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ID: 1507663569 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 201 (190)
Sequences: 890 (661.4)
Seq/Len: 4.684
Nf(neff/√len): 48.0

Jackhmmer Results: (2016_04)
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: 4.684).

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
89_M116_A3.9001.00
96_A116_A2.9991.00
73_L88_T2.4751.00
96_A113_T2.4671.00
28_G67_G2.3331.00
34_S102_K2.2811.00
156_L182_G2.2381.00
43_R107_E2.1161.00
35_G63_A1.9111.00
102_K108_E1.8751.00
25_F71_L1.8281.00
61_F188_G1.8111.00
89_M120_A1.7831.00
32_L67_G1.7341.00
20_L77_L1.7311.00
93_L116_A1.7170.99
85_W120_A1.6910.99
75_Q141_Y1.6460.99
66_I91_L1.6420.99
62_G98_L1.5580.99
17_A80_R1.5240.98
146_V150_G1.5180.98
56_I175_L1.4870.98
34_S108_E1.4710.98
117_V121_I1.4580.98
77_L85_W1.4290.97
27_S112_M1.3910.97
76_G84_A1.3880.97
40_I58_A1.3760.97
20_L122_F1.3760.97
105_D108_E1.3730.97
90_V94_V1.3540.96
192_L196_V1.3280.96
88_T92_L1.3200.95
81_L128_R1.3160.95
25_F74_A1.2880.95
35_G64_S1.2870.94
102_K105_D1.2800.94
82_S131_R1.2780.94
37_T108_E1.2730.94
116_A120_A1.2550.93
65_L74_A1.2380.93
53_H57_D1.2370.93
24_V115_T1.2090.92
92_L95_G1.2090.92
59_S103_G1.2060.92
21_A78_R1.1950.91
187_L190_A1.1840.91
25_F148_V1.1780.90
173_F180_P1.1670.90
181_R184_R1.1440.88
27_S95_G1.1440.88
62_G94_V1.1340.88
74_A92_L1.1250.87
103_G108_E1.1200.87
106_W110_S1.1170.87
142_L195_I1.1150.87
35_G43_R1.1130.87
110_S114_M1.1060.86
43_R102_K1.1020.86
24_V77_L1.0950.85
158_F165_Y1.0880.85
77_L119_L1.0880.85
34_S105_D1.0770.84
148_V194_V1.0720.84
63_A108_E1.0700.84
79_R87_L1.0680.83
188_G193_L1.0680.83
188_G192_L1.0670.83
19_V147_C1.0550.82
105_D109_A1.0530.82
17_A57_D1.0510.82
32_L36_A1.0490.82
62_G65_L1.0440.81
68_V88_T1.0430.81
143_V190_A1.0390.81
85_W198_L1.0360.81
159_A176_D1.0310.80
26_L29_V1.0280.80
47_I52_P1.0250.80
95_G105_D1.0100.78
43_R105_D1.0100.78
85_W89_M1.0090.78
34_S43_R1.0070.78
27_S44_L1.0060.78
33_F61_F1.0040.78
81_L85_W1.0030.78
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  
3qsvA40.20916.70.933Contact Map
3wajA10.85575.30.947Contact Map
1lnqA80.31843.90.95Contact Map
3nd0A20.32843.60.951Contact Map
4o6yA20.71643.60.951Contact Map
2q67A20.42792.60.954Contact Map
3kmpA20.21392.40.955Contact Map
3vouA20.42792.30.956Contact Map
4eneA20.3932.20.956Contact Map
4ytpC101.90.958Contact 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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