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OPENSEQ.org

ser 2 seq

ID: 1416320920 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 490 (447)
Sequences: 792 (471.2)
Seq/Len: 1.772
Nf(neff/√len): 22.3

HHblits Results: (2013_03)
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: 1.772).

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
79_D82_N3.3041.00
120_I142_V3.1761.00
45_H107_F2.7191.00
228_D231_S2.5191.00
103_N106_D2.3811.00
83_Q90_W2.0160.99
133_V136_S1.9310.98
79_D83_Q1.8440.97
134_G137_P1.8160.97
42_L50_Y1.7410.96
224_L228_D1.7280.96
97_D100_L1.7070.95
334_R338_K1.6880.95
46_L50_Y1.6750.95
138_N141_Y1.6650.94
170_P176_C1.6630.94
212_G294_L1.6140.93
172_D176_C1.6070.93
50_Y56_P1.6070.93
135_K138_N1.6020.93
95_W121_W1.5850.92
70_A89_I1.5840.92
269_G297_V1.5820.92
187_I234_S1.5680.92
42_L46_L1.5640.92
269_G285_T1.5300.90
95_W102_W1.5290.90
230_E233_G1.5170.90
211_Q247_R1.5140.90
131_V367_L1.5090.90
56_P66_V1.5000.89
133_V138_N1.4980.89
224_L237_E1.4980.89
109_N163_S1.4920.89
192_I238_M1.4920.89
215_E247_R1.4910.89
261_F294_L1.4790.88
104_P146_H1.4750.88
284_I304_T1.4660.88
135_K139_I1.4420.87
128_N312_S1.4410.86
115_I144_V1.4300.86
68_I178_L1.4250.86
230_E234_S1.4230.86
162_C176_C1.4160.85
182_S251_Y1.4050.85
246_R258_P1.4040.85
347_L351_H1.3970.84
266_D330_I1.3950.84
42_L66_V1.3920.84
288_L294_L1.3860.83
136_S139_I1.3820.83
338_K343_Q1.3800.83
97_D121_W1.3720.83
171_F174_Q1.3710.83
353_V358_A1.3700.82
210_N215_E1.3690.82
96_T103_N1.3680.82
121_W124_D1.3680.82
162_C172_D1.3620.82
128_N237_E1.3540.81
266_D325_S1.3470.81
250_F255_L1.3440.81
114_S143_Y1.3410.81
95_W123_P1.3360.80
38_A41_R1.3330.80
278_E282_F1.3300.80
288_L298_S1.3280.80
80_E83_Q1.3190.79
80_E91_Y1.3110.78
102_W123_P1.3080.78
354_L363_L1.3030.78
466_F469_Y1.2960.77
104_P142_V1.2950.77
81_K87_T1.2940.77
265_V319_M1.2930.77
162_C171_F1.2780.76
165_D181_T1.2770.76
162_C174_Q1.2690.75
211_Q253_V1.2590.74
42_L56_P1.2570.74
166_I300_T1.2490.74
57_V99_F1.2490.74
311_I330_I1.2440.73
254_T284_I1.2420.73
38_A108_D1.2390.73
461_L472_A1.2360.73
338_K358_A1.2360.73
308_T332_I1.2270.72
343_Q358_A1.2260.72
231_S234_S1.2260.72
161_A320_A1.2260.72
443_K448_R1.2250.72
165_D263_M1.2220.71
83_Q86_T1.2190.71
170_P174_Q1.2180.71
343_Q353_V1.2160.71
105_E146_H1.2140.71
262_L288_L1.2100.70
171_F176_C1.2080.70
281_S285_T1.2080.70
453_D463_K1.2060.70
456_R459_S1.2030.70
134_G138_N1.2020.69
90_W124_D1.2020.69
102_W121_W1.2010.69
50_Y55_R1.2000.69
204_D289_G1.1950.69
97_D123_P1.1940.69
285_T288_L1.1920.69
317_V353_V1.1920.69
90_W310_L1.1890.68
97_D116_P1.1860.68
47_L115_I1.1810.68
167_Y307_G1.1790.67
79_D168_N1.1710.67
241_Y276_S1.1630.66
169_F176_C1.1620.66
185_H256_L1.1620.66
162_C170_P1.1510.65
144_V329_T1.1490.64
