May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
av1 25-210 15-170 1-110
ID: 1513195145 Query Sequence

 Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 110 (110)
Sequences: 180 (50.2)
Seq/Len: 1.636
Nf(neff/√len): 4.8
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: 1.636).

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
91_V99_E2.0510.99
92_D99_E1.8720.97
98_G103_M1.5580.90
13_C16_P1.4750.87
11_R14_E1.4630.86
97_F103_M1.4550.86
48_H52_K1.4250.84
75_N78_N1.3870.82
61_V83_F1.3730.81
64_K77_T1.3450.79
13_C20_Q1.3230.77
71_I80_V1.3220.77
94_P105_D1.3160.77
24_S31_I1.3130.77
91_V95_Q1.2900.75
48_H53_R1.2740.73
49_R57_K1.2610.72
101_F106_N1.2570.72
46_L95_Q1.2500.71
103_M106_N1.2450.71
96_D100_V1.2290.70
105_D110_T1.2050.67
102_N107_E1.2040.67
17_C20_Q1.2030.67
10_P13_C1.1930.66
50_V54_F1.1900.66
101_F107_E1.1890.66
26_H35_M1.1830.65
100_V104_F1.1820.65
69_E72_K1.1750.65
83_F93_K1.1630.63
2_R5_R1.1490.62
16_P20_Q1.1460.62
71_I75_N1.1460.62
94_P107_E1.1340.60
47_T52_K1.1250.60
1_Y7_P1.1230.59
10_P16_P1.1160.59
94_P97_F1.1080.58
98_G101_F1.1030.57
98_G104_F1.0980.57
14_E21_S1.0840.55
96_D99_E1.0830.55
1_Y8_D1.0820.55
10_P15_G1.0810.55
56_V79_S1.0740.54
60_Y63_G1.0730.54
3_M46_L1.0600.53
55_C58_S1.0530.52
26_H33_K1.0510.52
70_N76_H1.0480.52
88_R94_P1.0430.51
8_D14_E1.0380.50
98_G106_N1.0240.49
47_T53_R1.0220.49
14_E17_C1.0120.48
96_D109_S1.0070.47
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  
1ansA10.16364.20.967Contact Map
4ob0A10.39093.40.969Contact Map
4wsbB10.69093.20.969Contact Map
1vtze300.845530.97Contact Map
2plxB10.236420.972Contact Map
2c5uA20.79091.80.973Contact Map
1u3dA10.29091.80.973Contact Map
2k8dA10.62731.80.973Contact Map
2l1uA10.61821.60.974Contact Map
2knpA10.29091.40.975Contact 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.
Page generated in 0.9645 seconds.