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OPENSEQ.org

1qz4

ID: 1453736963 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 213 (202)
Sequences: 391 (259.6)
Seq/Len: 1.936
Nf(neff/√len): 18.3

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: 1.936).

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
92_L174_G3.8781.00
55_F177_A3.5971.00
14_G177_A3.2881.00
14_G39_S2.6501.00
25_L163_V2.4281.00
19_A174_G2.4031.00
49_S53_A2.3351.00
105_A141_V2.0940.99
96_E182_H2.0800.99
15_I93_M2.0790.99
39_S55_F1.9970.99
112_R140_D1.9830.99
136_A140_D1.9440.99
112_R137_I1.8520.98
99_L109_L1.6940.96
156_A159_Q1.6520.95
40_L134_M1.6310.95
141_V144_P1.6270.94
7_D51_T1.6170.94
142_I175_I1.5210.91
25_L170_T1.4980.91
9_T201_Q1.4970.90
106_L109_L1.4910.90
8_I147_P1.4890.90
40_L169_A1.4800.90
112_R150_Q1.4790.90
66_L205_I1.4210.87
46_M113_I1.4190.87
91_S193_F1.3890.86
45_D53_A1.3580.84
155_P159_Q1.3580.84
88_Y149_I1.3150.81
19_A92_L1.3080.80
128_E162_Q1.3060.80
27_H84_E1.2830.79
148_R151_V1.2770.78
96_E179_V1.2410.75
53_A66_L1.2350.75
199_T202_A1.2310.75
8_I198_L1.2180.73
115_G118_R1.2130.73
38_V56_G1.2120.73
42_S177_A1.2070.73
113_I147_P1.2050.72
140_D150_Q1.2000.72
120_L130_L1.1970.72
143_S171_L1.1940.71
8_I90_L1.1820.70
157_V191_L1.1790.70
137_I140_D1.1690.69
50_S53_A1.1650.69
91_S149_I1.1530.67
45_D48_P1.1510.67
43_I46_M1.1430.67
25_L128_E1.1370.66
92_L135_A1.1300.65
25_L31_C1.1170.64
23_Q179_V1.1150.64
42_S145_L1.1060.63
16_C164_Q1.1050.63
10_L66_L1.1030.62
55_F82_N1.1020.62
99_L106_L1.1020.62
9_T202_A1.0960.62
141_V189_L1.0930.61
37_H41_N1.0930.61
132_S136_A1.0890.61
119_Q123_F1.0790.60
157_V192_M1.0780.60
163_V174_G1.0780.60
43_I114_N1.0720.59
13_A135_A1.0700.59
51_T184_V1.0690.59
163_V170_T1.0620.58
9_T67_E1.0600.58
72_V82_N1.0590.58
36_L145_L1.0570.58
98_K132_S1.0510.57
9_T198_L1.0490.57
43_I113_I1.0470.56
69_L91_S1.0460.56
100_S182_H1.0430.56
129_T154_S1.0430.56
18_S76_S1.0390.56
179_V182_H1.0310.55
40_L116_L1.0290.55
12_L90_L1.0240.54
72_V90_L1.0160.53
83_A91_S1.0150.53
12_L165_A1.0110.53
33_A145_L1.0050.52
72_V86_T1.0040.52
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  
1sdiA111000.014Contact Map
1o20A10.2316.50.965Contact Map
4asvA20.31929.50.968Contact Map
2w96A10.3385.90.971Contact Map
4cpgA20.29585.40.972Contact Map
4cgcA30.13624.80.972Contact Map
3ci9A20.22544.60.973Contact Map
3b34A10.61034.60.973Contact Map
4qhpA10.61034.30.973Contact Map
3af5A10.43194.30.973Contact 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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