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Bilge Ercan

ID: 1501081324 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 260 (256)
Sequences: 3269 (1744.9)
Seq/Len: 12.770
Nf(neff/√len): 109.1

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: 12.770).

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
212_T249_L6.0851.00
216_I245_A4.7111.00
48_L154_S3.6721.00
44_L149_W3.6271.00
224_A234_A3.2881.00
151_G214_T2.9401.00
44_L153_I2.7991.00
30_A148_F2.6781.00
60_V161_I2.5461.00
98_E205_K2.4471.00
63_G162_F2.2991.00
106_L243_S2.1371.00
120_I143_V2.1351.00
98_E250_D2.1121.00
95_L166_G2.0181.00
208_V253_L2.0171.00
49_Y54_L1.9761.00
148_F211_I1.9761.00
205_K250_D1.8471.00
64_V169_G1.8301.00
170_G185_F1.8141.00
113_G217_S1.7911.00
50_N54_L1.7381.00
117_T238_T1.7271.00
100_G163_V1.7231.00
220_N241_H1.7221.00
44_L48_L1.7001.00
51_V116_L1.6941.00
152_V211_I1.6601.00
152_V210_A1.6501.00
159_T163_V1.6301.00
171_S182_S1.6131.00
208_V249_L1.6101.00
139_P222_Y1.5941.00
171_S175_V1.5921.00
171_S186_W1.5661.00
140_L144_I1.5491.00
124_R129_L1.5291.00
220_N237_R1.5201.00
124_R222_Y1.5191.00
55_S112_A1.5101.00
70_L94_S1.5081.00
160_V203_L1.4671.00
159_T202_C1.4631.00
56_M161_I1.4491.00
229_A233_R1.4481.00
60_V165_V1.4461.00
61_V244_L1.4181.00
74_G90_L1.4060.99
224_A230_G1.3990.99
26_M140_L1.3920.99
227_T231_I1.3810.99
96_L167_I1.3760.99
25_L29_N1.3690.99
65_F102_V1.3620.99
108_F155_L1.3490.99
7_A11_H1.3310.99
124_R223_D1.3200.99
27_L215_W1.3130.99
43_L46_R1.3130.99
212_T245_A1.3010.99
128_Q243_S1.2900.99
212_T216_I1.2860.99
48_L153_I1.2850.99
10_G14_I1.2790.99
129_L143_V1.2780.99
47_Q147_R1.2580.99
125_A231_I1.2540.99
209_F250_D1.2500.99
159_T206_S1.2470.99
91_V170_G1.2380.98
98_E209_F1.2290.98
6_L10_G1.2250.98
220_N223_D1.2110.98
23_A215_W1.1860.98
253_L257_M1.1720.98
116_L218_L1.1690.97
32_V36_E1.1670.97
167_I189_M1.1490.97
14_I18_R1.1340.97
79_T84_E1.1340.97
71_G91_V1.1330.97
155_L159_T1.1160.96
93_L97_R1.1140.96
207_V211_I1.1020.96
124_R133_E1.1000.96
163_V202_C1.0970.96
137_V142_R1.0950.96
92_A189_M1.0930.96
155_L210_A1.0790.95
33_G145_S1.0730.95
97_R198_D1.0690.95
152_V207_V1.0640.95
69_V94_S1.0570.95
133_E139_P1.0530.95
217_S242_S1.0520.95
201_N257_M1.0520.95
122_L228_S1.0510.94
122_L231_I1.0470.94
22_R223_D1.0400.94
26_M144_I1.0380.94
24_G28_F1.0330.94
104_A162_F1.0310.94
47_Q50_N1.0250.93
138_D141_R1.0200.93
145_S148_F1.0200.93
219_F223_D1.0180.93
57_L61_V1.0060.93
200_V204_I1.0060.93
46_R229_A1.0050.93
205_K209_F1.0030.93
112_A115_A1.0020.92
111_R235_T1.0020.92
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  
2zy9A20.55387.10.963Contact Map
2mgyA10.39236.70.964Contact Map
1rh5C10.12313.40.969Contact Map
3ze3A60.28461.70.973Contact Map
4xp4A101.60.973Contact Map
2ls2A10.09621.60.974Contact Map
2a65A10.75381.50.974Contact Map
4u9nA20.48461.40.975Contact Map
2nwlA30.37691.30.975Contact Map
1h2sB10.21541.30.975Contact 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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