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T0814 -force run

ID: 1404849462 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 424 (412)
Sequences: 232 (210.3)
Seq/Len: 0.563
Nf(neff/√len): 10.4

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: 0.563).

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
348_N355_E6.0111.00
82_N86_T4.0041.00
160_E410_R3.6771.00
277_D369_Y3.0791.00
402_R409_D2.7940.99
167_A397_I2.6790.98
134_S160_E2.5430.98
186_F397_I2.4250.97
290_D392_Q2.1960.93
74_Y151_I2.0720.90
327_S344_K2.0590.90
345_M356_K2.0420.89
396_S414_V1.9110.85
157_S411_L1.9030.84
195_I202_L1.8840.84
66_G74_Y1.8600.82
141_V152_F1.8110.80
82_N408_Y1.7920.79
211_R214_N1.7280.76
271_N315_H1.7060.74
80_H88_S1.7030.74
398_Y411_L1.6980.74
340_D343_S1.6820.73
40_V154_A1.6770.72
40_V60_I1.6500.71
329_Y343_S1.6430.70
244_E392_Q1.6350.70
40_V62_I1.6220.69
260_V274_L1.6180.68
112_G345_M1.6060.68
244_E292_D1.6000.67
403_P406_A1.5690.65
163_V193_F1.5560.64
88_S198_P1.5520.64
157_S398_Y1.5500.64
151_I165_I1.5470.63
219_L237_L1.5050.60
244_E290_D1.4790.58
203_K402_R1.4500.56
94_E407_R1.4490.56
297_I326_G1.4230.54
202_L229_I1.4210.54
202_L399_V1.4190.54
62_I154_A1.4150.53
245_Y344_K1.4140.53
165_I399_V1.3980.52
253_N312_Y1.3890.51
133_V310_D1.3570.49
92_P100_Q1.3440.48
182_Q393_N1.3340.47
280_R385_E1.3280.46
276_T317_T1.3200.46
176_D181_H1.3200.46
207_Y212_R1.3190.46
335_F343_S1.3170.45
134_S184_V1.3050.45
52_I60_I1.3020.44
63_N306_D1.2980.44
241_A389_Y1.2920.43
11_M51_Y1.2900.43
153_T236_N1.2720.42
292_D392_Q1.2710.42
329_Y344_K1.2670.42
14_F19_G1.2600.41
250_F312_Y1.2580.41
207_Y398_Y1.2570.41
78_V180_S1.2410.40
79_V140_Q1.2410.40
23_Q330_L1.2340.39
106_D121_R1.2250.38
35_I344_K1.2220.38
76_Y126_N1.2090.37
206_V347_Y1.2080.37
122_L139_I1.2080.37
360_L365_Y1.2040.37
270_Y389_Y1.2020.37
95_Y158_V1.2010.37
82_N409_D1.1960.36
213_D399_V1.1890.36
171_G178_N1.1860.35
195_I201_D1.1850.35
12_M373_P1.1830.35
127_D188_I1.1830.35
299_C302_C1.1810.35
141_V309_A1.1810.35
76_Y98_G1.1760.35
162_V241_A1.1690.34
283_G317_T1.1690.34
101_G133_V1.1680.34
316_F360_L1.1670.34
66_G139_I1.1670.34
256_N260_V1.1670.34
207_Y396_S1.1660.34
131_F284_T1.1650.34
93_I287_Y1.1620.34
193_F401_Y1.1580.33
74_Y152_F1.1560.33
351_T355_E1.1550.33
204_I301_D1.1490.33
318_L384_I1.1480.33
53_A330_L1.1440.32
124_L131_F1.1400.32
252_S310_D1.1380.32
85_W136_N1.1310.32
216_V260_V1.1310.32
28_T31_N1.1310.32
97_N130_Q1.1310.32
166_S360_L1.1300.31
38_L62_I1.1300.31
9_L16_L1.1290.31
330_L358_V1.1290.31
246_R385_E1.1260.31
176_D369_Y1.1210.31
171_G251_L1.1210.31
188_I413_G1.1150.30
206_V237_L1.1150.30
55_G166_S1.1140.30
188_I399_V1.1100.30
343_S358_V1.1060.30
100_Q152_F1.1030.30
37_T195_I1.1010.30
54_L137_Y1.0990.29
186_F204_I1.0980.29
35_I74_Y1.0960.29
165_I415_T1.0920.29
77_N108_A1.0910.29
183_Q238_I1.0910.29
31_N152_F1.0840.28
94_E309_A1.0750.28
366_N403_P1.0730.28
136_N400_Y1.0680.27
213_D370_L1.0660.27
13_L21_N1.0650.27
98_G126_N1.0640.27
196_T245_Y1.0570.27
280_R369_Y1.0570.27
90_L260_V1.0550.27
247_R364_S1.0530.26
86_T346_G1.0530.26
86_T350_E1.0500.26
51_Y132_K1.0490.26
138_A278_Y1.0480.26
188_I276_T1.0480.26
28_T251_L1.0480.26
66_G212_R1.0480.26
8_L14_F1.0480.26
131_F252_S1.0470.26
117_Y213_D1.0460.26
167_A186_F1.0460.26
215_A401_Y1.0450.26
313_I357_A1.0410.26
184_V356_K1.0400.26
141_V224_I1.0400.26
403_P410_R1.0390.26
245_Y337_N1.0370.25
21_N345_M1.0330.25
165_I397_I1.0310.25
386_G393_N1.0310.25
40_V249_E1.0300.25
119_N341_E1.0290.25
249_E288_D1.0290.25
198_P203_K1.0290.25
138_A206_V1.0280.25
168_S185_S1.0280.25
54_L367_Y1.0270.25
362_Q409_D1.0240.25
241_A350_E1.0240.25
207_Y384_I1.0230.25
102_T163_V1.0170.24
89_Q403_P1.0170.24
213_D375_G1.0170.24
84_D190_N1.0160.24
328_V358_V1.0160.24
16_L132_K1.0140.24
187_N262_N1.0100.24
181_H240_P1.0070.24
181_H387_N1.0070.24
45_E220_Q1.0070.24
107_F203_K1.0070.24
251_L364_S1.0040.24
183_Q246_R1.0040.24
35_I66_G1.0030.23
13_L89_Q1.0030.23
121_R359_L1.0010.23
8_L36_K1.0010.23
315_H365_Y1.0000.23
245_Y298_R1.0000.23
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  
4r7fA10.93631000.063Contact Map
2qlvB20.2028970.953Contact Map
4aeeA20.2925970.953Contact Map
4aefA20.280796.40.956Contact Map
1z0nA30.202896.30.957Contact Map
2lu3A10.245395.50.959Contact Map
1ac0A10.238294.40.962Contact Map
4cfeB20.224193.90.963Contact Map
2z0bA60.254790.50.966Contact Map
4pyhA10.59271.40.973Contact 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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