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1upm

ID: 1516170826 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 475 (431)
Sequences: 458 (262.3)
Seq/Len: 1.063
Nf(neff/√len): 12.6

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: 1.063).

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
422_V452_S3.5111.00
422_V454_E2.9631.00
187_R191_E2.9551.00
411_W457_A2.7541.00
224_A228_A2.7131.00
38_A135_L2.6561.00
190_Y228_A2.5881.00
191_E414_A2.1010.97
190_Y227_K2.0340.96
448_A452_S2.0150.96
137_D316_K2.0110.96
271_T297_M1.8940.94
456_A460_E1.8770.94
152_P281_S1.8280.93
86_H100_Y1.8070.92
35_D102_A1.7990.92
183_K216_D1.7540.90
297_M309_M1.7430.90
190_Y231_E1.7210.89
447_E450_K1.7110.89
183_K220_F1.6810.88
155_I365_T1.6710.87
116_M144_Y1.6670.87
40_F57_V1.6590.87
170_L424_L1.6340.86
459_C466_K1.6140.85
426_A448_A1.6120.85
291_L310_H1.5860.83
85_Y102_A1.5600.82
412_G416_G1.5570.82
256_F260_L1.5510.81
154_G217_R1.5420.81
167_R198_D1.5300.80
50_P97_Y1.5270.80
419_A462_W1.4820.77
407_L413_N1.4730.77
426_A449_T1.4700.76
202_D217_R1.4680.76
145_V320_L1.4670.76
418_V454_E1.4630.76
270_L274_F1.4620.76
450_K456_A1.4550.75
422_V448_A1.4480.75
458_A462_W1.4240.73
161_K425_E1.4170.73
404_G408_G1.4160.72
193_L236_K1.4010.71
227_K231_E1.3980.71
190_Y224_A1.3890.70
329_G378_A1.3850.70
375_L399_V1.3820.70
295_R327_H1.3450.67
61_S176_P1.3130.64
39_A139_R1.3100.64
443_T446_R1.3090.64
116_M120_I1.3080.64
194_R228_A1.3050.63
384_V419_A1.2970.63
354_T358_R1.2950.62
164_K227_K1.2940.62
381_G404_G1.2920.62
234_E421_R1.2870.62
150_G195_G1.2830.61
189_V225_L1.2790.61
156_Q373_G1.2780.61
193_L225_L1.2730.61
225_L263_P1.2640.60
182_A212_M1.2620.60
156_Q372_P1.2490.58
295_R329_G1.2460.58
216_D219_L1.2450.58
426_A442_N1.2430.58
41_R136_E1.2330.57
150_G319_R1.2290.56
115_N118_T1.2250.56
224_A227_K1.2220.56
156_Q160_D1.2210.56
387_M407_L1.2200.56
409_H416_G1.2190.56
216_D460_E1.2190.56
75_T78_D1.2180.55
314_L323_G1.2150.55
185_Y221_C1.2140.55
148_F208_S1.2120.55
155_I364_F1.2110.55
191_E194_R1.2080.55
113_V210_P1.2050.54
281_S286_D1.2030.54
126_G295_R1.1990.54
268_D298_H1.1980.54
176_P186_G1.1920.53
43_S138_L1.1820.52
440_E447_E1.1790.52
320_L371_T1.1690.51
442_N448_A1.1670.51
173_T401_Q1.1640.50
160_D227_K1.1600.50
66_W241_N1.1550.50
262_V290_L1.1530.49
149_Q285_R1.1510.49
37_L148_F1.1470.49
172_C192_C1.1460.49
227_K442_N1.1440.49
156_Q166_G1.1440.49
266_M314_L1.1360.48
274_F297_M1.1360.48
217_R324_D1.1320.47
154_G202_D1.1310.47
109_E209_Q1.1310.47
453_P457_A1.1300.47
125_F295_R1.1250.47
66_W202_D1.1250.47
224_A321_S1.1240.47
145_V369_V1.1220.46
36_I320_L1.1210.46
266_M329_G1.1210.46
123_N333_G1.1180.46
426_A452_S1.1180.46
443_T456_A1.1170.46
173_T239_Y1.1160.46
160_D165_Y1.1120.46
37_L100_Y1.1090.45
62_S315_A1.1070.45
84_C398_S1.1060.45
209_Q212_M1.1050.45
292_H327_H1.1040.45
430_A456_A1.1030.45
114_T137_D1.0990.44
120_I135_L1.0960.44
409_H412_G1.0950.44
105_L144_Y1.0940.44
190_Y194_R1.0900.43
177_K211_F1.0890.43
442_N454_E1.0880.43
251_M254_A1.0870.43
82_G103_Y1.0860.43
440_E460_E1.0860.43
249_D252_K1.0850.43
205_N302_D1.0830.43
154_G324_D1.0820.43
62_S82_G1.0800.43
361_G456_A1.0800.43
325_H377_V1.0790.42
169_L375_L1.0770.42
118_T271_T1.0760.42
442_N452_S1.0740.42
164_K252_K1.0740.42
258_R413_N1.0740.42
136_E140_I1.0700.42
446_R456_A1.0680.41
36_I361_G1.0680.41
173_T402_F1.0670.41
442_N447_E1.0650.41
58_A65_T1.0640.41
164_K168_P1.0620.41
43_S409_H1.0620.41
169_L387_M1.0610.41
258_R264_I1.0600.41
385_W463_K1.0560.40
101_V208_S1.0550.40
301_I456_A1.0540.40
293_I323_G1.0530.40
142_V442_N1.0510.40
176_P380_G1.0490.40
219_L411_W1.0480.40
59_A221_C1.0470.40
239_Y264_I1.0450.39
104_P416_G1.0450.39
113_V399_V1.0430.39
327_H383_H1.0410.39
125_F378_A1.0400.39
442_N450_K1.0400.39
350_R358_R1.0390.39
65_T211_F1.0380.39
171_G295_R1.0360.39
109_E212_M1.0350.38
126_G177_K1.0340.38
379_S405_G1.0330.38
57_V267_H1.0330.38
370_S397_D1.0310.38
325_H399_V1.0300.38
460_E464_E1.0290.38
99_C453_P1.0290.38
257_A262_V1.0260.38
84_C87_I1.0250.38
54_G387_M1.0250.38
25_Y28_E1.0240.37
159_R202_D1.0230.37
60_E123_N1.0230.37
173_T379_S1.0220.37
337_G341_I1.0220.37
36_I42_V1.0200.37
264_I325_H1.0140.37
138_L222_A1.0140.37
278_T374_V1.0130.37
116_M140_I1.0120.36
197_L325_H1.0120.36
123_N380_G1.0120.36
150_G404_G1.0110.36
157_V324_D1.0100.36
295_R378_A1.0090.36
113_V314_L1.0080.36
143_A210_P1.0080.36
442_N446_R1.0070.36
425_E446_R1.0070.36
167_R371_T1.0050.36
442_N453_P1.0030.36
333_G380_G1.0030.36
339_R460_E1.0030.36
446_R464_E1.0030.36
363_Y456_A1.0010.35
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  
1wddA20.97681000.117Contact Map
4f0hA10.93681000.14Contact Map
3kdnA100.91161000.195Contact Map
2d69A40.89471000.205Contact Map
2qygA40.86741000.227Contact Map
1ykwA20.83791000.227Contact Map
3nwrA10.80421000.228Contact Map
2oemA20.84211000.229Contact Map
4nasA40.83161000.229Contact Map
2zviA40.83581000.23Contact 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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