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OPENSEQ.org

R1

ID: 1504189409 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 396 (359)
Sequences: 412 (324.1)
Seq/Len: 1.148
Nf(neff/√len): 17.1

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: 1.148).

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
316_F320_L2.3440.99
170_T218_A2.2020.98
357_E361_N2.1960.98
106_I316_F2.1610.98
158_M161_W2.1590.98
214_G265_L2.1370.98
102_M118_M2.1230.98
108_A260_I2.0950.98
95_H321_R2.0890.98
276_D282_R2.0870.97
288_E291_N2.0780.97
240_R277_Q2.0560.97
25_E233_W2.0530.97
235_E261_Q2.0040.97
237_K261_Q1.9850.96
254_K261_Q1.9840.96
162_G166_E1.9310.96
162_G261_Q1.8880.95
100_R215_E1.8570.94
217_D235_E1.8530.94
64_Q194_M1.8320.94
120_A332_I1.8150.93
100_R261_Q1.7940.93
27_T80_A1.7800.92
109_T116_W1.7720.92
45_K195_E1.7540.92
99_W214_G1.7320.91
166_E235_E1.7160.90
162_G217_D1.6980.90
63_W193_N1.6970.90
166_E217_D1.6930.90
235_E254_K1.6360.87
166_E261_Q1.6310.87
57_S279_G1.6300.87
101_G104_T1.6280.87
162_G235_E1.6220.87
254_K275_R1.6210.87
120_A127_I1.6090.86
215_E261_Q1.5880.85
178_V182_E1.5580.84
332_I343_L1.5530.83
25_E199_S1.5300.82
355_I360_M1.5210.81
179_S182_E1.5060.81
162_G275_R1.5010.80
166_E215_E1.4810.79
32_D38_H1.4800.79
162_G215_E1.4660.78
100_R237_K1.4490.77
251_F254_K1.4280.75
162_G238_T1.4170.75
100_R254_K1.4140.74
304_W309_C1.4070.74
217_D261_Q1.4020.74
100_R166_E1.4000.73
161_W279_G1.3970.73
215_E273_G1.3840.72
261_Q275_R1.3770.72
256_L309_C1.3700.71
107_M110_P1.3700.71
180_R184_E1.3570.70
201_V265_L1.3560.70
79_A358_E1.3550.70
217_D275_R1.3490.69
215_E275_R1.3410.69
119_N331_R1.3410.69
100_R162_G1.3410.69
107_M260_I1.3260.68
258_Y313_A1.3190.67
100_R217_D1.3020.65
235_E275_R1.3000.65
166_E275_R1.2970.65
217_D237_K1.2910.64
48_Y128_F1.2910.64
101_G254_K1.2850.64
96_V317_L1.2760.63
46_W174_P1.2700.63
38_H42_R1.2650.62
215_E235_E1.2630.62
133_H138_R1.2600.62
165_F273_G1.2280.59
141_M144_S1.2280.59
235_E238_T1.2240.58
55_D273_G1.2210.58
269_R286_E1.2210.58
75_D216_V1.2160.58
235_E262_S1.2120.57
100_R275_R1.2100.57
128_F359_F1.2080.57
104_T131_E1.2040.56
261_Q273_G1.1990.56
239_S242_I1.1980.56
100_R235_E1.1940.56
99_W265_L1.1910.55
94_A211_C1.1880.55
104_T257_K1.1840.55
101_G214_G1.1810.54
166_E237_K1.1740.54
120_A343_L1.1730.54
215_E254_K1.1720.53
172_P271_I1.1700.53
46_W101_G1.1620.52
32_D36_R1.1610.52
98_T102_M1.1610.52
162_G165_F1.1580.52
320_L343_L1.1580.52
351_H354_I1.1570.52
64_Q192_N1.1540.52
192_N195_E1.1540.52
262_S304_W1.1510.51
217_D254_K1.1430.51
237_K254_K1.1420.51
252_D258_Y1.1410.50
53_P320_L1.1390.50
23_P30_S1.1380.50
175_W180_R1.1340.50
165_F261_Q1.1320.50
162_G237_K1.1310.50
110_P308_V1.1300.49
163_Y166_E1.1260.49
53_P323_N1.1260.49
279_G304_W1.1200.48
180_R183_I1.1170.48
220_W269_R1.1130.48
56_L261_Q1.1110.48
162_G254_K1.1100.47
118_M284_M1.1080.47
167_T197_Y1.1010.47
35_R72_E1.1000.47
359_F363_R1.0990.46
289_T293_P1.0990.46
81_I92_I1.0950.46
50_A101_G1.0900.46
76_G97_T1.0880.45
127_I359_F1.0780.44
56_L100_R1.0770.44
61_Q294_Y1.0740.44
66_H356_T1.0740.44
99_W198_C1.0740.44
98_T281_L1.0730.44
162_G273_G1.0730.44
218_A341_I1.0700.44
361_N365_K1.0700.44
98_T235_E1.0640.43
100_R273_G1.0630.43
98_T163_Y1.0530.42
253_Q277_Q1.0510.42
98_T105_K1.0510.42
234_V238_T1.0510.42
23_P266_G1.0500.42
263_F266_G1.0490.42
283_S306_G1.0490.42
72_E279_G1.0480.42
31_Y130_E1.0480.42
196_Q214_G1.0450.41
107_M313_A1.0440.41
142_M210_V1.0360.40
106_I320_L1.0320.40
164_K292_I1.0300.40
81_I97_T1.0290.40
105_K239_S1.0280.40
101_G131_E1.0270.40
166_E262_S1.0230.39
212_L258_Y1.0200.39
215_E238_T1.0200.39
80_A114_E1.0190.39
112_D115_E1.0180.39
173_R177_E1.0170.39
40_G300_G1.0150.39
300_G305_D1.0140.38
33_R112_D1.0140.38
56_L166_E1.0130.38
243_T247_I1.0130.38
268_P309_C1.0120.38
56_L215_E1.0080.38
361_N364_I1.0060.38
40_G107_M1.0050.38
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  
5btoA201000.251Contact Map
5budA201000.274Contact Map
5btbA101000.292Contact Map
4j7nA10.86871000.294Contact Map
3fqiA10.86361000.303Contact Map
3fqgA10.76521000.306Contact Map
4gpsA10.72981000.373Contact Map
1piiA10.171710.80.977Contact Map
3uipD10.13896.30.979Contact Map
1ob8A20.31575.20.98Contact 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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