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scEMC4

ID: 1504851107 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 190 (177)
Sequences: 358 (251.5)
Seq/Len: 2.023
Nf(neff/√len): 18.9

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: 2.023).

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
87_N109_L2.4191.00
72_K75_Q2.0810.99
89_F93_M1.9980.99
142_F146_V1.9420.99
101_I165_I1.9360.99
94_S108_M1.9030.98
84_I151_L1.7890.97
90_M148_Q1.7600.97
121_R141_M1.7370.97
104_M108_M1.7340.97
99_Q155_G1.6460.95
20_E23_N1.6000.94
123_A144_Y1.5750.94
85_P109_L1.5430.93
163_G166_P1.5400.93
165_I170_G1.5310.92
32_S72_K1.5200.92
109_L151_L1.4950.91
71_Q105_T1.4880.91
85_P173_L1.4740.90
85_P92_Y1.4710.90
91_S101_I1.4520.89
157_R160_N1.4470.89
87_N112_G1.4290.88
87_N115_K1.4140.88
119_S144_Y1.4040.87
85_P162_M1.3490.84
106_A140_A1.3250.83
98_L159_L1.2820.80
112_G115_K1.2620.78
136_Q150_V1.2550.78
87_N108_M1.2520.77
143_M146_V1.2490.77
76_I79_Q1.2390.76
85_P99_Q1.2360.76
166_P171_D1.2310.76
149_G153_Y1.2110.74
164_L170_G1.2090.74
158_K172_W1.2070.74
124_F141_M1.1990.73
93_M103_I1.1970.73
99_Q102_P1.1930.73
75_Q175_W1.1920.72
81_A109_L1.1850.72
109_L155_G1.1830.72
81_A87_N1.1810.71
174_P183_N1.1800.71
96_T161_S1.1610.70
85_P108_M1.1560.69
73_A127_V1.1520.69
160_N170_G1.1500.69
137_V140_A1.1480.68
27_S40_S1.1460.68
106_A152_M1.1440.68
142_F145_I1.1410.68
110_L156_Y1.1380.67
91_S117_I1.1330.67
55_Q154_I1.1230.66
64_Q72_K1.1160.65
94_S144_Y1.1150.65
148_Q151_L1.1130.65
169_K176_E1.0990.63
101_I167_N1.0920.63
103_I181_Y1.0900.62
13_L103_I1.0870.62
108_M112_G1.0870.62
91_S104_M1.0810.61
7_Y92_Y1.0660.60
154_I158_K1.0650.60
164_L174_P1.0610.59
92_Y109_L1.0590.59
87_N127_V1.0580.59
99_Q148_Q1.0490.58
102_P127_V1.0480.58
168_A179_A1.0450.58
106_A159_L1.0430.57
98_L156_Y1.0420.57
155_G158_K1.0410.57
87_N102_P1.0320.56
162_M172_W1.0290.56
114_I119_S1.0220.55
108_M113_P1.0210.55
98_L175_W1.0190.55
68_L85_P1.0140.54
163_G171_D1.0110.54
63_N142_F1.0080.54
69_Q99_Q1.0050.53
113_P173_L1.0040.53
94_S99_Q1.0010.53
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  
4ardA20.30532.80.97Contact Map
2v4xA10.35262.60.971Contact Map
1em9A20.35262.60.971Contact Map
2mc7A10.15791.50.974Contact Map
3tirA10.33161.50.974Contact Map
2kgfA10.35791.40.975Contact Map
1jb0K10.12111.40.975Contact Map
1g92A10.12111.30.975Contact Map
2fq3A10.11051.20.976Contact Map
4rsxA10.342110.977Contact 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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