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PhD

ID: 1516033769 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 128 (123)
Sequences: 3792 (2953.4)
Seq/Len: 30.829
Nf(neff/√len): 266.3

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: 30.829).

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
53_F99_G3.4401.00
12_S120_D2.9751.00
38_Y41_G2.2481.00
20_P36_K2.1811.00
112_E115_L2.1321.00
36_K55_E2.1141.00
22_Y34_R2.0731.00
34_R57_S2.0501.00
105_R108_L1.8951.00
70_V100_Y1.8641.00
88_F92_F1.7531.00
27_Q32_C1.7461.00
7_V121_T1.6661.00
34_R55_E1.6601.00
42_N97_C1.6291.00
55_E97_C1.6211.00
52_V124_L1.5791.00
54_L68_Y1.5571.00
6_F37_V1.5271.00
115_L118_Q1.5151.00
114_Y117_P1.5091.00
71_E125_R1.5081.00
109_L122_V1.4981.00
15_R110_A1.4871.00
49_Y102_R1.3900.99
72_M104_F1.3810.99
22_Y36_K1.3670.99
63_T91_D1.3330.99
16_Q40_D1.3300.99
37_V50_L1.3180.99
4_A24_P1.2900.99
25_P32_C1.2770.99
66_Y92_F1.2170.98
44_V47_G1.2130.98
48_Y106_L1.1870.98
56_L62_E1.1750.98
68_Y90_S1.1690.97
10_N13_T1.1540.97
42_N53_F1.1500.97
31_L56_L1.1450.97
7_V123_I1.1390.97
53_F100_Y1.1380.97
25_P57_S1.1340.97
45_V49_Y1.1290.97
114_Y118_Q1.1240.97
45_V48_Y1.1190.96
85_I89_A1.0710.95
33_W54_L1.0630.95
61_P64_S1.0540.95
37_V52_V1.0450.94
6_F23_S1.0420.94
11_F110_A1.0400.94
5_T125_R1.0380.94
51_S99_G1.0370.94
41_G51_S1.0360.94
90_S97_C1.0250.93
60_L63_T1.0250.93
5_T123_I1.0210.93
85_I88_F1.0190.93
36_K97_C1.0140.93
81_T86_R1.0020.92
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  
3ivvA10.976699.90.231Contact Map
1flkA20.968899.90.242Contact Map
4ghuA10.968899.90.248Contact Map
1ca9A60.960999.90.251Contact Map
1d00A80.960999.90.252Contact Map
3zjbA30.984499.90.254Contact Map
3hqiA20.960999.90.256Contact Map
1lb6A10.984499.90.258Contact Map
2f1zA20.960999.90.261Contact Map
2fojA10.906299.90.269Contact 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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