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OPENSEQ.org

1uch

ID: 1452700720 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 230 (230)
Sequences: 1163 (788.7)
Seq/Len: 5.057
Nf(neff/√len): 52.0

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: 5.057).

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
179_H192_N6.1551.00
20_L25_L2.8591.00
10_E13_P2.5541.00
39_P203_E2.5381.00
126_S137_Y2.4921.00
83_S177_D2.4471.00
120_K124_E2.4191.00
105_A123_L2.2301.00
4_Q145_R2.1841.00
85_Y126_S2.1141.00
51_A103_A2.0821.00
131_P134_R2.0551.00
37_M224_A2.0521.00
17_N21_K2.0491.00
103_A172_A2.0391.00
30_Q230_A1.9641.00
20_L104_I1.9201.00
41_L44_M1.8481.00
20_L100_L1.8291.00
20_L31_F1.8281.00
122_F144_I1.7971.00
34_V226_A1.7641.00
136_R139_E1.7441.00
136_R140_N1.7351.00
22_Q150_T1.7061.00
130_S133_E1.6981.00
16_T53_L1.6680.99
64_V68_E1.6500.99
32_V228_S1.6330.99
56_F184_D1.6270.99
84_V176_V1.6110.99
180_L191_I1.5920.99
55_L170_F1.5810.99
181_Y193_H1.5700.99
14_E17_N1.5000.99
43_S47_R1.4640.98
34_V224_A1.4420.98
66_R70_E1.4280.98
52_V202_L1.4280.98
121_K125_E1.4240.98
193_H208_V1.4140.98
50_C229_A1.4100.98
175_H201_L1.3820.97
101_I138_L1.3800.97
122_F126_S1.3580.97
16_T99_G1.3510.97
11_A223_N1.3300.96
204_D208_V1.2930.95
53_L99_G1.2830.95
212_F215_R1.2830.95
76_Q81_T1.2510.94
118_T143_A1.2500.94
95_C106_N1.2240.93
182_E193_H1.2220.93
26_H114_E1.2200.93
126_S129_M1.2180.93
58_I168_L1.2020.92
6_W10_E1.2020.92
179_H195_E1.1970.92
49_V226_A1.1960.92
58_I63_E1.1940.92
122_F131_P1.1900.92
12_N15_V1.1820.92
97_T148_H1.1600.91
196_T204_D1.1560.90
209_C224_A1.1410.90
5_R92_S1.1410.90
213_M216_D1.1360.89
9_L157_T1.1300.89
40_E43_S1.1220.89
9_L100_L1.1160.88
36_G41_L1.1130.88
58_I62_Y1.1080.88
13_P201_L1.1060.88
94_A98_I1.1020.87
147_T151_S1.1000.87
49_V201_L1.0980.87
95_C99_G1.0980.87
79_D82_S1.0950.87
8_P12_N1.0870.86
45_V103_A1.0850.86
8_P13_P1.0840.86
16_T98_I1.0810.86
86_F189_F1.0790.86
93_N184_D1.0790.86
185_G190_P1.0710.85
114_E120_K1.0650.85
145_R151_S1.0620.85
96_G102_H1.0620.85
47_R200_T1.0520.84
36_G48_P1.0490.84
119_L122_F1.0370.83
15_V20_L1.0370.83
135_A145_R1.0350.82
69_E193_H1.0270.82
29_W107_N1.0260.82
205_A208_V1.0250.82
56_F62_Y1.0220.81
117_S120_K1.0200.81
103_A117_S1.0200.81
15_V94_A1.0200.81
65_F215_R1.0140.81
18_Q22_Q1.0100.80
159_A162_I1.0080.80
101_I119_L1.0070.80
142_D146_V1.0050.80
36_G206_I1.0050.80
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  
1xd3A20.9957100-0.021Contact Map
4jkjA20.96521000.001Contact Map
2wdtA20.88261000.038Contact Map
4wlrA10.89571000.039Contact Map
3riiA20.91741000.046Contact Map
4ig7A10.82611000.047Contact Map
4i6nA20.91741000.049Contact Map
1cmxA20.87831000.053Contact Map
3o65A40.565255.10.948Contact Map
3j7yj10.256521.90.958Contact 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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