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ser all seq clustal

ID: 1416330352 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 490 (453)
Sequences: 893 (515.4)
Seq/Len: 1.971
Nf(neff/√len): 24.2

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: 1.971).

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_N3.4871.00
120_I142_V3.1631.00
45_H107_F3.0101.00
228_D231_S2.5821.00
103_N106_D2.5091.00
479_T482_T2.2601.00
478_I482_T2.1971.00
137_P141_Y2.1170.99
224_L237_E2.0490.99
79_D83_Q2.0160.99
42_L46_L1.9710.99
478_I481_V1.9440.99
42_L50_Y1.9120.98
479_T483_L1.9020.98
334_R338_K1.8590.98
476_Y479_T1.8510.98
95_W102_W1.8460.98
46_L50_Y1.8350.98
172_D176_C1.7560.97
138_N141_Y1.7360.97
269_G285_T1.6870.96
70_A89_I1.6760.96
102_W123_P1.6580.95
97_D100_L1.6490.95
170_P176_C1.6460.95
95_W121_W1.6420.95
135_K139_I1.6250.95
104_P146_H1.6180.94
187_I234_S1.6130.94
121_W124_D1.6110.94
269_G297_V1.5880.94
95_W123_P1.5750.93
50_Y56_P1.5490.93
171_F176_C1.5290.92
231_S234_S1.5230.92
212_G294_L1.5170.91
476_Y481_V1.5160.91
97_D121_W1.5000.91
114_S143_Y1.4850.90
215_E247_R1.4840.90
317_V353_V1.4710.90
135_K141_Y1.4660.90
83_Q90_W1.4560.89
278_E282_F1.4250.88
68_I178_L1.4230.88
162_C176_C1.4190.87
291_S298_S1.4160.87
38_A108_D1.4080.87
162_C174_Q1.4050.87
246_R258_P1.4050.87
128_N237_E1.4010.87
102_W121_W1.4000.86
97_D123_P1.3980.86
284_I304_T1.3890.86
192_I238_M1.3820.86
56_P66_V1.3800.85
97_D102_W1.3770.85
182_S192_I1.3760.85
338_K343_Q1.3650.85
386_G389_L1.3620.84
261_F294_L1.3600.84
210_N215_E1.3490.84
162_C172_D1.3420.83
80_E91_Y1.3380.83
477_S482_T1.3270.82
95_W124_D1.3230.82
170_P174_Q1.3080.81
254_T284_I1.2960.80
208_F223_F1.2870.79
353_V457_V1.2860.79
165_D181_T1.2850.79
42_L56_P1.2810.79
109_N163_S1.2800.79
347_L351_H1.2770.79
171_F174_Q1.2740.78
288_L294_L1.2730.78
162_C170_P1.2710.78
50_Y55_R1.2660.78
466_F469_Y1.2620.78
354_L363_L1.2620.78
221_T240_F1.2620.78
266_D330_I1.2610.77
162_C171_F1.2530.77
461_L472_A1.2490.77
343_Q358_A1.2480.76
353_V358_A1.2460.76
47_L115_I1.2460.76
343_Q353_V1.2440.76
477_S481_V1.2380.76
115_I144_V1.2360.75
262_L266_D1.2340.75
191_N213_E1.2310.75
230_E234_S1.2310.75
182_S251_Y1.2290.75
224_L228_D1.2260.75
38_A41_R1.2250.75
454_W462_D1.2250.75
102_W124_D1.2210.74
443_K448_R1.2180.74
41_R49_D1.2170.74
456_R459_S1.2160.74
217_L245_R1.2090.73
169_F180_F1.2080.73
211_Q247_R1.2030.73
302_P309_P1.1900.72
128_N181_T1.1870.71
277_G293_F1.1850.71
80_E83_Q1.1810.71
478_I483_L1.1790.71
250_F255_L1.1750.70
285_T288_L1.1740.70
283_K301_L1.1700.70
114_S129_E1.1700.70
142_V150_V1.1690.70
319_M327_A1.1680.69
434_L438_R1.1640.69
