| d4lfnc_ |
| ID: | 1448772838 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 142 (140) | ||
| Sequences: | 2770 (1731) | ||
| Seq/Len: | 19.786 | ||
| Nf(neff/√len): | 146.3 |
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: 19.786).
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 | 137_M | 3.641 | 1.00 |
| 132_Q | 136_D | 3.246 | 1.00 |
| 21_Y | 119_Q | 2.827 | 1.00 |
| 16_E | 19_K | 2.515 | 1.00 |
| 4_I | 56_A | 2.134 | 1.00 |
| 81_T | 103_A | 2.129 | 1.00 |
| 32_V | 50_K | 2.118 | 1.00 |
| 4_I | 32_V | 2.034 | 1.00 |
| 95_E | 127_A | 1.974 | 1.00 |
| 6_G | 47_V | 1.973 | 1.00 |
| 14_M | 114_A | 1.934 | 1.00 |
| 64_R | 107_G | 1.924 | 1.00 |
| 17_Q | 111_Y | 1.919 | 1.00 |
| 87_E | 116_V | 1.899 | 1.00 |
| 91_H | 95_E | 1.857 | 1.00 |
| 110_G | 113_R | 1.806 | 1.00 |
| 82_A | 93_T | 1.764 | 1.00 |
| 85_E | 89_T | 1.736 | 1.00 |
| 11_G | 62_F | 1.696 | 1.00 |
| 61_M | 73_S | 1.657 | 1.00 |
| 2_D | 28_R | 1.641 | 1.00 |
| 45_L | 141_M | 1.616 | 1.00 |
| 50_K | 55_D | 1.603 | 1.00 |
| 61_M | 69_S | 1.582 | 1.00 |
| 19_K | 23_E | 1.569 | 1.00 |
| 52_L | 76_V | 1.545 | 1.00 |
| 15_K | 31_D | 1.515 | 1.00 |
| 12_F | 16_E | 1.466 | 1.00 |
| 61_M | 103_A | 1.451 | 1.00 |
| 48_T | 79_M | 1.438 | 1.00 |
| 30_A | 56_A | 1.433 | 1.00 |
| 88_N | 92_M | 1.429 | 1.00 |
| 13_A | 106_T | 1.429 | 1.00 |
| 86_E | 89_T | 1.425 | 1.00 |
| 99_A | 121_Y | 1.415 | 1.00 |
| 17_Q | 115_L | 1.404 | 0.99 |
| 10_D | 107_G | 1.397 | 0.99 |
| 4_I | 50_K | 1.392 | 0.99 |
| 45_L | 49_K | 1.391 | 0.99 |
| 44_S | 69_S | 1.390 | 0.99 |
| 119_Q | 123_D | 1.386 | 0.99 |
| 39_D | 133_I | 1.338 | 0.99 |
| 45_L | 76_V | 1.285 | 0.99 |
| 52_L | 79_M | 1.277 | 0.99 |
| 21_Y | 115_L | 1.267 | 0.99 |
| 58_K | 121_Y | 1.239 | 0.98 |
| 37_A | 133_I | 1.227 | 0.98 |
| 91_H | 116_V | 1.212 | 0.98 |
| 88_N | 108_I | 1.202 | 0.98 |
| 47_V | 59_A | 1.194 | 0.98 |
| 120_R | 124_T | 1.193 | 0.98 |
| 49_K | 53_N | 1.181 | 0.98 |
| 136_D | 140_K | 1.181 | 0.98 |
| 95_E | 124_T | 1.177 | 0.98 |
| 93_T | 121_Y | 1.175 | 0.98 |
| 63_D | 69_S | 1.172 | 0.98 |
| 81_T | 101_A | 1.162 | 0.97 |
| 24_E | 119_Q | 1.161 | 0.97 |
| 44_S | 61_M | 1.149 | 0.97 |
| 6_G | 32_V | 1.133 | 0.97 |
| 23_E | 29_V | 1.128 | 0.97 |
| 112_D | 115_L | 1.127 | 0.97 |
| 60_I | 118_I | 1.112 | 0.96 |
| 67_V | 82_A | 1.111 | 0.96 |
| 93_T | 99_A | 1.110 | 0.96 |
| 48_T | 52_L | 1.106 | 0.96 |
| 5_I | 19_K | 1.105 | 0.96 |
| 84_V | 102_I | 1.105 | 0.96 |
| 20_K | 23_E | 1.098 | 0.96 |
| 92_M | 95_E | 1.093 | 0.96 |
| 70_A | 83_V | 1.079 | 0.95 |
| 4_I | 54_S | 1.076 | 0.95 |
| 75_K | 139_E | 1.076 | 0.95 |
| 1_M | 27_Y | 1.048 | 0.94 |
| 70_A | 103_A | 1.047 | 0.94 |
| 87_E | 120_R | 1.040 | 0.94 |
| 14_M | 111_Y | 1.030 | 0.94 |
| 4_I | 57_H | 1.023 | 0.93 |
| 2_D | 30_A | 1.006 | 0.93 |
| 90_A | 117_I | 1.005 | 0.93 |
| 76_V | 141_M | 1.002 | 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 | |
| 3s5pA | 2 | 0.9296 | 100 | -0.019 | Contact Map |
| 2vvrA | 6 | 1 | 100 | -0.013 | Contact Map |
| 4lflB | 2 | 1 | 100 | -0.013 | Contact Map |
| 3he8A | 2 | 1 | 100 | -0.011 | Contact Map |
| 4lflA | 2 | 0.993 | 100 | -0.01 | Contact Map |
| 3ph3A | 2 | 1 | 100 | -0.009 | Contact Map |
| 1o1xA | 1 | 0.9859 | 100 | -0.006 | Contact Map |
| 3sgwA | 1 | 1 | 100 | -0.005 | Contact Map |
| 2vvpA | 5 | 1 | 100 | -0.005 | Contact Map |
| 3k7pA | 2 | 1 | 100 | -0.001 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)