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OPENSEQ.org

b1

ID: 1456067006 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 269 (221)
Sequences: 19895 (13505.7)
Seq/Len: 90.023
Nf(neff/√len): 908.5

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: 90.023).

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
100_C114_G2.9641.00
58_L71_T2.7711.00
52_S70_S2.7361.00
142_S155_A2.7301.00
120_V154_I2.5561.00
236_R249_S2.4261.00
60_A102_T2.4021.00
78_Y87_C2.3411.00
102_T144_A2.2591.00
94_H113_S2.2491.00
185_L198_A2.2481.00
77_I113_S2.2121.00
230_Q248_S2.2081.00
112_A152_L2.1601.00
153_L162_F2.1491.00
69_A79_I2.1341.00
144_A187_R2.1241.00
161_H170_P2.1161.00
30_Q68_L2.0901.00
78_Y90_S2.0711.00
69_A111_I2.0561.00
69_A103_F2.0211.00
154_I163_W1.9991.00
112_A145_F1.9831.00
160_I197_T1.9811.00
30_Q61_F1.9571.00
179_E197_T1.9521.00
153_L188_F1.9481.00
213_I248_S1.9471.00
99_W116_L1.8701.00
136_S154_I1.8501.00
57_F73_V1.8501.00
214_P223_Y1.8401.00
189_D239_L1.8071.00
214_P226_R1.8051.00
114_G140_I1.7891.00
187_R238_P1.7261.00
153_L186_V1.7231.00
121_R130_E1.7201.00
161_H173_V1.6741.00
153_L195_L1.6721.00
62_S103_F1.6611.00
112_A122_I1.6611.00
38_R70_S1.6601.00
104_H145_F1.6411.00
197_T216_D1.6331.00
113_S123_W1.6261.00
69_A101_V1.6231.00
112_A143_L1.6101.00
81_E84_T1.5911.00
146_H188_F1.5821.00
124_D127_G1.5771.00
217_G220_L1.5671.00
196_L239_L1.5351.00
30_Q59_L1.5231.00
184_R209_D1.5051.00
164_D167_R1.4661.00
155_A186_V1.4301.00
196_L215_I1.4281.00
71_T101_V1.4171.00
155_A183_V1.3800.99
70_S80_T1.3770.99
240_L244_L1.3290.99
235_R251_S1.3200.99
31_E40_M1.3170.99
52_S72_H1.3040.99
187_R237_T1.3020.99
41_K44_G1.2960.99
71_T98_P1.2660.99
185_L236_R1.2590.99
170_P173_V1.2590.99
114_G143_L1.2430.98
142_S185_L1.2390.98
136_S156_T1.2360.98
106_T109_G1.2290.98
196_L246_M1.2120.98
58_L100_C1.2070.98
136_S140_I1.1940.98
93_G123_W1.1880.98
62_S66_T1.1850.98
196_L237_T1.1640.97
144_A186_V1.1640.97
230_Q234_V1.1320.97
223_Y226_R1.1320.97
33_V37_T1.1290.97
121_R132_W1.1260.97
81_E88_V1.1180.96
198_A234_V1.1140.96
102_T143_L1.1100.96
76_N90_S1.1050.96
66_T83_K1.1050.96
39_W48_E1.0990.96
208_D212_E1.0820.96
67_L88_V1.0820.96
109_G126_H1.0650.95
94_H115_C1.0570.95
52_S56_T1.0520.95
156_T159_E1.0520.95
61_F82_V1.0500.94
189_D194_Y1.0500.94
72_H76_N1.0480.94
187_R239_L1.0360.94
189_D193_H1.0340.94
190_P243_F1.0250.93
152_L165_W1.0240.93
240_L245_H1.0160.93
100_C143_L1.0130.93
198_A237_T1.0070.93
32_L56_T1.0030.93
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  
1vyhC100.91451000.284Contact Map
4j87A10.92571000.301Contact Map
4wjuA20.91451000.313Contact Map
4j73A10.94051000.314Contact Map
1gotB10.91451000.314Contact Map
3w15A10.91821000.319Contact Map
4bpeR10.94421000.319Contact Map
3frxA40.94421000.327Contact Map
3dm0A10.95171000.327Contact Map
3fm0A10.94421000.328Contact 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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