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JULY30_eIF2B_human_alpha

ID: 1501460665 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 305 (280)
Sequences: 2916 (1716)
Seq/Len: 10.414
Nf(neff/√len): 102.6

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: 10.414).

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
206_I281_I3.4981.00
213_N222_Q3.4361.00
221_A280_L2.7751.00
128_H153_T2.7281.00
123_A192_L2.6171.00
71_L96_R2.6031.00
139_E171_L2.5941.00
216_A280_L2.5901.00
221_A279_S2.4821.00
179_L182_A2.4821.00
194_I229_V2.4311.00
111_I229_V2.3881.00
53_I73_L2.3701.00
152_V175_V2.3611.00
184_G214_Q2.3551.00
53_I69_G2.2551.00
200_V230_A2.2501.00
119_I192_L2.1801.00
72_F93_M2.1541.00
57_C66_S2.0581.00
195_V226_F2.0561.00
193_V219_A2.0141.00
57_C70_E2.0111.00
71_L103_R1.9991.00
149_S176_T1.9991.00
177_V263_G1.9211.00
195_V212_T1.9031.00
50_T73_L1.8991.00
126_L153_T1.8991.00
241_L245_D1.8781.00
175_V266_L1.8431.00
124_T191_D1.8331.00
106_L110_K1.8171.00
241_L244_Q1.7971.00
137_V229_V1.7881.00
177_V266_L1.7621.00
116_H144_A1.7481.00
123_A191_D1.7271.00
225_P282_T1.7191.00
49_L76_I1.7171.00
149_S174_P1.6681.00
207_I246_V1.6571.00
124_T149_S1.6421.00
126_L190_A1.6301.00
124_T151_Y1.6101.00
50_T77_S1.5981.00
113_D140_A1.5861.00
197_A200_V1.5731.00
102_R106_L1.5691.00
158_D162_K1.5671.00
206_I228_V1.5631.00
235_F291_L1.5441.00
195_V228_V1.5441.00
182_A271_P1.5431.00
186_I269_E1.5321.00
140_A144_A1.5301.00
212_T276_T1.5211.00
113_D117_T1.5191.00
120_K123_A1.5071.00
41_T44_G1.4991.00
165_A177_V1.4931.00
117_T144_A1.4861.00
205_G278_P1.4811.00
201_V239_F1.4721.00
213_N277_A1.4711.00
58_G66_S1.4591.00
197_A230_A1.4561.00
110_K113_D1.4421.00
126_L215_M1.4301.00
183_V214_Q1.4281.00
261_Q265_D1.4251.00
143_A171_L1.4201.00
151_Y190_A1.4070.99
109_N113_D1.3800.99
217_V221_A1.3800.99
48_N51_S1.3500.99
232_S287_D1.3490.99
178_V186_I1.3460.99
119_I123_A1.3390.99
123_A146_K1.3370.99
124_T148_F1.3200.99
292_T295_A1.3170.99
188_E244_Q1.3120.99
174_P267_K1.3070.99
220_K223_N1.2780.99
107_S232_S1.2770.99
166_K170_H1.2760.99
149_S175_V1.2630.99
79_A92_I1.2600.99
240_P245_D1.2580.99
85_D88_K1.2570.99
112_A140_A1.2530.99
116_H146_K1.2410.98
66_S70_E1.2400.98
141_A148_F1.2310.98
150_V168_L1.2300.98
75_F96_R1.2290.98
184_G217_V1.2290.98
50_T54_E1.1890.98
123_A141_A1.1850.98
140_A143_A1.1840.98
227_Y283_L1.1770.98
158_D272_W1.1660.97
130_Y140_A1.1630.97
227_Y282_T1.1630.97
109_N140_A1.1620.97
95_E99_L1.1550.97
96_R99_L1.1520.97
67_S233_F1.1500.97
291_L295_A1.1470.97
239_F245_D1.1430.97
45_L90_K1.1420.97
44_G48_N1.1290.97
94_I98_E1.1280.97
69_G73_L1.1280.97
115_C137_V1.1250.97
184_G218_C1.1240.97
122_G147_R1.1220.97
187_M193_V1.1170.96
91_K95_E1.1150.96
141_A192_L1.1130.96
136_R139_E1.1120.96
186_I190_A1.1120.96
109_N143_A1.0950.96
291_L296_V1.0900.96
183_V215_M1.0860.96
199_G236_V1.0840.96
66_S69_G1.0810.95
57_C69_G1.0790.95
187_M219_A1.0730.95
187_M222_Q1.0700.95
67_S71_L1.0660.95
98_E101_L1.0650.95
184_G213_N1.0600.95
122_G148_F1.0500.94
142_V147_R1.0470.94
205_G275_Y1.0400.94
121_D147_R1.0390.94
227_Y285_F1.0340.94
193_V215_M1.0230.93
153_T215_M1.0220.93
112_A136_R1.0050.93
104_I108_R1.0010.92
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  
3ecsA80.97381000.149Contact Map
3a11A60.98361000.197Contact Map
2yvkA40.97381000.252Contact Map
1t5oA40.96721000.253Contact Map
4ldrA20.98691000.256Contact Map
1t9kA40.96391000.269Contact Map
2a0uA20.99021000.273Contact Map
1vb5A20.88851000.369Contact Map
1w2wB40.52461000.472Contact Map
1w2wA40.478799.40.812Contact 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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