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T0827

ID: 1403288143 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 407 (365)
Sequences: 365 (294)
Seq/Len: 1.000
Nf(neff/√len): 15.4

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: 1.000).

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_L4.2961.00
106_D131_S3.8001.00
198_A202_A2.5360.99
144_P173_A2.3450.99
93_V98_L2.3440.99
132_E157_K2.2600.98
98_L124_I2.2020.98
135_A150_L1.9040.94
32_D71_R1.8920.93
62_V93_V1.7990.91
255_I260_F1.7820.90
130_V135_A1.7780.90
138_L146_V1.7710.90
15_A26_L1.7630.90
136_D162_G1.7540.89
80_G84_R1.7480.89
135_A162_G1.7310.89
129_G155_L1.6960.87
140_E169_A1.6790.86
65_R89_D1.6600.86
251_N260_F1.6450.85
78_M83_V1.5860.82
130_V134_V1.5520.80
151_L176_L1.5450.80
259_P262_S1.5350.79
270_G278_I1.5230.78
87_L101_S1.5170.78
135_A158_L1.5170.78
321_Q342_E1.5070.77
362_Y365_W1.4930.76
113_L124_I1.4910.76
259_P288_L1.4850.76
14_E29_R1.4810.75
113_L155_L1.4630.74
305_L308_L1.4580.74
99_V126_Q1.4470.73
158_L162_G1.4320.72
89_D93_V1.4180.71
93_V110_I1.4140.71
91_L120_H1.4110.70
153_N156_V1.3860.68
110_I131_S1.3720.67
124_I137_A1.3720.67
98_L155_L1.3710.67
30_L113_L1.3630.66
176_L303_E1.3220.63
87_L97_L1.3200.63
59_D64_E1.3110.62
335_G340_N1.3030.61
251_N258_S1.2990.61
254_A281_E1.2940.61
93_V261_N1.2900.60
202_A206_I1.2860.60
41_I296_I1.2810.59
83_V101_S1.2760.59
90_E116_A1.2740.59
34_V356_A1.2720.59
136_D141_V1.2630.58
340_N346_T1.2620.58
23_R30_L1.2550.57
138_L353_V1.2530.57
244_F251_N1.2520.57
358_T362_Y1.2510.57
195_F199_D1.2460.56
136_D206_I1.2450.56
27_L31_A1.2430.56
25_T283_S1.2380.55
110_I121_R1.2360.55
146_V307_I1.2250.54
21_R297_F1.2230.54
124_I158_L1.2210.54
180_L266_A1.2180.54
270_G319_V1.2150.53
340_N345_L1.2140.53
121_R141_V1.2130.53
256_A259_P1.2130.53
98_L146_V1.2110.53
103_K202_A1.2090.53
98_L262_S1.2090.53
69_A309_C1.2050.52
122_R138_L1.2010.52
53_L146_V1.1970.52
266_A294_A1.1950.52
122_R146_V1.1920.51
41_I49_T1.1920.51
14_E26_L1.1870.51
69_A255_I1.1840.50
364_N367_L1.1810.50
158_L322_L1.1660.49
151_L166_I1.1650.49
93_V326_L1.1650.49
348_Y351_I1.1610.48
125_A364_N1.1580.48
362_Y366_S1.1570.48
97_L281_E1.1510.47
14_E17_R1.1500.47
202_A278_I1.1490.47
151_L304_P1.1470.47
37_P41_I1.1450.47
159_S162_G1.1450.47
94_A117_T1.1440.47
268_A305_L1.1430.47
140_E171_R1.1250.45
76_N103_K1.1220.45
97_L101_S1.1210.45
150_L270_G1.1170.44
66_E92_P1.1170.44
145_A286_S1.1160.44
252_R256_A1.1160.44
148_E151_L1.1110.44
27_L32_D1.1100.44
186_L283_S1.1070.43
43_A138_L1.1040.43
340_N343_R1.1040.43
177_I202_A1.0970.42
114_Y158_L1.0960.42
178_P282_I1.0940.42
113_L141_V1.0920.42
113_L121_R1.0880.42
355_R362_Y1.0850.41
82_L285_L1.0850.41
98_L123_L1.0830.41
357_Q361_R1.0820.41
61_N116_A1.0780.41
179_L198_A1.0770.41
27_L64_E1.0760.41
203_R293_G1.0760.41
98_L310_K1.0700.40
104_L283_S1.0700.40
120_H146_V1.0690.40
286_S293_G1.0690.40
111_S114_Y1.0680.40
35_C301_G1.0680.40
57_L223_D1.0660.40
166_I224_V1.0650.40
138_L150_L1.0650.40
24_S32_D1.0640.40
104_L155_L1.0570.39
105_S312_T1.0560.39
72_L198_A1.0550.39
25_T28_K1.0530.39
11_E31_A1.0530.39
341_L345_L1.0530.39
14_E18_A1.0520.38
64_E186_L1.0500.38
353_V357_Q1.0490.38
258_S281_E1.0490.38
53_L68_V1.0490.38
150_L158_L1.0470.38
69_A293_G1.0460.38
141_V162_G1.0450.38
268_A285_L1.0430.38
117_T159_S1.0380.37
69_A236_P1.0360.37
118_T143_E1.0360.37
130_V150_L1.0330.37
101_S124_I1.0330.37
143_E155_L1.0310.37
148_E152_R1.0280.36
69_A178_P1.0280.36
61_N149_T1.0250.36
158_L186_L1.0220.36
40_R82_L1.0220.36
147_I173_A1.0210.36
52_L309_C1.0190.36
102_E313_G1.0160.35
120_H170_T1.0130.35
69_A131_S1.0130.35
93_V96_A1.0110.35
64_E261_N1.0070.35
121_R278_I1.0050.34
354_D357_Q1.0040.34
151_L266_A1.0000.34
46_R186_L1.0000.34
18_A56_M1.0000.34
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  
1lrvA10.363690.60.944Contact Map
2jdqA20.412837.30.964Contact Map
4lacA10.253136.70.964Contact Map
3ltmA20.4335.10.964Contact Map
1oyzA10.439833.90.965Contact Map
4g3aA20.530729.10.966Contact Map
3ltjA10.442326.50.967Contact Map
1b3uA20.184325.50.967Contact Map
4db6A10.292422.20.968Contact Map
1te4A10.25820.60.968Contact 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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