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T0814 120-424 -force run

ID: 1404851082 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 305 (299)
Sequences: 234 (210)
Seq/Len: 0.783
Nf(neff/√len): 12.1

Jackhmmer Results: (2014_04_16)
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: 0.783).

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
229_N236_E6.1091.00
41_E291_R3.7231.00
158_D250_Y3.2041.00
283_R290_D2.8881.00
15_S41_E2.6850.99
48_A278_I2.6290.99
67_F278_I2.3990.98
226_M237_K2.2480.97
208_S225_K2.2000.96
171_D273_Q2.1900.96
277_S295_V2.0110.93
22_V33_F1.9820.93
76_I83_L1.9370.91
38_S292_L1.9340.91
152_N196_H1.8460.89
279_Y292_L1.8180.87
92_R95_N1.7200.83
221_D224_S1.6980.82
141_V155_L1.6940.82
210_Y224_S1.6780.81
284_P287_A1.6650.80
100_L118_L1.6530.80
125_E273_Q1.6310.79
44_V74_F1.6230.78
38_S279_Y1.6140.77
125_E173_D1.6100.77
32_I46_I1.6100.77
134_N193_Y1.5500.73
88_Y93_R1.4880.69
84_K283_R1.4860.69
46_I280_V1.4830.69
157_T198_T1.4830.69
125_E171_D1.4820.69
83_L110_I1.4550.66
161_R266_E1.4200.64
126_Y225_K1.4130.63
83_L280_V1.4010.62
178_I207_G1.3910.61
131_F193_Y1.3690.59
3_L20_I1.3550.58
88_Y279_Y1.3540.58
88_Y277_S1.3370.57
14_V191_D1.3340.57
15_S65_V1.3340.57
34_T117_N1.3260.56
210_Y225_K1.3020.54
8_D69_I1.2960.53
94_D280_V1.2900.53
63_Q274_N1.2760.52
173_D273_Q1.2740.51
22_V190_A1.2710.51
216_F224_S1.2710.51
43_V122_A1.2660.51
211_L239_V1.2600.50
122_A270_Y1.2510.49
127_R266_E1.2380.48
74_F282_Y1.2310.48
12_F165_T1.2280.47
199_L265_I1.2230.47
57_D62_H1.2170.46
197_F241_L1.2160.46
76_I82_D1.2060.45
180_C183_C1.2020.45
87_V118_L1.2000.45
57_D250_Y1.1950.45
52_G59_N1.1920.44
232_T236_E1.1920.44
11_Q178_I1.1840.44
241_L246_Y1.1770.43
224_S239_V1.1650.42
87_V228_Y1.1650.42
46_I278_I1.1610.42
77_T126_Y1.1600.42
12_F133_S1.1520.41
19_A159_Y1.1520.41
151_Y270_Y1.1460.40
52_G132_L1.1460.40
69_I185_D1.1430.40
64_Q119_I1.1340.39
137_N141_V1.1330.39
85_I182_D1.1310.39
97_V141_V1.1270.39
17_N281_Y1.1240.39
243_Q290_D1.1230.38
133_S191_D1.1200.38
67_F85_I1.1080.37
47_S241_L1.1070.37
194_I238_A1.1000.37
19_A87_V1.0980.36
122_A231_E1.0980.36
128_R245_S1.0940.36
68_N143_N1.0920.36
2_R240_L1.0900.36
62_H121_P1.0860.35
96_A282_Y1.0830.35
130_E169_D1.0820.35
96_A193_Y1.0790.35
61_S68_N1.0790.35
79_P84_K1.0780.35
22_V214_E1.0700.34
69_I280_V1.0660.34
247_N284_P1.0660.34
24_N138_G1.0580.33
95_N280_V1.0570.33
108_N259_V1.0560.33
76_I84_K1.0540.33
215_L224_S1.0520.33
267_G274_N1.0480.32
203_P230_F1.0460.32
33_F127_R1.0420.32
69_I157_T1.0360.32
153_V193_Y1.0340.31
46_I296_T1.0340.31
36_C214_E1.0340.31
126_Y218_N1.0290.31
21_Q126_Y1.0270.31
49_S66_S1.0270.31
254_P258_S1.0250.31
69_I294_G1.0240.31
65_V237_K1.0220.31
5_L12_F1.0210.30
96_A99_D1.0160.30
46_I279_Y1.0150.30
78_Y81_T1.0120.30
193_Y296_T1.0050.29
132_L245_S1.0040.29
126_Y179_R1.0030.29
161_R250_Y1.0030.29
177_F277_S1.0030.29
219_V268_N1.0020.29
127_R158_D1.0020.29
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  
4r7fA10.98361000.029Contact Map
2qlvB20.28296.80.936Contact Map
4aeeA20.406696.70.937Contact Map
4aefA20.390296.20.94Contact Map
1z0nA30.28296.10.94Contact Map
2lu3A10.34195.70.942Contact Map
1ac0A10.331195.20.944Contact Map
4cfeB20.308292.70.95Contact Map
2z0bA60.363990.80.953Contact Map
4rkkA20.363968.90.963Contact 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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