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OPENSEQ.org

FerA

ID: 1491934118 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 114 (114)
Sequences: 180 (123.2)
Seq/Len: 1.579
Nf(neff/√len): 11.5

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: 1.579).

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
7_N16_L2.1150.99
52_S86_A1.8320.96
9_L16_L1.8260.96
105_D109_R1.6710.93
80_S83_T1.4980.87
111_R114_A1.4810.86
1_H106_W1.4630.85
19_G43_L1.4510.85
12_I15_R1.4260.83
109_R113_L1.4110.82
3_I103_A1.3640.79
100_L110_L1.3510.78
2_R7_N1.3330.77
32_S37_D1.2860.73
73_Q109_R1.2790.73
8_Q39_L1.2600.71
44_T96_L1.2560.71
104_E110_L1.2470.70
65_T68_D1.2410.70
30_Q71_L1.2360.69
85_A98_A1.2340.69
40_V63_S1.2310.69
44_T61_T1.2300.69
6_Q13_A1.2280.68
1_H65_T1.2110.67
108_L113_L1.1990.66
67_L110_L1.1990.66
93_H99_A1.1940.65
37_D48_I1.1830.64
9_L90_K1.1770.64
79_L105_D1.1560.62
81_Q85_A1.1510.61
43_L104_E1.1450.61
46_E77_H1.1410.60
65_T70_Y1.1340.59
7_N14_D1.1310.59
27_L87_L1.1290.59
23_V40_V1.1270.59
46_E57_D1.1270.59
19_G50_G1.1270.59
108_L112_A1.1220.58
13_A33_T1.1170.58
54_P80_S1.1170.58
2_R110_L1.1110.57
8_Q12_I1.0960.56
28_K45_D1.0960.56
50_G56_G1.0900.55
56_G75_R1.0780.54
103_A108_L1.0770.54
11_G91_L1.0730.53
9_L55_L1.0710.53
72_Y76_T1.0660.52
24_H97_P1.0660.52
2_R16_L1.0600.52
6_Q16_L1.0520.51
22_Q109_R1.0480.50
45_D53_Q1.0470.50
46_E50_G1.0460.50
54_P79_L1.0430.50
52_S57_D1.0420.50
59_H70_Y1.0360.49
48_I91_L1.0360.49
65_T105_D1.0330.49
29_A36_V1.0290.49
36_V40_V1.0230.48
47_L54_P1.0060.46
52_S79_L1.0030.46
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  
1io1A10.350919.20.906Contact Map
2yn7A20.745612.70.913Contact Map
4nx9A10.333311.30.915Contact Map
2l81A10.72816.20.925Contact Map
3pwxA20.55.30.927Contact Map
3ilwA20.89475.20.927Contact Map
2o8rA20.33334.80.928Contact Map
4po2A20.92984.60.929Contact Map
3v47C20.29824.60.929Contact Map
4i3hA20.85964.50.929Contact 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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