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av1_cp

ID: 1513917391 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 50% gaps before running GREMLIN.
Length: 256 (254)
Sequences: 259 (72.7)
Seq/Len: 1.020
Nf(neff/√len): 4.6

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: 1.020).

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 > 50% 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
147_D154_E2.0210.96
146_V154_E1.9430.95
138_F180_R1.9210.94
213_Q228_M1.8030.91
153_G158_M1.7670.90
207_N210_V1.7210.89
185_T194_K1.5970.83
147_D151_D1.4960.77
151_D155_V1.4860.76
6_A10_I1.4510.74
181_K185_T1.4160.71
138_F148_K1.4100.71
232_A236_A1.4090.71
1_M4_R1.4060.70
8_I12_T1.4030.70
83_I88_K1.3830.69
180_R185_T1.3750.68
78_E92_I1.3690.68
29_S32_A1.3650.67
5_A8_I1.3620.67
48_P52_K1.3600.67
27_Y30_R1.3570.67
17_V36_V1.3490.66
119_K132_T1.3460.66
151_D154_E1.3450.66
240_V243_T1.3360.65
101_L172_H1.3330.65
13_P18_R1.3230.64
138_F159_F1.3220.64
238_N241_Y1.3200.63
52_K56_Y1.3170.63
68_C75_Q1.3090.62
18_R26_P1.3040.62
247_R252_D1.2900.61
13_P25_S1.2880.61
18_R24_G1.2750.59
247_R251_Y1.2750.59
14_A30_R1.2690.59
130_N133_N1.2510.57
68_C71_P1.2500.57
44_W47_R1.2370.56
201_K208_Y1.2300.55
249_Y253_S1.2210.55
236_A242_A1.2060.53
138_F172_H1.2010.53
232_A237_S1.1980.52
81_H90_M1.1940.52
224_E227_L1.1900.52
171_V228_M1.1890.52
7_D11_S1.1790.51
234_T242_A1.1760.50
3_K11_S1.1740.50
219_Y225_N1.1730.50
71_P75_Q1.1650.49
174_D177_Q1.1600.49
36_V61_S1.1600.49
243_T250_F1.1570.49
2_S8_I1.1500.48
232_A242_A1.1500.48
171_V213_Q1.1480.48
237_S240_V1.1460.48
55_M58_M1.1400.47
101_L180_R1.1360.47
5_A10_I1.1350.47
55_M101_L1.1340.46
47_R52_K1.1310.46
141_R144_R1.1290.46
163_P166_A1.1280.46
13_P26_P1.1270.46
103_H107_K1.1220.45
129_K190_Q1.1170.45
243_T247_R1.1170.45
18_R25_S1.1110.44
154_E171_V1.1080.44
120_I132_T1.1080.44
232_A235_H1.1070.44
187_T192_A1.1070.44
46_N52_K1.1020.43
4_R11_S1.0990.43
46_N49_M1.0970.43
1_M11_S1.0940.43
102_T107_K1.0940.43
15_S18_R1.0900.42
80_R153_G1.0870.42
14_A29_S1.0840.42
187_T197_A1.0840.42
247_R250_F1.0830.42
27_Y55_M1.0830.42
225_N240_V1.0800.41
138_F203_V1.0780.41
243_T252_D1.0760.41
249_Y252_D1.0760.41
5_A9_V1.0740.41
2_S6_A1.0710.41
79_S90_M1.0700.41
128_T190_Q1.0700.41
236_A240_V1.0680.40
146_V171_V1.0670.40
7_D10_I1.0640.40
81_H191_Y1.0640.40
234_T237_S1.0630.40
150_Q179_L1.0620.40
75_Q94_D1.0610.40
116_V172_H1.0610.40
48_P56_Y1.0610.40
28_T45_T1.0590.40
78_E82_D1.0590.40
243_T249_Y1.0590.40
25_S35_I1.0580.39
17_V30_R1.0560.39
10_I17_V1.0520.39
147_D176_Y1.0510.39
186_V195_E1.0500.39
139_L153_G1.0470.38
28_T42_Q1.0460.38
187_T190_Q1.0420.38
129_K192_A1.0400.38
77_F92_I1.0400.38
14_A32_A1.0380.38
117_L153_G1.0370.38
78_E181_K1.0350.37
1_M6_A1.0340.37
56_Y63_D1.0340.37
232_A240_V1.0320.37
240_V250_F1.0290.37
7_D12_T1.0280.37
16_K30_R1.0260.37
13_P24_G1.0250.37
16_K29_S1.0240.36
79_S86_I1.0240.36
237_S242_A1.0220.36
225_N229_L1.0160.36
174_D178_V1.0110.35
177_Q194_K1.0100.35
222_H228_M1.0090.35
2_S5_A1.0060.35
92_I114_V1.0060.35
238_N243_T1.0050.35
103_H108_G1.0040.35
72_C75_Q1.0020.35
111_V114_V1.0010.35
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: (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  
3zqxA10.19145.60.985Contact Map
2knpA10.1255.30.985Contact Map
2b4wA10.19923.90.986Contact Map
3zucA10.20313.70.987Contact Map
2dw0A20.21483.60.987Contact Map
3k7nA10.22663.30.987Contact Map
3k7lA10.24613.20.987Contact Map
1a9xA40.23442.90.987Contact Map
2plxB10.10162.80.987Contact Map
2ddiA10.12892.80.987Contact 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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