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1BKR

ID: 1465993738 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 109 (107)
Sequences: 1427 (904.3)
Seq/Len: 13.336
Nf(neff/√len): 87.4

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: 13.336).

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
58_N61_Y3.3421.00
38_N65_N2.9381.00
64_Q68_N2.5081.00
24_I36_A2.4221.00
68_N72_Q2.1571.00
64_Q78_K2.0991.00
26_N29_T1.8501.00
45_R48_L1.6581.00
26_N30_S1.6531.00
19_Y42_H1.6401.00
76_L102_Y1.6201.00
68_N78_K1.5901.00
92_E100_V1.5761.00
39_A51_F1.5681.00
15_K43_K1.5671.00
69_L73_H1.4811.00
70_A102_Y1.4751.00
95_I99_V1.4701.00
90_P95_I1.4461.00
8_L11_W1.4321.00
85_I95_I1.4291.00
60_H82_P1.4010.99
37_F67_F1.3670.99
5_K92_E1.3440.99
27_F99_V1.3060.99
64_Q82_P1.2990.99
59_A86_S1.2860.99
57_S62_N1.2650.99
91_D97_T1.2650.99
41_I102_Y1.2550.99
18_G21_N1.2250.98
49_I65_N1.2200.98
6_D10_L1.2060.98
50_D53_K1.1720.98
37_F63_L1.1440.97
16_T19_Y1.1320.97
55_K58_N1.1320.97
90_P99_V1.1210.97
41_I69_L1.1140.96
51_F54_L1.0980.96
35_M54_L1.0960.96
12_C24_I1.0670.95
27_F31_W1.0620.95
15_K44_H1.0590.95
3_S6_D1.0580.95
62_N66_A1.0500.94
96_I100_V1.0460.94
67_F82_P1.0390.94
81_D84_D1.0340.94
28_T89_H1.0200.93
25_H29_T1.0130.93
22_V36_A1.0080.93
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  
1bkrA10.9908100-0.03Contact Map
1bhdA21100-0.023Contact Map
1wyqA11100-0.018Contact Map
2d87A111000.007Contact Map
2d88A111000.018Contact Map
2d89A10.99081000.028Contact Map
1wylA10.99081000.028Contact Map
3f7pA20.98171000.049Contact Map
4d1eA10.97251000.05Contact Map
4q57B10.972599.90.055Contact 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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