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4pgr

ID: 1500382148 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 207 (205)
Sequences: 3304 (1976.5)
Seq/Len: 16.117
Nf(neff/√len): 138.0

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: 16.117).

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
155_G197_N3.2631.00
12_L167_L3.2161.00
107_G167_L2.5951.00
121_W165_Y2.5941.00
18_T65_V2.3101.00
98_S202_F2.2501.00
156_T194_L2.1881.00
12_L107_G2.1651.00
44_E72_S2.1321.00
135_G151_Y2.0541.00
153_V201_F2.0511.00
80_V92_V2.0371.00
105_V129_L2.0191.00
166_D190_D2.0071.00
83_Y203_G1.9461.00
106_L160_S1.8931.00
163_I194_L1.8671.00
22_A188_Y1.8491.00
124_L161_L1.8451.00
42_I46_A1.8331.00
95_A198_L1.7911.00
196_I200_R1.7551.00
124_L165_Y1.7411.00
95_A201_F1.7291.00
46_A50_L1.7101.00
50_L54_M1.6781.00
131_L155_G1.6771.00
16_V104_A1.6651.00
38_L42_I1.6511.00
125_L129_L1.6441.00
166_D169_Q1.6421.00
154_I158_V1.6291.00
189_L193_N1.5951.00
108_T112_K1.5951.00
107_G111_A1.5881.00
23_T97_G1.5491.00
101_V133_V1.5381.00
153_V157_I1.5251.00
146_A150_A1.4861.00
137_F141_S1.4551.00
97_G101_V1.4421.00
187_L190_D1.4321.00
160_S194_L1.4131.00
149_M201_F1.4101.00
117_L164_L1.3980.99
63_A67_T1.3960.99
169_Q186_S1.3910.99
166_D189_L1.3750.99
44_E75_T1.3610.99
150_A154_I1.3360.99
113_M117_L1.3320.99
60_V64_F1.3300.99
131_L158_V1.3280.99
110_G168_N1.3260.99
95_A98_S1.3070.99
148_M200_R1.3050.99
98_S198_L1.2910.99
62_Y66_Y1.2880.99
113_M168_N1.2840.99
25_G70_F1.2730.99
134_V151_Y1.2650.99
68_F72_S1.2640.99
109_I113_M1.2610.99
109_I115_K1.2580.99
169_Q190_D1.2530.99
128_V132_A1.2530.99
157_I161_L1.2410.98
10_R180_I1.2280.98
4_K7_I1.2110.98
3_S174_H1.2030.98
168_N172_H1.2010.98
102_I106_L1.1970.98
60_V63_A1.1950.98
132_A136_I1.1920.98
129_L133_V1.1880.98
84_A91_V1.1720.98
198_L202_F1.1650.97
138_N144_N1.1540.97
14_V62_Y1.1500.97
159_F193_N1.1450.97
147_A150_A1.1380.97
120_L124_L1.1250.97
4_K174_H1.1220.97
18_T69_A1.1090.96
138_N141_S1.1030.96
49_I53_W1.0950.96
152_S200_R1.0940.96
149_M153_V1.0930.96
170_I187_L1.0910.96
93_L97_G1.0890.96
58_K62_Y1.0850.96
44_E48_I1.0800.95
159_F166_D1.0760.95
76_L196_I1.0760.95
197_N200_R1.0740.95
50_L64_F1.0630.95
47_M64_F1.0610.95
159_F189_L1.0600.95
136_I139_I1.0580.95
67_T71_V1.0570.95
103_F191_F1.0550.95
123_F127_A1.0470.94
27_F31_F1.0460.94
91_V202_F1.0360.94
102_I105_V1.0260.94
129_L132_A1.0180.93
119_F122_S1.0060.93
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  
4pgrA10.99521000.077Contact Map
4i0uA100.28028.70.942Contact Map
4ev6A50.28998.40.942Contact Map
3w9iA60.72955.90.946Contact Map
4dx5A30.77294.20.95Contact Map
3ne5A10.72464.20.95Contact Map
2xq2A10.78262.90.954Contact Map
1r8hA60.14012.20.957Contact Map
3b5dA20.02421.90.958Contact Map
4mt1A10.72461.80.958Contact 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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