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OPENSEQ.org

CSN4 from Hsapien paranoid

ID: 1481078522 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 445 (422)
Sequences: 823 (442.3)
Seq/Len: 1.950
Nf(neff/√len): 21.5

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: 1.950).

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
152_K155_E3.7781.00
233_E236_E2.6911.00
174_S215_S1.9690.99
79_L125_V1.8380.98
148_K185_E1.8220.98
373_E398_K1.8180.98
144_V426_I1.8130.98
71_K74_D1.7590.97
145_E149_E1.7390.97
133_E143_L1.6490.95
241_L281_I1.6470.95
98_Q135_E1.6120.94
423_L427_E1.6040.94
228_S240_Y1.5750.93
8_K12_D1.5710.93
220_Y244_I1.5240.92
99_K102_E1.4740.90
73_D117_S1.4640.89
214_E249_A1.4630.89
372_T375_Q1.4530.89
10_D18_K1.4500.89
12_D15_Q1.4460.89
366_N373_E1.4130.87
13_Y44_K1.3870.86
14_S20_E1.3860.86
431_H435_K1.3760.85
285_Q391_A1.3760.85
425_H429_I1.3720.85
8_K14_S1.3670.84
371_L384_V1.3650.84
123_R279_D1.3650.84
74_D77_E1.3590.84
36_L92_S1.3520.84
18_K28_A1.3510.83
62_I96_M1.3510.83
164_Q184_M1.3510.83
9_A445_K1.3500.83
267_F312_P1.3350.82
15_Q19_E1.3260.82
17_L39_L1.3260.82
72_W132_V1.3260.82
377_E395_R1.3150.81
354_S389_I1.3110.81
178_Q219_E1.3070.81
161_C195_Q1.3070.81
275_N279_D1.2990.80
182_E185_E1.2990.80
103_Y111_D1.2880.79
12_D19_E1.2790.79
278_N341_L1.2780.79
350_L396_P1.2770.78
156_A364_R1.2700.78
384_V391_A1.2700.78
189_L226_K1.2660.78
144_V160_L1.2610.77
87_G100_V1.2510.76
316_K319_E1.2490.76
74_D124_V1.2440.76
371_L427_E1.2370.75
39_L444_A1.2330.75
14_S18_K1.2320.75
253_D256_K1.2310.75
10_D16_I1.2260.74
44_K47_R1.2250.74
14_S44_K1.2230.74
286_N412_L1.2210.74
229_L234_Y1.2130.73
12_D37_D1.2100.73
147_K155_E1.2100.73
201_R423_L1.2080.73
221_Y243_E1.2070.73
8_K15_Q1.2040.72
76_N267_F1.2000.72
43_E47_R1.1940.72
121_T124_V1.1940.72
294_E399_I1.1910.71
137_A175_E1.1900.71
349_N360_I1.1870.71
35_A39_L1.1840.71
11_K15_Q1.1820.70
20_E28_A1.1820.70
101_M312_P1.1810.70
15_Q18_K1.1810.70
234_Y237_V1.1780.70
19_E29_Q1.1780.70
8_K18_K1.1780.70
10_D28_A1.1760.70
9_A12_D1.1730.70
38_Q43_E1.1720.70
11_K35_A1.1710.69
19_E28_A1.1700.69
11_K18_K1.1680.69
35_A38_Q1.1670.69
10_D19_E1.1660.69
363_L398_K1.1640.69
11_K14_S1.1610.68
123_R351_R1.1610.68
177_I366_N1.1550.68
34_S38_Q1.1500.67
73_D77_E1.1470.67
44_K54_S1.1450.67
198_V201_R1.1430.67
8_K28_A1.1420.67
189_L336_H1.1410.67
92_S95_Y1.1390.66
83_S121_T1.1350.66
36_L62_I1.1320.66
127_E416_S1.1310.66
120_E237_V1.1300.65
9_A290_L1.1280.65
261_L270_L1.1260.65
9_A16_I1.1250.65
353_I365_L1.1240.65
15_Q35_A1.1220.65
242_Q280_L1.1210.65
19_E34_S1.1200.64
18_K31_D1.1190.64
