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2wvoA

ID: 1504790096 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 50% gaps before running GREMLIN.
Length: 233 (207)
Sequences: 1195 (937.3)
Seq/Len: 5.773
Nf(neff/√len): 65.1

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: 5.773).

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 > 50% 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
3_E6_E4.1411.00
37_D153_G2.3731.00
5_F9_A2.2821.00
2_S7_I2.2441.00
10_G13_G2.2271.00
4_P8_V2.2151.00
16_G19_N1.8791.00
56_G60_Q1.7131.00
48_A167_V1.6581.00
44_R162_Q1.6481.00
16_G20_N1.6311.00
88_L92_E1.6250.99
48_A164_A1.6060.99
44_R165_G1.6010.99
87_I163_V1.5720.99
48_A169_E1.4720.99
1_M4_P1.4350.98
5_F10_G1.4330.98
18_F56_G1.4330.98
2_S6_E1.4240.98
51_R172_K1.4110.98
9_A13_G1.4070.98
25_F163_V1.4020.98
127_R130_K1.3910.98
161_D165_G1.3880.98
51_R171_E1.3750.98
6_E10_G1.3690.98
197_L200_L1.3580.98
1_M13_G1.3560.98
3_E7_I1.3480.97
34_F38_Y1.3290.97
153_G157_E1.3290.97
193_D196_S1.3240.97
27_Y149_A1.3200.97
51_R168_D1.3120.97
3_E13_G1.2960.96
31_G34_F1.2740.96
52_L57_E1.2520.95
194_E198_T1.2350.95
6_E9_A1.2290.95
25_F167_V1.2290.95
51_R56_G1.2190.95
124_A131_D1.2180.95
151_Y163_V1.2180.95
195_A199_I1.2070.94
188_I192_E1.2050.94
125_L132_L1.2050.94
55_W87_I1.1970.94
13_G16_G1.1960.94
48_A177_E1.1840.93
26_E154_K1.1680.93
44_R164_A1.1680.93
152_D155_S1.1670.93
41_C48_A1.1660.93
5_F14_V1.1650.93
34_F37_D1.1640.93
190_E195_A1.1570.92
167_V170_L1.1450.92
35_G137_Q1.1440.92
51_R55_W1.1350.91
18_F80_A1.1340.91
41_C160_V1.1210.91
6_E13_G1.1160.90
3_E8_V1.1070.90
192_E195_A1.0980.89
141_S145_K1.0960.89
101_Y152_D1.0880.89
4_P7_I1.0870.89
162_Q169_E1.0850.89
152_D156_L1.0840.89
193_D197_L1.0840.89
8_V11_A1.0840.89
55_W80_A1.0800.88
184_A210_A1.0800.88
56_G61_I1.0790.88
7_I13_G1.0760.88
147_A152_D1.0710.88
80_A174_F1.0690.88
128_R131_D1.0620.87
77_V80_A1.0590.87
47_I83_I1.0590.87
121_I125_L1.0580.87
184_A205_G1.0510.86
180_C205_G1.0480.86
34_F97_T1.0480.86
9_A14_V1.0480.86
193_D205_G1.0450.86
144_K152_D1.0450.86
164_A168_D1.0390.86
36_R89_L1.0380.86
195_A206_G1.0360.85
183_L191_V1.0340.85
110_L113_F1.0320.85
182_K205_G1.0310.85
189_E210_A1.0290.85
188_I193_D1.0260.85
118_M121_I1.0250.85
18_F21_C1.0250.85
124_A127_R1.0240.85
152_D163_V1.0190.84
122_G126_H1.0170.84
90_L163_V1.0140.84
115_D118_M1.0130.84
126_H132_L1.0100.83
38_Y148_W1.0080.83
15_A45_L1.0060.83
55_W60_Q1.0030.83
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  
2wvqA20.91421000.121Contact Map
4btfA10.652417.80.909Contact Map
2msvA10.605213.70.914Contact Map
4ogqG10.15026.20.926Contact Map
1q90G10.12025.10.929Contact Map
4abxA40.5154.30.932Contact Map
2kncB10.29182.40.94Contact Map
5rubA20.24462.30.941Contact Map
2ifoA10.10732.20.941Contact Map
1y14A20.4122.10.941Contact 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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