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OPENSEQ.org
dhd -force run
ID: 1513454133 Query Sequence

 Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 105 (105)
Sequences: 95 (71)
Seq/Len: 0.905
Nf(neff/√len): 6.9
HHblits Results: (2016_02)
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: 0.905).

Sequences per length for each position, AFTER the coverage/gap filter was applied
Legend: If visible, the positions blocked in grey are regions that have > 75% gaps and were automatically trimmed and excluded in the GREMLIN analysis.
Trim query Generate MSA using: Filter MSA GREMLIN
Start: End: E-value: Iterations: Coverage: Remove gaps: Prior:
GREMLIN Results:
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.

ij Scaled score Prob
55_D74_N2.3570.98
61_E100_F2.1000.96
35_P74_N1.8690.92
42_I54_F1.7980.89
56_I63_Y1.7560.88
11_G16_E1.7410.87
10_Y16_E1.5300.76
9_V12_P1.4780.72
54_F72_F1.4190.68
75_G94_V1.3950.66
18_K25_L1.3900.66
4_R17_G1.3850.65
19_T23_K1.3830.65
67_G98_A1.3550.63
55_D58_R1.3060.59
31_A51_I1.3010.58
70_E73_K1.2900.57
22_A33_Y1.2780.56
66_Y73_K1.2740.56
4_R14_G1.2740.56
64_L74_N1.2670.55
43_C71_E1.2490.53
23_K28_T1.2100.50
75_G92_V1.2080.50
7_I15_G1.1970.49
22_A55_D1.1830.48
46_Y97_M1.1720.47
46_Y100_F1.1520.45
67_G94_V1.1470.44
66_Y70_E1.1440.44
15_G91_Y1.1260.42
15_G22_A1.1210.42
4_R18_K1.1200.42
57_P86_L1.1180.42
43_C77_I1.1140.41
12_P57_P1.1100.41
2_C5_R1.1060.41
1_P101_L1.0940.40
65_N95_I1.0890.39
79_S84_P1.0870.39
11_G84_P1.0860.39
19_T74_N1.0850.39
68_L77_I1.0620.37
71_E76_I1.0600.37
20_T23_K1.0600.37
72_F83_E1.0550.36
76_I86_L1.0530.36
84_P92_V1.0440.35
8_W11_G1.0410.35
64_L103_K1.0380.35
19_T55_D1.0360.35
75_G89_V1.0330.34
65_N85_V1.0330.34
14_G58_R1.0280.34
8_W32_F1.0250.34
73_K79_S1.0180.33
68_L94_V1.0160.33
73_K99_N1.0090.33
4_R8_W1.0090.33
Legend: Only predictions with Scaled Score > 1 are listed. For all 3L/2 predictions, click on one of the links below.
Prob = P(contact | scaled_score, seq/len).
Scaled Score = (raw_score/average(raw_scores)).
NEW Features 		HHsearch Results: (06Aug15)
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  
1tueA60.952487.30.89Contact Map
1in4A10.838184.60.894Contact Map
1u0jA10.866781.10.898Contact Map
4d2uA60.971477.90.901Contact Map
2qgzA10.790576.50.903Contact Map
3co5A20.866775.40.903Contact Map
1hqcA20.98172.90.905Contact Map
3n70A80.866772.70.905Contact Map
4ciuA10.942971.60.906Contact Map
3pfiA20.8952690.908Contact Map
M = number of chains, if homo-oligomer
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)
Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.
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