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PilN

ID: 1513362476 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 180 (170)
Sequences: 1813 (1486.5)
Seq/Len: 10.665
Nf(neff/√len): 114.0

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: 10.665).

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
65_K68_E3.6711.00
118_Q142_E2.7751.00
109_V153_K2.6831.00
119_V137_S2.3451.00
78_Q82_E2.2771.00
74_Q77_E2.1451.00
135_G174_F2.0351.00
70_K73_A1.8641.00
55_L59_K1.8131.00
109_V113_N1.6421.00
43_S47_S1.6201.00
91_E95_S1.6081.00
83_N87_K1.6001.00
108_D112_S1.5871.00
57_K60_T1.5861.00
150_L176_A1.5391.00
107_L110_V1.5201.00
68_E72_V1.5171.00
118_Q138_A1.4631.00
81_K84_E1.4491.00
84_E88_R1.4481.00
109_V112_S1.4421.00
60_T63_E1.4151.00
79_L83_N1.4070.99
84_E87_K1.3900.99
47_S51_Q1.3850.99
75_K78_Q1.3730.99
80_E84_E1.3690.99
71_M74_Q1.3620.99
147_L162_I1.3460.99
61_T65_K1.3420.99
113_N153_K1.3280.99
104_L108_D1.3020.99
44_G48_M1.2920.99
60_T64_T1.2910.99
78_Q81_K1.2910.99
90_I94_L1.2760.99
40_V44_G1.2660.99
6_N9_P1.2540.99
109_V156_I1.2410.98
114_L146_Y1.2340.98
140_M162_I1.2290.98
74_Q78_Q1.2250.98
53_K56_I1.2210.98
85_E88_R1.1990.98
81_K85_E1.1950.98
146_Y150_L1.1910.98
50_K53_K1.1870.98
85_E89_R1.1760.98
123_L134_E1.1650.97
42_L46_I1.1640.97
140_M165_V1.1630.97
42_L45_I1.1400.97
103_I126_I1.1360.97
56_I60_T1.1360.97
32_P35_I1.1290.97
119_V142_E1.1230.97
67_K70_K1.1190.96
55_L58_E1.1170.96
121_F146_Y1.1160.96
63_E67_K1.1140.96
126_I131_T1.1020.96
25_R29_L1.0920.96
147_L151_E1.0920.96
70_K143_V1.0910.96
87_K90_I1.0870.96
104_L137_S1.0820.96
96_L100_R1.0810.95
61_T64_T1.0500.94
134_E175_Q1.0490.94
84_E112_S1.0460.94
95_S114_L1.0460.94
105_K155_D1.0410.94
120_Y136_I1.0390.94
143_V167_K1.0340.94
140_M144_G1.0310.94
29_L64_T1.0240.93
120_Y138_A1.0230.93
84_E95_S1.0160.93
140_M147_L1.0130.93
70_K74_Q1.0050.93
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  
4bhqA20.438999.60.436Contact Map
2rjzA20.6595.20.788Contact Map
2w7vA20.433387.30.831Contact Map
2dq0A20.922254.90.87Contact Map
3qneA10.883345.20.877Contact Map
2dq3A20.922235.20.885Contact Map
3lssA20.922227.70.891Contact Map
2j5uA20.644416.30.902Contact Map
4bgnA20.316712.70.906Contact Map
4c4vA10.338911.30.909Contact 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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