319_M325_S1.1640.69
132_D169_F1.1620.69
90_W310_L1.1620.69
169_F176_C1.1610.69
311_I330_I1.1610.69
453_D456_R1.1550.68
87_T160_T1.1520.68
128_N312_S1.1500.68
104_P142_V1.1500.68
288_L298_S1.1500.68
187_I236_A1.1490.68
169_F172_D1.1480.68
245_R310_L1.1460.67
271_Y434_L1.1450.67
349_L353_V1.1440.67
289_G329_T1.1400.67
430_L433_E1.1360.66
100_L124_D1.1350.66
100_L121_W1.1350.66
104_P117_T1.1300.66
338_K358_A1.1280.66
266_D325_S1.1240.65
97_D116_P1.1230.65
319_M336_V1.1190.65
175_N248_P1.1170.64
154_K179_T1.1160.64
279_R282_F1.1150.64
110_I113_L1.1140.64
219_V248_P1.1130.64
308_T332_I1.1100.64
39_L212_G1.1060.63
455_L473_V1.1060.63
251_Y262_L1.1030.63
148_G176_C1.1030.63
42_L66_V1.1020.63
275_D278_E1.0980.63
169_F174_Q1.0960.62
312_S319_M1.0940.62
456_R466_F1.0870.61
281_S285_T1.0840.61
96_T149_E1.0840.61
289_G455_L1.0840.61
239_K330_I1.0800.61
254_T304_T1.0800.61
455_L460_V1.0800.61
228_D237_E1.0770.60
76_L259_S1.0720.60
97_D107_F1.0710.60
221_T337_H1.0680.59
176_C182_S1.0630.59
96_T103_N1.0620.59
131_V183_W1.0620.59
299_D329_T1.0610.59
363_L366_Q1.0600.58
265_V319_M1.0600.58
191_N223_F1.0600.58
392_A403_P1.0570.58
254_T268_V1.0570.58
298_S301_L1.0570.58
47_L120_I1.0540.58
322_L333_V1.0540.58
228_D234_S1.0540.58
429_G442_E1.0530.58
230_E237_E1.0520.58
182_S185_H1.0520.58
266_D307_G1.0520.58
133_V152_N1.0480.57
136_S141_Y1.0480.57
338_K342_Q1.0480.57
212_G297_V1.0460.57
171_F182_S1.0450.57
345_V456_R1.0440.57
97_D124_D1.0440.57
212_G254_T1.0420.57
97_D129_E1.0420.57
282_F469_Y1.0400.56
83_Q86_T1.0400.56
46_L56_P1.0380.56
211_Q253_V1.0360.56
113_L453_D1.0330.56
394_G397_C1.0320.55
103_N124_D1.0320.55
365_E453_D1.0290.55
125_I475_A1.0290.55
322_L336_V1.0280.55
120_I128_N1.0270.55
55_R66_V1.0260.55
210_N242_V1.0250.55
272_L319_M1.0230.54
224_L230_E1.0220.54
105_E146_H1.0210.54
127_I152_N1.0190.54
177_S248_P1.0170.54
281_S284_I1.0160.54
70_A74_A1.0150.54
290_Y325_S1.0140.53
191_N236_A1.0140.53
36_R39_L1.0120.53
301_L329_T1.0120.53
81_K87_T1.0110.53
185_H256_L1.0090.53
315_F326_L1.0070.53
269_G318_C1.0070.53
101_Q120_I1.0030.52
126_L457_V1.0030.52
212_G244_I1.0020.52
322_L466_F1.0020.52
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  
4pirA50.78161000.253Contact Map
4aq5C10.73881000.27Contact Map
4aq5E10.74491000.276Contact Map
4aq5B10.74291000.28Contact Map
4aq5A20.74691000.284Contact Map
2bg9A20.74691000.367Contact Map
2bg9E10.74291000.37Contact Map
2bg9C10.73671000.373Contact Map
2bg9B10.74081000.375Contact Map
4cofA50.67351000.478Contact 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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