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ID: 1518378913 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 298 (288)
Sequences: 12278 (7165)
Seq/Len: 42.632
Nf(neff/√len): 422.2

Jackhmmer Results: (2016_04)
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: 42.632).

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
262_A270_F3.3691.00
165_F173_L3.1201.00
62_P70_F3.0821.00
162_T166_K2.9551.00
256_D260_K2.8981.00
159_N163_K2.6811.00
260_K264_D2.6601.00
259_R263_K2.6381.00
95_Y126_T2.6331.00
261_I269_A2.5661.00
155_T159_N2.5631.00
59_V63_K2.5611.00
163_K167_S2.4311.00
258_W270_F2.4281.00
56_D60_R2.3661.00
164_I172_G2.2761.00
234_V258_W2.2221.00
251_Y257_C2.1431.00
38_V143_A2.0591.00
60_R64_E2.0561.00
226_L274_A2.0371.00
154_F160_C2.0081.00
95_Y122_A1.9911.00
121_G185_I1.9861.00
265_E269_A1.9711.00
262_A267_P1.9701.00
251_Y256_D1.9641.00
253_G256_D1.9491.00
91_F95_Y1.9271.00
286_F290_L1.9251.00
156_G159_N1.9231.00
168_D172_G1.8791.00
237_R265_E1.8651.00
161_I173_L1.8501.00
154_F159_N1.8401.00
117_L189_A1.8361.00
33_K37_Q1.8061.00
51_Y57_C1.7841.00
202_L216_I1.7771.00
58_V70_F1.7481.00
140_R168_D1.7291.00
252_T256_D1.7001.00
35_L65_Q1.6851.00
194_V223_V1.6801.00
159_N162_T1.6071.00
265_E272_K1.5741.00
61_I69_S1.5741.00
32_V58_V1.5701.00
94_K98_I1.5591.00
17_V294_I1.5551.00
95_Y119_S1.5421.00
170_L174_Y1.5371.00
198_A219_T1.5371.00
30_E33_K1.5371.00
27_A31_R1.5241.00
52_K56_D1.5061.00
51_Y56_D1.4981.00
87_L91_F1.4981.00
190_A227_V1.4891.00
255_V259_R1.4801.00
114_A118_A1.4661.00
99_F119_S1.4501.00
195_Y292_D1.4461.00
21_I290_L1.4361.00
103_V115_G1.4281.00
290_L294_I1.4261.00
65_Q72_R1.4121.00
165_F170_L1.4060.99
31_R35_L1.4040.99
24_T74_N1.4040.99
198_A216_I1.4020.99
65_Q69_S1.4000.99
197_T201_M1.3550.99
16_G82_F1.3310.99
168_D175_Q1.3150.99
137_A161_I1.3130.99
215_M219_T1.3080.99
20_A78_V1.2870.99
87_L130_F1.2840.99
138_R142_A1.2830.99
208_V212_V1.2790.99
91_F126_T1.2780.99
96_K196_D1.2780.99
255_V258_W1.2750.99
56_D59_V1.2740.99
251_Y260_K1.2700.99
197_T200_G1.2480.99
121_G189_A1.2410.98
11_D93_D1.2370.98
125_A181_V1.2350.98
158_G162_T1.2250.98
14_A294_I1.2250.98
13_L16_G1.2040.98
234_V270_F1.1830.98
191_Y288_L1.1630.97
74_N78_V1.1590.97
235_R239_M1.1570.97
132_Y136_F1.1540.97
122_A126_T1.1480.97
25_A286_F1.1470.97
194_V198_A1.1440.97
218_Q282_M1.1420.97
232_D235_R1.1330.97
93_D96_K1.1300.97
187_Y224_A1.1230.97
99_F122_A1.1110.96
136_F140_R1.1080.96
17_V21_I1.1070.96
129_C177_F1.1070.96
112_Y115_G1.1040.96
55_I59_V1.0990.96
120_G189_A1.0970.96
177_F181_V1.0870.96
27_A71_W1.0810.95
51_Y60_R1.0750.95
15_G19_A1.0730.95
169_G172_G1.0730.95
209_H212_V1.0660.95
213_S292_D1.0660.95
256_D259_R1.0640.95
61_I65_Q1.0630.95
210_I293_E1.0620.95
274_A278_V1.0610.95
163_K166_K1.0590.95
111_R115_G1.0550.95
266_G269_A1.0500.94
215_M218_Q1.0490.94
120_G124_G1.0410.94
217_A285_A1.0300.94
154_F163_K1.0280.94
84_T88_N1.0240.93
181_V185_I1.0190.93
122_A125_A1.0180.93
259_R262_A1.0160.93
164_I168_D1.0140.93
80_R84_T1.0140.93
94_K97_Q1.0130.93
267_P271_F1.0120.93
39_Q51_Y1.0100.93
66_G69_S1.0090.93
62_P67_F1.0080.93
30_E138_R1.0080.93
137_A160_C1.0040.93
143_A240_M1.0030.93
92_K196_D1.0020.92
21_I24_T1.0000.92
160_C164_I1.0000.92
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  
1okcA10.97991000.113Contact Map
4c9gA10.88591000.166Contact Map
2lckA10.93961000.183Contact Map
4i5lB20.238321.30.953Contact Map
2b0jA10.34980.961Contact Map
4jjfA20.30877.30.962Contact Map
2jvwA10.20474.20.966Contact Map
1t10A10.17113.60.967Contact Map
3j9xA5803.40.967Contact Map
1l3lA40.20472.80.969Contact 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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