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OPENSEQ.org

p5

ID: 1496119871 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 482 (459)
Sequences: 643 (375.4)
Seq/Len: 1.401
Nf(neff/√len): 17.5

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: 1.401).

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
167_S184_F3.2751.00
349_K364_T2.8611.00
393_D396_K2.8221.00
343_K346_I2.7171.00
235_V299_S2.5221.00
359_A396_K2.4991.00
123_G177_F2.3170.99
186_E232_Y2.2370.99
174_L179_A2.2120.99
170_I234_V2.1570.99
311_I341_A2.0780.98
1_M5_H2.0750.98
280_F328_N2.0700.98
171_T334_K2.0590.98
274_L281_S2.0510.98
312_T319_I2.0350.98
10_R13_F1.9790.97
167_S332_A1.9470.97
259_A320_R1.8800.96
444_V448_K1.8360.96
114_T117_D1.8190.95
212_A225_I1.8030.95
184_F234_V1.8030.95
213_P229_T1.7470.94
10_R15_K1.7270.93
393_D397_C1.7190.93
11_R15_K1.6940.92
167_S333_P1.6850.92
211_E228_D1.6830.92
303_E340_G1.6730.92
187_I195_I1.6310.90
181_S237_T1.6230.90
64_E388_N1.6190.90
216_S225_I1.6190.90
181_S312_T1.6160.90
169_M329_L1.6040.89
1_M7_I1.6030.89
184_F334_K1.6020.89
350_K448_K1.6020.89
9_S13_F1.5980.89
350_K447_D1.5710.88
305_G311_I1.5660.88
183_S301_L1.5580.88
469_P472_G1.5580.88
174_L270_L1.5510.87
171_T184_F1.5480.87
35_R39_E1.5410.87
1_M6_S1.5380.87
303_E344_F1.5370.87
232_Y330_P1.5340.86
1_M4_F1.5320.86
256_A320_R1.5290.86
390_W397_C1.5250.86
210_E225_I1.5240.86
184_F331_V1.5230.86
434_A437_T1.5150.86
205_P217_F1.4880.84
438_M441_S1.4730.83
279_Y344_F1.4690.83
160_Q166_A1.4570.82
426_H429_V1.4420.81
312_T317_P1.4190.80
210_E216_S1.4160.80
443_F446_M1.4080.79
360_L393_D1.4030.79
187_I326_I1.4030.79
366_L450_F1.3980.79
5_H8_V1.3860.78
307_L317_P1.3840.78
294_G297_V1.3790.77
358_G362_K1.3710.77
441_S445_N1.3710.77
4_F12_D1.3610.76
353_D362_K1.3600.76
167_S334_K1.3540.75
436_T440_N1.3510.75
181_S314_G1.3450.75
306_R344_F1.3210.73
386_G397_C1.3160.73
236_H270_L1.3110.72
179_A266_A1.3100.72
345_C355_C1.3020.71
29_A33_V1.3010.71
215_P280_F1.3000.71
23_G28_A1.2980.71
5_H9_S1.2870.70
4_F8_V1.2840.70
440_N443_F1.2770.69
352_A360_L1.2720.69
443_F447_D1.2690.69
162_T166_A1.2670.68
278_G327_V1.2630.68
1_M9_S1.2620.68
240_Q412_Q1.2530.67
349_K353_D1.2530.67
233_A324_M1.2450.66
161_G165_E1.2430.66
274_L330_P1.2320.65
240_Q245_S1.2190.64
240_Q260_Y1.2180.64
307_L310_L1.2150.64
230_G326_I1.2110.63
368_W386_G1.2030.63
397_C408_C1.2000.62
106_T114_T1.1990.62
468_F474_H1.1880.61
278_G352_A1.1830.61
4_F7_I1.1810.60
215_P282_V1.1780.60
293_V310_L1.1770.60
237_T321_Q1.1760.60
11_R14_M1.1760.60
12_D23_G1.1740.60
447_D451_G1.1720.60
5_H10_R1.1720.60
270_L274_L1.1660.59
303_E336_P1.1640.59
419_K447_D1.1530.58
12_D15_K1.1510.57
292_I324_M1.1420.57
1_M12_D1.1390.56
116_R169_M1.1370.56
346_I365_E1.1310.55
233_A295_W1.1260.55
162_T343_K1.1260.55
34_F38_D1.1250.55
182_V188_N1.1250.55
5_H12_D1.1250.55
59_D335_K1.1180.54
8_V12_D1.1130.54
14_M17_L1.1100.53
5_H14_M1.1090.53
180_S239_R1.1070.53
333_P337_I1.1070.53
397_C411_C1.1070.53
279_Y426_H1.1070.53
227_P273_F1.1010.52
399_R402_N1.1000.52
103_A108_S1.0990.52
288_G331_V1.0960.52
424_S432_T1.0950.52
164_E337_I1.0940.52
252_S418_S1.0900.51
408_C411_C1.0860.51
252_S320_R1.0850.51
352_A362_K1.0830.51
240_Q320_R1.0800.50
344_F355_C1.0790.50
305_G432_T1.0780.50
360_L450_F1.0760.50
163_P386_G1.0750.50
162_T165_E1.0710.49
231_I330_P1.0670.49
39_E57_E1.0660.49
62_T67_W1.0660.49
312_T320_R1.0590.48
64_E365_E1.0590.48
1_M8_V1.0590.48
278_G426_H1.0550.48
318_M418_S1.0540.48
327_V344_F1.0510.47
466_N472_G1.0510.47
278_G344_F1.0510.47
344_F352_A1.0510.47
18_G36_D1.0490.47
62_T66_D1.0480.47
218_N223_K1.0470.47
249_G360_L1.0470.47
12_D16_A1.0440.47
165_E273_F1.0430.47
240_Q296_G1.0420.46
32_P37_L1.0410.46
398_N401_W1.0400.46
279_Y313_P1.0380.46
181_S315_W1.0370.46
470_V473_I1.0370.46
338_D344_F1.0360.46
306_R349_K1.0350.46
30_V33_V1.0340.46
9_S16_A1.0330.46
320_R401_W1.0320.45
163_P330_P1.0300.45
164_E332_A1.0290.45
6_S12_D1.0280.45
293_V309_H1.0280.45
89_E93_I1.0250.45
6_S9_S1.0240.45
32_P56_K1.0210.44
235_V301_L1.0210.44
436_T439_L1.0210.44
166_A298_M1.0200.44
208_I226_I1.0190.44
416_V419_K1.0190.44
426_H452_Y1.0150.44
439_L443_F1.0130.44
89_E92_A1.0110.43
1_M13_F1.0100.43
290_G326_I1.0070.43
115_L274_L1.0070.43
167_S234_V1.0040.43
72_R195_I1.0030.43
32_P36_D1.0020.42
231_I246_S1.0010.42
344_F426_H1.0010.42
349_K362_K1.0010.42
182_V330_P1.0000.42
58_V61_P1.0000.42
383_N388_N1.0000.42
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  
4uquA20.82371000.562Contact Map
4rasA30.82991000.579Contact Map
7fd1A10.213798.50.935Contact Map
2v2kA20.205498.10.942Contact Map
1hfeL20.280198.10.943Contact Map
3i9v920.290597.80.946Contact Map
1xerA10.211697.70.947Contact Map
2zvsA30.143297.50.949Contact Map
3gyxB60.232497.50.949Contact Map
1jnrB20.232497.40.95Contact 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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