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fniii

ID: 1446557530 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 122 (119)
Sequences: 5364 (3590.1)
Seq/Len: 45.076
Nf(neff/√len): 329.1

HHblits Results: (2015_06)
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: 45.076).

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
96_Q103_T3.1041.00
50_G98_F2.8451.00
54_G94_V2.7451.00
98_F103_T2.6211.00
96_Q106_S2.5481.00
56_R92_G2.4281.00
28_T31_S2.4031.00
21_D37_K2.2791.00
94_V106_S2.2381.00
82_L93_V2.1731.00
53_I80_Y2.1251.00
44_Q48_I2.0391.00
32_I112_A1.9971.00
52_Q98_F1.9741.00
12_E100_R1.9061.00
57_E86_K1.9011.00
85_L91_Y1.8391.00
82_L85_L1.8061.00
55_Y82_L1.7921.00
99_N102_G1.7911.00
52_Q96_Q1.7701.00
53_I95_V1.6601.00
90_Q113_T1.6571.00
89_A114_T1.6371.00
33_Q81_T1.6221.00
32_I93_V1.5871.00
52_Q103_T1.5691.00
24_L112_A1.5511.00
54_G106_S1.5361.00
57_E89_A1.4981.00
47_V99_N1.4941.00
33_Q79_V1.4911.00
23_T35_T1.4751.00
96_Q104_G1.4731.00
88_F116_E1.4311.00
92_G109_E1.4111.00
87_K117_S1.3980.99
55_Y93_V1.3970.99
17_G43_L1.3860.99
97_A104_G1.3480.99
11_E101_A1.3390.99
22_V34_V1.3390.99
49_R98_F1.3210.99
54_G96_Q1.3170.99
16_D45_N1.3110.99
58_N92_G1.2730.99
38_A51_Y1.2660.99
46_G99_N1.2460.98
58_N90_Q1.1950.98
22_V107_S1.1190.96
23_T37_K1.1170.96
99_N104_G1.0920.96
31_S81_T1.0730.95
90_Q111_N1.0640.95
26_P115_L1.0240.93
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  
1va9A1199.60.054Contact Map
1uenA10.975499.50.093Contact Map
1x5hA10.967299.40.144Contact Map
4n68A10.811599.40.144Contact Map
2edxA10.983699.40.152Contact Map
4pbxA10.95999.40.175Contact Map
4n5uA10.885299.30.18Contact Map
1x5gA10.91899.30.181Contact Map
2dbjA10.975499.30.194Contact Map
2ee2A10.942699.30.194Contact 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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