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OPENSEQ.org
Precursor HVI-2
ID: 1509209456 Query Sequence

 Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 135 (112)
Sequences: 151 (122.6)
Seq/Len: 1.348
Nf(neff/√len): 11.6
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: 1.348).

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
6_Y9_P2.3260.99
9_P21_T1.9160.97
78_W130_P1.8990.96
53_G56_L1.8290.95
112_E116_R1.5670.87
28_W33_I1.4990.84
12_A25_T1.4790.83
11_L15_G1.4600.82
6_Y21_T1.4400.80
30_L37_P1.3690.76
27_E31_E1.3650.75
19_E45_W1.3480.74
9_P17_F1.3410.73
46_T78_W1.3370.73
12_A16_E1.3250.72
6_Y99_W1.3230.72
81_D134_T1.3150.71
99_W110_T1.2990.70
83_R102_L1.2960.70
96_L130_P1.2850.69
29_G34_F1.2760.68
44_P98_G1.2660.67
11_L16_E1.2280.64
14_V30_L1.2090.62
14_V33_I1.2050.62
109_L118_L1.1960.61
42_Q73_R1.1930.60
11_L21_T1.1920.60
3_K59_G1.1920.60
104_K108_W1.1410.55
12_A34_F1.1370.55
24_Y33_I1.1330.54
47_A53_G1.1300.54
25_T69_L1.1110.52
11_L109_L1.1090.52
12_A15_G1.1030.51
5_K115_E1.0940.51
83_R98_G1.0910.50
75_L78_W1.0910.50
58_A70_A1.0870.50
20_A69_L1.0850.50
54_H58_A1.0840.50
59_G104_K1.0770.49
25_T39_F1.0760.49
55_R135_R1.0710.48
71_D131_L1.0690.48
43_R64_E1.0600.47
107_P132_A1.0530.46
10_Q24_Y1.0510.46
53_G118_L1.0450.46
57_L104_K1.0440.46
70_A126_E1.0420.45
48_L110_T1.0340.45
107_P116_R1.0240.44
75_L79_L1.0210.43
12_A27_E1.0210.43
15_G21_T1.0180.43
6_Y17_F1.0180.43
30_L35_V1.0170.43
7_T108_W1.0150.43
74_D108_W1.0040.42
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  
2bivA30.47411.90.932Contact Map
4c5eA40.48891.80.933Contact Map
3nehA20.34811.40.938Contact Map
4c2wC20.18521.20.941Contact Map
3ut1A10.46671.10.942Contact Map
2lp1A1010.942Contact Map
4cnkA20.333310.943Contact Map
4c5iA20.466710.943Contact Map
3hkwA30.80.90.944Contact Map
5aftc10.08890.80.947Contact 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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