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VV_TRAP_Small_subunit

ID: 1515972590 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 172 (157)
Sequences: 7837 (6091.6)
Seq/Len: 49.917
Nf(neff/√len): 486.2

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: 49.917).

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
82_P85_I2.6851.00
75_T79_D2.6041.00
97_V145_Q2.3961.00
31_W43_S2.2741.00
65_A70_T2.1691.00
98_L142_V2.1111.00
34_A39_L2.1031.00
109_Y113_E1.9661.00
81_L85_I1.8931.00
29_L50_A1.8901.00
81_L89_L1.8491.00
91_L149_M1.8401.00
91_L153_V1.8231.00
84_K87_L1.8191.00
56_Y133_S1.8141.00
105_I142_V1.8131.00
102_F106_Y1.8121.00
101_I138_G1.7411.00
14_E144_R1.7371.00
106_Y110_Q1.7051.00
34_A38_L1.6581.00
101_I141_M1.6141.00
102_F142_V1.6141.00
112_V132_Y1.6121.00
66_I141_M1.5721.00
126_S129_W1.5701.00
35_T39_L1.5631.00
144_R147_Q1.5561.00
31_W35_T1.5511.00
85_I88_L1.5451.00
62_C141_M1.5431.00
116_A128_K1.5381.00
120_L123_L1.5081.00
84_K88_L1.4501.00
98_L149_M1.4241.00
94_E152_I1.4231.00
115_T131_N1.4060.99
69_G148_K1.4050.99
78_S90_V1.3930.99
35_T43_S1.3760.99
12_N16_I1.3680.99
105_I139_L1.3550.99
88_L92_S1.3480.99
101_I142_V1.3110.99
150_V154_T1.3060.99
120_L127_S1.3030.99
48_E120_L1.2810.99
66_I145_Q1.2770.99
87_L156_F1.2750.99
113_E117_F1.2570.99
108_G138_G1.2520.99
112_V135_P1.2360.98
105_I138_G1.2350.98
21_L53_L1.2320.98
52_V120_L1.2300.98
15_E64_I1.2240.98
104_I138_G1.2140.98
105_I109_Y1.2130.98
108_G135_P1.2100.98
63_A137_G1.1870.98
12_N15_E1.1800.98
64_I68_R1.1730.98
32_Q47_E1.1530.97
63_A144_R1.1450.97
54_F58_S1.1450.97
52_V130_M1.1400.97
132_Y136_L1.1270.97
30_T34_A1.1260.97
47_E51_R1.1210.97
69_G73_N1.1120.96
5_M8_K1.1080.96
110_Q114_R1.1070.96
9_I12_N1.1030.96
28_V53_L1.0970.96
101_I145_Q1.0930.96
94_E149_M1.0870.96
24_A53_L1.0840.96
23_A27_V1.0790.95
108_G134_L1.0700.95
63_A140_F1.0600.95
49_L123_L1.0560.95
33_I37_W1.0530.95
98_L145_Q1.0490.94
25_L57_M1.0300.94
22_M57_M1.0270.94
87_L155_E1.0170.93
27_V31_W1.0150.93
32_Q46_S1.0110.93
52_V127_S1.0060.93
91_L152_I1.0030.93
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  
2wswA10.529110.20.924Contact Map
4c7rA30.936100.925Contact Map
2kncA10.3147.80.928Contact Map
2ov2I80.1866.80.93Contact Map
4xp4A106.70.93Contact Map
2odbB10.1866.50.931Contact Map
4uvmA10.85474.90.935Contact Map
2l8sA10.25584.90.935Contact Map
3w4tA10.77334.40.936Contact Map
4ysxC203.70.938Contact 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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