | 183_A | 2.659 | 1.00 |
| 21_G | 165_G | 2.532 | 1.00 |
| 70_D | 183_A | 2.480 | 1.00 |
| 23_K | 163_Q | 2.475 | 1.00 |
| 58_D | 174_V | 2.395 | 1.00 |
| 26_F | 37_G | 2.284 | 1.00 |
| 168_Y | 172_F | 2.118 | 1.00 |
| 61_T | 74_V | 2.109 | 1.00 |
| 63_W | 175_F | 2.018 | 1.00 |
| 40_Y | 168_Y | 1.991 | 1.00 |
| 117_T | 129_S | 1.962 | 1.00 |
| 63_W | 72_V | 1.923 | 1.00 |
| 40_Y | 172_F | 1.873 | 1.00 |
| 24_L | 39_L | 1.806 | 1.00 |
| 49_E | 54_K | 1.795 | 1.00 |
| 42_E | 45_K | 1.784 | 1.00 |
| 169_P | 172_F | 1.745 | 1.00 |
| 115_Y | 133_F | 1.580 | 1.00 |
| 131_Y | 145_D | 1.503 | 0.99 |
| 135_T | 142_H | 1.496 | 0.99 |
| 29_N | 158_L | 1.482 | 0.99 |
| 58_D | 61_T | 1.467 | 0.99 |
| 144_V | 159_I | 1.462 | 0.99 |
| 145_D | 154_M | 1.457 | 0.99 |
| 143_Q | 156_T | 1.444 | 0.99 |
| 25_A | 38_V | 1.442 | 0.99 |
| 165_G | 168_Y | 1.432 | 0.99 |
| 129_S | 147_A | 1.431 | 0.99 |
| 47_V | 54_K | 1.420 | 0.99 |
| 55_T | 64_S | 1.413 | 0.99 |
| 134_V | 141_L | 1.374 | 0.98 |
| 23_K | 40_Y | 1.365 | 0.98 |
| 134_V | 140_R | 1.343 | 0.98 |
| 66_V | 69_A | 1.330 | 0.98 |
| 21_G | 167_S | 1.323 | 0.98 |
| 23_K | 38_V | 1.304 | 0.97 |
| 10_E | 14_E | 1.293 | 0.97 |
| 113_V | 142_H | 1.284 | 0.97 |
| 117_T | 131_Y | 1.282 | 0.97 |
| 148_P | 153_Y | 1.282 | 0.97 |
| 25_A | 160_D | 1.266 | 0.97 |
| 57_F | 77_P | 1.261 | 0.97 |
| 135_T | 138_T | 1.260 | 0.97 |
| 100_L | 118_M | 1.256 | 0.97 |
| 26_F | 48_V | 1.252 | 0.97 |
| 53_M | 75_S | 1.244 | 0.96 |
| 28_V | 37_G | 1.241 | 0.96 |
| 143_Q | 158_L | 1.227 | 0.96 |
| 130_V | 146_L | 1.219 | 0.96 |
| 72_V | 177_K | 1.211 | 0.96 |
| 27_T | 158_L | 1.192 | 0.95 |
| 22_V | 162_Y | 1.186 | 0.95 |
| 22_V | 41_L | 1.185 | 0.95 |
| 93_L | 97_G | 1.174 | 0.95 |
| 21_G | 166_Q | 1.166 | 0.94 |
| 38_V | 49_E | 1.155 | 0.94 |
| 163_Q | 166_Q | 1.155 | 0.94 |
| 63_W | 74_V | 1.145 | 0.94 |
| 101_K | 117_T | 1.127 | 0.93 |
| 119_T | 161_S | 1.107 | 0.92 |
| 14_E | 18_K | 1.102 | 0.92 |
| 7_N | 11_R | 1.100 | 0.92 |
| 39_L | 132_L | 1.099 | 0.92 |
| 11_R | 14_E | 1.091 | 0.91 |
| 171_S | 174_V | 1.091 | 0.91 |
| 176_D | 181_P | 1.089 | 0.91 |
| 63_W | 177_K | 1.087 | 0.91 |
| 94_Y | 100_L | 1.085 | 0.91 |
| 15_A | 19_A | 1.083 | 0.91 |
| 14_E | 17_R | 1.075 | 0.90 |
| 26_F | 50_T | 1.065 | 0.90 |
| 112_S | 174_V | 1.065 | 0.90 |
| 86_N | 153_Y | 1.063 | 0.90 |
| 65_Y | 181_P | 1.051 | 0.89 |
| 74_V | 187_D | 1.045 | 0.89 |
| 103_S | 117_T | 1.031 | 0.88 |
| 49_E | 52_G | 1.027 | 0.88 |
| 65_Y | 175_F | 1.022 | 0.87 |
| 65_Y | 72_V | 1.022 | 0.87 |
| 72_V | 183_A | 1.022 | 0.87 |
| 25_A | 36_A | 1.019 | 0.87 |
| 147_A | 154_M | 1.019 | 0.87 |
| 145_D | 156_T | 1.011 | 0.86 |
| 177_K | 182_T | 1.005 | 0.86 |
| 32_Q | 70_D | 1.000 | 0.86 |
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 | |
| 4mxtA | 1 | 0.9894 | 100 | 0.204 | Contact Map |
| 2w7qA | 2 | 0.9312 | 100 | 0.308 | Contact Map |
| 1iwlA | 1 | 0.8836 | 100 | 0.318 | Contact Map |
| 2yzyA | 1 | 0.8042 | 99.9 | 0.377 | Contact Map |
| 3buuA | 2 | 0.9471 | 99.9 | 0.467 | Contact Map |
| 3m4wA | 4 | 0.9577 | 99.9 | 0.489 | Contact Map |
| 3bk5A | 1 | 0.9471 | 99.8 | 0.503 | Contact Map |
| 3mh9C | 2 | 0.9259 | 99.2 | 0.678 | Contact Map |
| 2byoA | 1 | 0.8466 | 98.5 | 0.757 | Contact Map |
| 3u1wA | 3 | 0.7725 | 18.9 | 0.93 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)