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T0806

ID: 1435255063 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 258 (256)
Sequences: 2251 (1551.3)
Seq/Len: 8.793
Nf(neff/√len): 97.0

Jackhmmer Results: (2015_01_07)
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: 8.793).

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
30_N150_I4.0211.00
52_I56_L3.1331.00
92_Q95_T3.0711.00
241_D244_S2.8431.00
142_D145_Q2.7731.00
100_D221_E2.5971.00
81_L101_F2.5401.00
60_N63_R2.5261.00
149_D153_N2.4531.00
97_S100_D2.4471.00
104_A220_I2.3491.00
3_I219_I2.3231.00
4_L167_V2.2791.00
217_R221_E2.2751.00
10_T84_K2.2411.00
47_S54_D2.2031.00
168_I219_I2.1911.00
17_L77_R2.1731.00
226_K229_Q2.1501.00
100_D223_R2.1271.00
244_S253_K2.0781.00
246_S249_E2.0591.00
196_E255_Y2.0281.00
241_D253_K2.0241.00
96_F217_R1.9911.00
187_E248_G1.9461.00
96_F100_D1.9171.00
192_V249_E1.8791.00
137_N140_G1.8741.00
151_I178_S1.8421.00
103_F107_H1.8401.00
13_Y82_A1.8201.00
26_E154_K1.7991.00
38_A64_F1.7641.00
228_E231_T1.7431.00
131_M178_S1.7331.00
61_A65_H1.7241.00
5_I216_S1.7201.00
26_E158_A1.6881.00
109_R158_A1.5971.00
105_Q121_L1.5871.00
141_K145_Q1.5481.00
227_P250_L1.5481.00
100_D220_I1.5441.00
31_S67_W1.5441.00
214_L236_E1.5391.00
194_L253_K1.5341.00
5_I108_L1.5331.00
103_F220_I1.5331.00
15_S77_R1.5291.00
231_T250_L1.4851.00
37_E135_L1.4781.00
5_I87_V1.4651.00
58_G62_A1.4631.00
84_K94_E1.4510.99
62_A66_D1.4460.99
219_I224_L1.4400.99
219_I230_L1.4130.99
86_D206_F1.3950.99
224_L229_Q1.3870.99
96_F104_A1.3700.99
8_A11_L1.3670.99
191_P250_L1.3480.99
59_I63_R1.3310.99
208_A212_R1.3100.99
104_A216_S1.3050.99
154_K157_E1.3040.99
207_Y254_R1.3020.99
90_G210_K1.3020.99
46_I52_I1.3010.99
151_I179_V1.2990.99
75_N125_Q1.2830.98
72_T75_N1.2690.98
96_F101_F1.2520.98
196_E201_F1.2450.98
118_L124_M1.2440.98
148_G180_K1.2410.98
2_L109_R1.2400.98
4_L155_L1.2390.98
240_F250_L1.2370.98
91_L216_S1.2310.98
27_L154_K1.2170.98
117_V154_K1.2150.98
113_G131_M1.2130.98
33_Q146_F1.2120.98
95_T217_R1.2080.97
96_F221_E1.2070.97
99_D223_R1.2000.97
77_R82_A1.1990.97
12_D84_K1.1900.97
37_E41_L1.1890.97
225_T229_Q1.1770.97
168_I191_P1.1750.97
2_L165_N1.1680.97
30_N146_F1.1670.97
76_A123_L1.1600.97
32_Q36_H1.1540.96
80_I91_L1.1490.96
52_I57_A1.1480.96
34_L137_N1.1430.96
47_S57_A1.1320.96
13_Y124_M1.1250.96
229_Q232_G1.1200.96
159_L186_A1.1000.95
239_F255_Y1.0970.95
221_E235_S1.0940.95
166_V187_E1.0910.95
168_I230_L1.0830.94
18_T81_L1.0830.94
33_Q37_E1.0640.94
134_R142_D1.0520.93
247_N250_L1.0510.93
95_T221_E1.0440.93
131_M174_E1.0440.93
30_N139_R1.0400.93
144_Y177_K1.0390.93
43_P58_G1.0330.92
47_S52_I1.0300.92
53_S56_L1.0280.92
195_D205_S1.0260.92
37_E138_A1.0260.92
80_I120_P1.0260.92
43_P61_A1.0200.92
12_D77_R1.0180.92
216_S220_I1.0100.91
101_F121_L1.0040.91
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: (31Jan15)
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  
3c65A10.034923.50.962Contact Map
4ou0A10.2287210.963Contact Map
4glxA10.32568.10.969Contact Map
2yfvC10.22097.80.969Contact Map
4pj0U20.35667.30.969Contact Map
2vqeB10.472970.97Contact Map
4e1pA20.15896.40.97Contact Map
2k9lA10.26366.30.97Contact Map
3sgiA106.10.97Contact Map
3eyiA20.240360.971Contact 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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