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CHMP3

ID: 1506627547 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 222 (220)
Sequences: 1073 (619.3)
Seq/Len: 4.877
Nf(neff/√len): 41.8

HHblits Results: (2016_02)
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: 4.877).

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
70_S73_A2.9301.00
42_E45_K2.6831.00
217_L220_L2.6211.00
50_D54_K2.6131.00
10_K18_E2.5431.00
41_E71_R2.4601.00
214_Q218_A2.2181.00
56_Q59_V1.9761.00
71_R171_E1.8761.00
23_I84_M1.8751.00
41_E45_K1.8211.00
119_K122_E1.8171.00
46_R50_D1.8031.00
11_P14_E1.7201.00
125_A129_E1.6990.99
133_E136_K1.6870.99
40_E43_K1.6690.99
144_L147_T1.6690.99
129_E132_K1.6670.99
57_K61_I1.6420.99
38_Q74_V1.6400.99
158_E162_E1.6260.99
218_A221_R1.6190.99
10_K15_L1.5970.99
38_Q42_E1.5130.99
215_S218_A1.5060.98
37_I73_A1.5010.98
11_P15_L1.4890.98
216_R219_T1.4460.98
145_E149_E1.4360.98
98_L102_G1.4320.98
44_V47_S1.3840.97
87_V127_M1.3790.97
48_V67_M1.3680.97
34_I78_Y1.3520.96
217_L221_R1.3200.96
124_Q128_R1.3110.96
113_A116_S1.2990.95
206_E209_A1.2820.95
94_Q98_L1.2710.94
46_R54_K1.2680.94
165_I169_L1.2540.94
132_K181_P1.2490.94
30_V64_A1.2400.93
19_W22_K1.2290.93
69_R80_S1.2140.92
170_F173_T1.2110.92
216_R221_R1.2070.92
39_R43_K1.1990.92
216_R220_L1.1980.92
2_G6_K1.1950.92
47_S50_D1.1900.91
80_S100_V1.1870.91
5_G16_V1.1830.91
43_K47_S1.1660.90
4_F12_P1.1640.90
117_L138_G1.1630.90
130_L134_M1.1590.90
2_G5_G1.1480.89
213_M216_R1.1450.89
40_E70_S1.1450.89
124_Q162_E1.1340.89
112_K129_E1.1340.89
25_K29_V1.1340.89
42_E46_R1.1320.89
31_D81_K1.1210.88
143_M146_D1.1190.88
34_I74_V1.1180.88
166_D170_F1.1140.87
61_I119_K1.1110.87
134_M164_E1.1030.87
136_K140_I1.1010.87
198_A201_E1.0990.86
175_G178_G1.0960.86
92_K96_A1.0930.86
69_R105_Q1.0930.86
92_K144_L1.0850.86
197_M200_S1.0850.86
48_V60_C1.0770.85
41_E181_P1.0750.85
27_M88_L1.0720.85
168_I171_E1.0700.84
181_P184_V1.0690.84
51_A54_K1.0580.84
204_E207_E1.0520.83
65_K81_K1.0510.83
68_I71_R1.0490.83
102_G106_K1.0470.83
14_E20_S1.0390.82
3_L6_K1.0360.82
40_E73_A1.0350.82
51_A59_V1.0340.82
132_K182_S1.0310.81
38_Q148_F1.0310.81
213_M220_L1.0300.81
51_A163_M1.0290.81
187_A197_M1.0240.81
205_E209_A1.0220.81
61_I163_M1.0200.80
1_M5_G1.0160.80
104_L131_S1.0160.80
26_E134_M1.0150.80
206_E210_L1.0140.80
205_E208_E1.0120.80
97_V107_S1.0110.80
87_V111_M1.0100.79
15_L18_E1.0060.79
111_M127_M1.0040.79
174_A213_M1.0010.79
41_E67_M1.0000.78
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  
3frtA20.63961000.197Contact Map
2gd5A40.72971000.298Contact Map
3eabG60.189298.20.826Contact Map
3frrA10.797395.90.88Contact Map
3um3B10.072191.20.901Contact Map
2xzeQ20.103690.30.903Contact Map
3ggyA20.752389.10.905Contact Map
2v6xB10.166756.10.929Contact Map
4abmA40.3559310.939Contact Map
2luhB10.265828.90.94Contact 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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