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T0827

ID: 1403290367 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 407 (371)
Sequences: 382 (299.8)
Seq/Len: 1.030
Nf(neff/√len): 15.6

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: 1.030).

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
130_V155_L3.6831.00
106_D131_S3.6451.00
198_A202_A2.7461.00
132_E157_K2.2350.98
98_L124_I2.2030.98
135_A150_L2.0910.97
144_P173_A2.0540.96
138_L146_V1.9510.95
87_L101_S1.9330.95
249_Q252_R1.8190.92
15_A26_L1.7720.90
140_E169_A1.7690.90
32_D71_R1.7610.90
130_V135_A1.7390.89
93_V98_L1.7050.88
78_M83_V1.6850.87
153_N156_V1.6720.87
127_R153_N1.6450.86
80_G84_R1.6410.85
129_G155_L1.6400.85
135_A162_G1.6400.85
130_V134_V1.6270.85
113_L124_I1.5980.83
65_R89_D1.5910.83
373_P376_L1.5760.82
241_A252_R1.5430.80
267_V275_N1.5380.80
372_T375_L1.5290.79
136_D162_G1.4970.77
62_V93_V1.4860.77
79_P127_R1.4840.76
158_L162_G1.4790.76
91_L120_H1.4710.76
150_L258_S1.4600.75
101_S153_N1.4200.72
103_K202_A1.3870.69
64_E259_P1.3700.68
89_D93_V1.3680.68
135_A158_L1.3680.68
56_M79_P1.3630.67
101_S127_R1.3520.66
376_L379_I1.3340.65
10_F13_P1.3230.64
124_I137_A1.3190.64
11_E33_V1.3170.63
375_L379_I1.3110.63
348_Y351_I1.3080.63
158_L186_L1.2850.61
99_V131_S1.2820.60
258_S281_E1.2770.60
79_P153_N1.2710.59
99_V126_Q1.2690.59
11_E14_E1.2680.59
260_F318_C1.2670.59
340_N346_T1.2640.59
260_F267_V1.2620.59
14_E29_R1.2520.58
151_L176_L1.2450.57
372_T376_L1.2420.57
102_E313_G1.2420.57
148_E152_R1.2340.56
11_E15_A1.2330.56
87_L153_N1.2310.56
176_L303_E1.2310.56
121_R141_V1.2300.56
7_T14_E1.2280.55
14_E26_L1.2260.55
355_R362_Y1.2180.55
27_L31_A1.2170.54
27_L32_D1.2170.54
90_E116_A1.2110.54
98_L155_L1.2080.54
8_P11_E1.2070.53
122_R146_V1.2060.53
305_L308_L1.2030.53
124_I158_L1.2030.53
125_A153_N1.2030.53
110_I131_S1.2030.53
122_R138_L1.1950.52
159_S162_G1.1940.52
321_Q342_E1.1900.52
120_H170_T1.1840.51
113_L155_L1.1730.50
59_D64_E1.1700.50
147_I151_L1.1700.50
25_T28_K1.1690.50
333_R337_T1.1690.50
343_R346_T1.1660.50
113_L121_R1.1660.50
41_I296_I1.1660.50
30_L162_G1.1640.49
110_I150_L1.1580.49
56_M256_A1.1580.49
79_P101_S1.1530.48
46_R186_L1.1510.48
125_A191_A1.1510.48
94_A117_T1.1440.48
241_A249_Q1.1430.48
120_H146_V1.1400.47
37_P41_I1.1370.47
73_A101_S1.1370.47
69_A131_S1.1360.47
151_L304_P1.1340.47
87_L97_L1.1340.47
97_L239_R1.1330.47
23_R30_L1.1300.46
94_A127_R1.1290.46
78_M101_S1.1240.46
40_R82_L1.1180.45
136_D141_V1.1170.45
125_A137_A1.1140.45
65_R186_L1.1040.44
296_I304_P1.1020.44
110_I121_R1.1010.44
41_I49_T1.0980.43
187_R259_P1.0970.43
134_V137_A1.0970.43
103_K274_F1.0920.43
357_Q361_R1.0910.43
358_T362_Y1.0880.42
94_A153_N1.0840.42
362_Y366_S1.0830.42
241_A245_I1.0820.42
69_A286_S1.0770.41
203_R263_L1.0760.41
188_P232_G1.0760.41
61_N248_R1.0740.41
56_M180_L1.0740.41
98_L260_F1.0740.41
179_L198_A1.0730.41
108_D125_A1.0690.41
136_D159_S1.0670.41
246_E284_Y1.0660.40
357_Q364_N1.0620.40
93_V110_I1.0600.40
202_A267_V1.0600.40
101_S124_I1.0600.40
305_L357_Q1.0600.40
134_V314_L1.0570.40
111_S114_Y1.0570.40
228_A282_I1.0570.40
146_V307_I1.0530.39
131_S135_A1.0530.39
141_V162_G1.0510.39
260_F275_N1.0510.39
126_Q149_T1.0490.39
14_E17_R1.0480.39
373_P379_I1.0470.39
143_E337_T1.0470.39
260_F263_L1.0470.39
162_G198_A1.0440.38
60_A125_A1.0430.38
362_Y365_W1.0430.38
148_E151_L1.0420.38
57_L181_L1.0420.38
340_N359_V1.0400.38
214_R220_A1.0370.38
341_L345_L1.0340.38
252_R258_S1.0340.38
267_V319_V1.0330.38
172_D326_L1.0310.37
79_P314_L1.0290.37
193_V286_S1.0280.37
353_V357_Q1.0260.37
147_I169_A1.0240.37
257_K288_L1.0230.37
252_R256_A1.0200.36
93_V198_A1.0200.36
138_L150_L1.0200.36
87_L156_V1.0160.36
158_L322_L1.0150.36
21_R297_F1.0140.36
79_P94_A1.0130.36
373_P377_K1.0110.36
351_I357_Q1.0110.36
242_L245_I1.0090.35
354_D361_R1.0040.35
69_A110_I1.0030.35
72_L198_A1.0010.35
355_R364_N1.0010.35
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: (14Jun14)
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  
1lrvA10.4816980.892Contact Map
3ltmA20.427594.80.925Contact Map
4l7mA20.461994.50.926Contact Map
1oyzA10.4447940.928Contact Map
4g3aA20.503793.60.929Contact Map
4lacA10.253192.30.932Contact Map
2jdqA20.395692.30.932Contact Map
3ltjA10.442391.70.933Contact Map
4db6A10.385790.70.935Contact Map
4jw3C20.22690.50.935Contact 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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