277_G292_V1.1490.64
463_K466_F1.1440.64
353_V457_V1.1420.64
62_K66_V1.1410.64
105_E117_T1.1390.63
266_D307_G1.1280.62
100_L121_W1.1270.62
295_I314_Y1.1250.62
79_D113_L1.1220.62
319_M325_S1.1170.61
454_W462_D1.1150.61
295_I348_W1.1120.61
212_G337_H1.1090.60
87_T160_T1.1080.60
289_G329_T1.1080.60
269_G326_L1.1070.60
345_V457_V1.1030.60
319_M336_V1.1020.60
426_A430_L1.1020.60
182_S185_H1.1010.60
114_S129_E1.0990.59
191_N213_E1.0960.59
322_L333_V1.0960.59
289_G455_L1.0960.59
126_L457_V1.0950.59
290_Y325_S1.0950.59
217_L245_R1.0930.59
181_T329_T1.0930.59
80_E311_I1.0930.59
96_T149_E1.0880.58
90_W255_L1.0860.58
125_I251_Y1.0840.58
411_R415_S1.0790.57
434_L437_I1.0790.57
46_L56_P1.0780.57
142_V150_V1.0730.57
269_G316_V1.0730.57
382_D385_S1.0720.56
150_V468_V1.0700.56
137_P141_Y1.0680.56
279_R338_K1.0670.56
138_N367_L1.0660.56
240_F298_S1.0660.56
345_V353_V1.0630.56
76_L259_S1.0620.55
216_L323_V1.0610.55
78_V83_Q1.0600.55
262_L266_D1.0590.55
247_R321_L1.0580.55
126_L156_L1.0570.55
272_L319_M1.0570.55
283_K301_L1.0560.55
50_Y74_A1.0550.55
208_F223_F1.0540.55
276_S461_L1.0520.54
239_K330_I1.0520.54
291_S298_S1.0510.54
212_G297_V1.0480.54
458_G466_F1.0480.54
282_F469_Y1.0470.54
453_D456_R1.0430.53
221_T240_F1.0420.53
438_R442_E1.0390.53
185_H305_A1.0380.53
283_K315_F1.0380.53
169_F172_D1.0370.53
338_K342_Q1.0370.53
175_N248_P1.0370.53
317_V345_V1.0360.53
86_T93_Q1.0360.53
325_S332_I1.0360.53
289_G299_D1.0350.53
101_Q147_Q1.0310.52
182_S192_I1.0300.52
106_D150_V1.0280.52
97_D102_W1.0270.52
178_L349_L1.0270.52
57_V77_S1.0260.52
174_Q182_S1.0240.51
113_L311_I1.0230.51
93_Q473_V1.0230.51
334_R343_Q1.0220.51
216_L465_L1.0210.51
248_P294_L1.0200.51
75_I85_L1.0190.51
110_I113_L1.0180.51
402_G418_P1.0180.51
126_L315_F1.0160.50
40_Q311_I1.0150.50
104_P117_T1.0130.50
44_D48_A1.0120.50
155_P166_I1.0120.50
97_D107_F1.0120.50
434_L438_R1.0110.50
96_T146_H1.0110.50
254_T304_T1.0100.50
460_V463_K1.0080.50
94_F151_Q1.0080.50
441_L451_A1.0080.50
68_I464_L1.0080.50
221_T224_L1.0080.50
253_V321_L1.0060.49
319_M327_A1.0050.49
178_L439_H1.0050.49
339_Q347_L1.0030.49
219_V248_P1.0030.49
133_V137_P1.0020.49
57_V66_V1.0020.49
279_R282_F1.0010.49
51_R78_V1.0000.49
39_L212_G1.0000.49
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: (06Sep14)
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  
4pirA50.78161000.258Contact Map
4aq5C10.73881000.285Contact Map
4aq5E10.74491000.287Contact Map
4aq5A20.74691000.291Contact Map
4aq5B10.74081000.292Contact Map
2bg9A20.74691000.373Contact Map
2bg9E10.74291000.377Contact Map
2bg9C10.73671000.38Contact Map
2bg9B10.74081000.383Contact Map
4cofA50.67351000.484Contact 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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