OPENSEQ.org
7_1qjppdb

ID: 1516869653 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 137 (134)
Sequences: 5822 (4046.5)
Seq/Len: 43.448
Nf(neff/√len): 349.6

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: 43.448).

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
121_Y126_G3.6871.00
79_G99_V3.6271.00
71_L109_Y3.0761.00
10_G27_F2.7461.00
76_R104_A2.6161.00
12_K25_G2.5291.00
60_T102_V2.4981.00
118_R131_G2.4951.00
116_A133_S2.4501.00
123_W126_G2.3121.00
42_Y55_Q2.2281.00
111_I117_T2.2181.00
13_L22_L2.1691.00
115_I134_Y2.1501.00
15_W20_N2.1211.00
71_L107_V2.1191.00
81_V97_T2.0711.00
103_F123_W1.9681.00
74_Y106_G1.9561.00
8_Y29_G1.8901.00
112_T115_I1.8661.00
41_G58_Q1.7291.00
7_W30_Y1.7271.00
14_G23_G1.6641.00
32_V38_F1.5941.00
74_Y120_E1.5921.00
115_I132_V1.5751.00
108_E116_A1.5571.00
81_V99_V1.5291.00
24_A44_W1.5101.00
60_T76_R1.5001.00
12_K43_D1.4761.00
27_F118_R1.4401.00
70_D109_Y1.4211.00
83_R95_H1.4161.00
35_Y63_L1.4151.00
74_Y118_R1.4000.99
72_D108_E1.3850.99
37_G64_G1.3830.99
7_W28_G1.3530.99
12_K27_F1.3240.99
78_G102_V1.3090.99
76_R122_Q1.3070.99
60_T122_Q1.2880.99
43_D56_G1.2650.99
108_E118_R1.2650.99
7_W11_A1.2490.99
101_P125_N1.2390.98
82_W100_S1.2340.98
116_A135_R1.2330.98
40_M59_L1.2110.98
12_K131_G1.1900.98
27_F133_S1.1870.98
80_M102_V1.1780.98
31_Q37_G1.1630.97
25_G43_D1.1580.97
6_T30_Y1.1570.97
27_F39_E1.1430.97
114_E134_Y1.1000.96
37_G62_K1.0780.95
67_I73_I1.0520.95
70_D110_A1.0460.94
120_E129_S1.0320.94
73_I107_V1.0210.93
83_R97_T1.0140.93
32_V36_V1.0050.93
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  
2jmmA10.985499.80.177Contact Map
1qjpA10.992799.80.179Contact Map
2k0lA1199.80.198Contact Map
1p4tA10.978199.70.24Contact Map
3nb3A30.985499.70.257Contact Map
2lhfA10.956299.60.27Contact Map
2mafA10.963599.60.274Contact Map
3qraA10.970899.60.291Contact Map
4rlcA1099.60.295Contact Map
2x27X1199.60.301Contact 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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