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T0814 -force run

ID: 1402517792 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 424 (412)
Sequences: 232 (211)
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_E6.0681.00
82_N86_T4.0641.00
160_E410_R3.5181.00
277_D369_Y3.0270.99
402_R409_D2.6850.98
167_A397_I2.6480.98
186_F397_I2.4530.97
134_S160_E2.3920.96
290_D392_Q2.2360.94
345_M356_K2.2330.94
74_Y151_I2.0800.90
327_S344_K2.0230.89
157_S411_L1.9320.86
195_I202_L1.8950.84
396_S414_V1.8940.84
66_G74_Y1.8840.84
82_N408_Y1.8420.82
211_R214_N1.7870.79
141_V152_F1.7650.78
112_G345_M1.7600.77
271_N315_H1.7540.77
329_Y343_S1.7340.76
244_E392_Q1.7010.74
40_V154_A1.6980.74
398_Y411_L1.6660.72
80_H88_S1.6550.71
40_V62_I1.6410.70
260_V274_L1.6170.68
244_E292_D1.5760.66
340_D343_S1.5650.65
157_S398_Y1.5640.65
40_V60_I1.5490.64
203_K402_R1.5370.63
94_E407_R1.5150.61
403_P406_A1.5150.61
88_S198_P1.5100.61
163_V193_F1.5050.60
151_I165_I1.5030.60
202_L229_I1.4970.60
297_I326_G1.4930.59
219_L237_L1.4680.57
244_E290_D1.4680.57
245_Y344_K1.4520.56
202_L399_V1.4340.55
165_I399_V1.4280.54
134_S184_V1.4260.54
62_I154_A1.4250.54
63_N306_D1.3800.50
241_A389_Y1.3780.50
14_F19_G1.3740.50
92_P100_Q1.3670.49
253_N312_Y1.3480.48
329_Y344_K1.3340.47
207_Y212_R1.3310.47
133_V310_D1.3310.47
335_F343_S1.3150.45
280_R385_E1.3150.45
9_L16_L1.3140.45
276_T317_T1.3080.45
292_D392_Q1.3020.44
122_L139_I1.2970.44
176_D181_H1.2890.43
38_L62_I1.2640.41
270_Y389_Y1.2520.40
207_Y398_Y1.2510.40
171_G178_N1.2500.40
82_N409_D1.2460.40
153_T236_N1.2430.40
79_V140_Q1.2400.39
252_S310_D1.2350.39
93_I287_Y1.2350.39
213_D399_V1.2280.39
360_L365_Y1.2270.38
171_G251_L1.2250.38
76_Y126_N1.2220.38
66_G139_I1.2130.37
35_I344_K1.2010.37
195_I201_D1.2000.36
141_V309_A1.1990.36
182_Q393_N1.1980.36
94_E309_A1.1870.36
256_N260_V1.1870.36
250_F312_Y1.1820.35
216_V260_V1.1810.35
206_V347_Y1.1800.35
76_Y98_G1.1790.35
52_I60_I1.1770.35
315_H365_Y1.1750.35
95_Y158_V1.1710.34
78_V180_S1.1670.34
193_F401_Y1.1640.34
351_T355_E1.1640.34
53_A330_L1.1590.34
176_D369_Y1.1530.33
106_D121_R1.1510.33
299_C302_C1.1480.33
160_E345_M1.1430.32
10_F13_L1.1430.32
74_Y152_F1.1380.32
162_V241_A1.1380.32
28_T31_N1.1380.32
207_Y396_S1.1380.32
204_I301_D1.1350.32
330_L358_V1.1340.32
37_T195_I1.1330.32
183_Q238_I1.1290.31
247_R364_S1.1250.31
166_S360_L1.1230.31
188_I399_V1.1160.31
318_L384_I1.1120.30
131_F284_T1.1120.30
66_G212_R1.1100.30
316_F360_L1.1080.30
246_R385_E1.1080.30
95_Y345_M1.1070.30
322_P330_L1.1060.30
77_N108_A1.1040.30
11_M51_Y1.1020.30
343_S358_V1.1010.30
157_S407_R1.0930.29
198_P203_K1.0900.29
165_I415_T1.0880.29
124_L131_F1.0860.29
188_I413_G1.0850.28
127_D188_I1.0850.28
97_N130_Q1.0840.28
101_G133_V1.0830.28
117_Y213_D1.0830.28
98_G126_N1.0800.28
40_V249_E1.0780.28
131_F252_S1.0750.28
366_N403_P1.0740.28
167_A186_F1.0710.28
38_L251_L1.0710.28
31_N152_F1.0710.28
328_V358_V1.0690.27
213_D370_L1.0660.27
215_A401_Y1.0630.27
188_I276_T1.0630.27
251_L364_S1.0630.27
184_V356_K1.0580.27
249_E288_D1.0580.27
82_N234_N1.0570.27
76_Y287_Y1.0570.27
212_R215_A1.0550.27
28_T251_L1.0510.26
196_T245_Y1.0500.26
55_G166_S1.0480.26
165_I397_I1.0440.26
107_F203_K1.0430.26
215_A218_D1.0410.26
245_Y337_N1.0390.26
52_I365_Y1.0350.25
45_E220_Q1.0340.25
37_T376_S1.0310.25
206_V237_L1.0270.25
292_D336_N1.0240.25
23_Q330_L1.0230.25
181_H387_N1.0220.25
35_I74_Y1.0220.25
86_T346_G1.0200.24
8_L22_A1.0190.24
280_R369_Y1.0180.24
138_A206_V1.0150.24
245_Y298_R1.0150.24
134_S345_M1.0140.24
403_P410_R1.0120.24
119_N341_E1.0120.24
38_L245_Y1.0110.24
213_D375_G1.0070.24
150_I260_V1.0070.24
186_F204_I1.0070.24
84_D190_N1.0070.24
89_Q403_P1.0070.24
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: (12Jul14)
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  
2qlvB20.2028970.953Contact Map
4aefA20.280796.20.957Contact Map
2lu3A10.245395.90.958Contact Map
4aeeA20.275995.40.96Contact Map
1z0nA30.205294.50.962Contact Map
1ac0A10.238294.30.962Contact Map
4cfeB20.224194.10.962Contact Map
2z0bA60.252488.60.968Contact Map
1m7xA40.294877.90.972Contact Map
4pyhA10.580271.90.973Contact 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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