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4pgr

ID: 1500381611 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 207 (207)
Sequences: 4199 (2408.5)
Seq/Len: 20.285
Nf(neff/√len): 167.4

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: 20.285).

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
155_G197_N3.1261.00
12_L167_L3.0971.00
107_G167_L2.4251.00
121_W165_Y2.4061.00
42_I46_A2.3711.00
83_Y203_G2.2341.00
156_T194_L2.1821.00
153_V157_I2.1721.00
80_V92_V2.1631.00
98_S202_F2.1341.00
18_T65_V2.0261.00
166_D190_D2.0151.00
131_L155_G1.9811.00
12_L107_G1.9481.00
43_L71_V1.9471.00
124_L161_L1.9421.00
106_L160_S1.9301.00
153_V201_F1.9201.00
44_E72_S1.9061.00
124_L165_Y1.8251.00
46_A50_L1.8171.00
125_L129_L1.8021.00
146_A150_A1.7841.00
105_V129_L1.7751.00
95_A198_L1.7601.00
163_I194_L1.7561.00
135_G151_Y1.7331.00
150_A154_I1.7001.00
129_L133_V1.6291.00
128_V162_Y1.6051.00
22_A188_Y1.5651.00
16_V104_A1.5641.00
107_G111_A1.5411.00
95_A201_F1.5111.00
166_D169_Q1.4781.00
108_T112_K1.4761.00
196_I200_R1.4751.00
102_I198_L1.4711.00
128_V132_A1.4601.00
63_A67_T1.4541.00
189_L193_N1.4491.00
131_L158_V1.4391.00
168_N172_H1.4241.00
60_V64_F1.4221.00
49_I53_W1.4151.00
98_S198_L1.4101.00
44_E75_T1.4101.00
23_T97_G1.4010.99
170_I187_L1.3990.99
198_L202_F1.3960.99
117_L164_L1.3770.99
91_V202_F1.3750.99
48_I52_F1.3730.99
154_I158_V1.3720.99
157_I161_L1.3680.99
101_V133_V1.3620.99
103_F191_F1.3330.99
67_T71_V1.3080.99
149_M201_F1.2770.99
132_A136_I1.2430.98
79_I196_I1.2330.98
187_L190_D1.2290.98
113_M117_L1.2130.98
25_G70_F1.2050.98
47_M71_V1.2030.98
27_F31_F1.2000.98
148_M200_R1.1910.98
97_G101_V1.1870.98
106_L164_L1.1830.98
137_F141_S1.1770.98
169_Q186_S1.1750.98
68_F72_S1.1730.98
197_N200_R1.1640.97
120_L124_L1.1640.97
149_M153_V1.1620.97
109_I115_K1.1580.97
79_I83_Y1.1520.97
95_A98_S1.1490.97
109_I113_M1.1450.97
38_L42_I1.1400.97
173_R183_M1.1200.96
4_K7_I1.1190.96
62_Y66_Y1.1140.96
134_V151_Y1.1090.96
102_I105_V1.1010.96
84_A91_V1.0910.96
159_F189_L1.0890.96
166_D189_L1.0830.96
10_R180_I1.0800.95
51_A64_F1.0750.95
94_E202_F1.0720.95
169_Q190_D1.0660.95
83_Y196_I1.0630.95
110_G168_N1.0600.95
159_F193_N1.0500.94
18_T69_A1.0460.94
47_M64_F1.0440.94
98_S156_T1.0420.94
50_L64_F1.0380.94
3_S174_H1.0270.94
145_S148_M1.0240.93
119_F122_S1.0220.93
103_F187_L1.0190.93
151_Y155_G1.0170.93
14_V62_Y1.0170.93
43_L46_A1.0060.93
7_I11_I1.0050.93
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  
4pgrA10.99521000.006Contact Map
4i0uA100.28025.80.935Contact Map
4ev6A50.28995.70.936Contact Map
1r8hA60.140130.944Contact Map
2xq2A10.77781.90.949Contact Map
4b4aA10.64731.90.949Contact Map
3w9iA60.72951.50.953Contact Map
4k0jA60.69081.40.953Contact Map
4n7wA20.431.20.955Contact Map
3b5dA20.01931.10.957Contact 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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