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OPENSEQ.org
3178
ID: 1407781649 Query Sequence

 Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 93 (89)
Sequences: 90 (72)
Seq/Len: 1.011
Nf(neff/√len): 7.6
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: 1.011).

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
51_H68_V1.7050.88
55_S61_E1.6990.88
28_I76_A1.6020.83
48_A70_V1.5160.78
77_V85_R1.4640.75
33_N85_R1.4570.74
54_A88_R1.4180.71
36_V53_Y1.3810.68
68_V90_R1.3810.68
85_R89_R1.3440.65
38_G50_Q1.3100.62
42_L83_A1.3070.62
8_L28_I1.3020.62
19_L64_S1.2970.61
52_T69_G1.2880.60
9_T85_R1.2590.58
17_T88_R1.2150.54
31_K87_V1.2130.54
17_T31_K1.2050.53
39_I44_L1.2030.53
67_I71_I1.2000.52
40_L67_I1.1990.52
15_G39_I1.1870.51
11_A55_S1.1870.51
41_G80_L1.1830.51
10_I13_A1.1750.50
44_L75_L1.1610.49
6_F19_L1.1600.49
13_A86_S1.1570.48
52_T56_A1.1570.48
5_Y75_L1.1570.48
55_S85_R1.1540.48
21_T55_S1.1320.46
54_A75_L1.1290.46
34_E65_A1.1280.46
78_V91_V1.1140.44
50_Q65_A1.1050.44
39_I78_V1.0940.43
48_A51_H1.0880.42
10_I66_W1.0590.39
18_M31_K1.0570.39
47_F63_T1.0570.39
75_L79_P1.0550.39
51_H66_W1.0540.39
62_Y83_A1.0510.39
12_L46_L1.0470.38
68_V72_V1.0400.38
11_A52_T1.0370.37
27_N78_V1.0350.37
54_A79_P1.0340.37
36_V54_A1.0320.37
69_G74_L1.0310.37
7_F56_A1.0190.36
4_I45_A1.0170.36
63_T81_L1.0170.36
12_L76_A1.0130.35
29_T77_V1.0120.35
12_L28_I1.0120.35
15_G30_L1.0080.35
45_A78_V1.0050.35
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: (17Jul14)
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  
2m20A20.34419.50.921Contact Map
3giaA10.9149.10.922Contact Map
2ks1B10.43018.40.923Contact Map
2rddB10.27967.50.925Contact Map
2l2tA20.41947.20.925Contact Map
1fftB20.47314.30.933Contact Map
4djkA20.92474.30.933Contact Map
4o6yA20.90323.60.936Contact Map
2jwaA20.43013.50.936Contact Map
3mk7A40.93553.20.937Contact 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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