350_L379_Y1.1170.64
362_L373_E1.1160.64
80_T117_S1.1130.64
228_S236_E1.1040.63
76_N118_V1.1040.63
15_Q31_D1.1040.63
217_K221_Y1.1020.63
13_Y20_E1.1010.62
188_I226_K1.1010.62
18_K34_S1.1010.62
11_K30_N1.1000.62
66_L74_D1.0990.62
203_I244_I1.0990.62
19_E30_N1.0980.62
287_D348_H1.0970.62
14_S37_D1.0960.62
394_N402_F1.0950.62
97_I384_V1.0950.62
10_D44_K1.0930.62
380_I400_V1.0910.61
8_K11_K1.0910.61
18_K30_N1.0870.61
16_I19_E1.0870.61
13_Y17_L1.0870.61
254_E372_T1.0850.61
28_A33_N1.0840.61
244_I260_V1.0840.61
30_N34_S1.0840.61
54_S57_E1.0830.61
272_P427_E1.0830.61
434_T442_L1.0830.61
16_I28_A1.0820.60
188_I196_A1.0810.60
270_L322_L1.0800.60
177_I206_K1.0760.60
14_S28_A1.0750.60
12_D290_L1.0740.60
28_A34_S1.0720.59
383_L389_I1.0690.59
293_L299_L1.0670.59
11_K19_E1.0670.59
232_R328_A1.0670.59
172_E308_L1.0670.59
56_K276_L1.0660.59
18_K27_L1.0630.58
73_D168_Y1.0630.58
138_R175_E1.0620.58
442_L445_K1.0620.58
12_D18_K1.0610.58
73_D81_L1.0600.58
204_L221_Y1.0580.58
15_Q37_D1.0570.58
154_D190_K1.0570.58
67_A102_E1.0540.57
157_A426_I1.0520.57
14_S19_E1.0510.57
184_M196_A1.0510.57
16_I35_A1.0480.57
46_T171_M1.0470.57
341_L344_R1.0460.57
28_A31_D1.0450.57
11_K290_L1.0440.56
234_Y264_I1.0440.56
86_H195_Q1.0420.56
71_K121_T1.0410.56
237_V241_L1.0400.56
419_V423_L1.0400.56
100_V322_L1.0400.56
55_S299_L1.0390.56
101_M131_F1.0390.56
10_D30_N1.0390.56
222_N226_K1.0370.56
29_Q34_S1.0350.55
91_L95_Y1.0340.55
283_K374_S1.0320.55
8_K31_D1.0290.55
357_Y377_E1.0280.55
188_I193_Y1.0260.54
78_Q81_L1.0240.54
76_N124_V1.0240.54
346_I379_Y1.0240.54
34_S432_L1.0230.54
18_K32_C1.0230.54
180_I203_I1.0220.54
142_D386_Q1.0220.54
76_N81_L1.0220.54
83_S354_S1.0220.54
10_D445_K1.0210.54
330_G333_A1.0180.54
384_V413_N1.0170.53
168_Y280_L1.0160.53
67_A156_A1.0160.53
220_Y224_L1.0150.53
434_T437_E1.0140.53
28_A43_E1.0130.53
29_Q37_D1.0120.53
14_S30_N1.0090.53
28_A290_L1.0090.53
63_V175_E1.0090.53
159_I162_E1.0080.52
27_L33_N1.0070.52
15_Q34_S1.0070.52
120_E123_R1.0040.52
227_I231_K1.0030.52
9_A61_K1.0030.52
118_V121_T1.0020.52
349_N402_F1.0010.52
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: (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  
4cr2P10.93261000.318Contact Map
4d10D20.85621000.473Contact Map
4d0pA10.77751000.51Contact Map
4cr2Q10.89661000.523Contact Map
3txnA10.76851000.537Contact Map
4d10B20.88541000.608Contact Map
4cr2R10.84491000.657Contact Map
4d10C20.87641000.672Contact Map
4d10A20.89211000.672Contact Map
4cr2O10.81000.692Contact 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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