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sfrp1

ID: 1501519635 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 124 (119)
Sequences: 857 (557.3)
Seq/Len: 7.202
Nf(neff/√len): 51.1

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: 7.202).

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
22_Y25_M2.5061.00
14_L67_A2.4651.00
8_V36_M2.1901.00
7_C17_C1.9161.00
55_H85_V1.7711.00
89_C106_C1.7601.00
19_N59_Q1.6681.00
93_M98_F1.6621.00
9_D24_K1.6081.00
79_R111_E1.6061.00
101_P104_L1.5711.00
57_G84_A1.5511.00
16_L50_L1.5070.99
29_N33_H1.4610.99
79_R83_E1.4510.99
101_P106_C1.4500.99
83_E86_R1.4330.99
84_A88_S1.3980.99
90_E94_Q1.3860.99
82_C89_C1.3790.99
63_C70_C1.3770.99
105_K108_K1.3760.99
54_C70_C1.3740.99
80_W111_E1.3700.99
119_T123_A1.3480.98
82_C106_C1.3470.98
28_P33_H1.3320.98
114_V120_P1.3130.98
76_Y114_V1.3040.98
63_C82_C1.2820.98
69_V118_M1.2540.97
55_H88_S1.2280.97
62_L66_F1.2200.96
68_P78_C1.2170.96
7_C22_Y1.2120.96
69_V81_L1.1810.95
120_P123_A1.1740.95
10_I22_Y1.1710.95
86_R100_W1.1630.95
14_L39_V1.1580.95
52_K96_F1.1490.95
27_L39_V1.1440.94
42_Q47_V1.1420.94
85_V88_S1.1170.93
17_C22_Y1.1140.93
100_W106_C1.1000.93
118_M123_A1.0980.93
25_M36_M1.0960.93
63_C68_P1.0880.92
10_I18_H1.0810.92
52_K92_V1.0710.91
56_A113_D1.0700.91
28_P31_L1.0670.91
75_I78_C1.0640.91
65_L109_F1.0610.91
70_C78_C1.0570.91
113_D119_T1.0520.90
63_C89_C1.0490.90
7_C10_I1.0450.90
113_D122_N1.0420.90
60_V81_L1.0300.89
50_L76_Y1.0290.89
65_L104_L1.0270.89
78_C82_C1.0260.89
46_W61_F1.0120.88
77_P118_M1.0090.88
118_M122_N1.0080.88
47_V51_N1.0070.88
88_S95_F1.0040.87
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  
1ijyA20.92741000.04Contact Map
5bpbA401000.041Contact Map
1ijxA60.92741000.052Contact Map
2mahA10.8791000.139Contact Map
4c7aA20.8791000.161Contact Map
3hklA20.951697.40.764Contact Map
3odnA10.895235.20.898Contact Map
4ywtA4034.40.898Contact Map
4x86B10.1292.60.94Contact Map
2nx7A10.225810.952Contact 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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