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OPENSEQ.org

AlpC

ID: 1456484099 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 91 (87)
Sequences: 168 (120.5)
Seq/Len: 1.931
Nf(neff/√len): 12.9

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: 1.931).

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
15_A78_L2.6221.00
9_T70_L2.5711.00
31_R81_R2.0950.99
23_Y28_A2.0530.99
21_I42_A1.9040.98
31_R85_A1.8070.97
21_I25_R1.6330.95
35_S85_A1.5600.93
51_G63_S1.5570.93
57_Y70_L1.4820.90
17_C20_L1.3840.85
12_V53_V1.3630.84
39_Y43_L1.3620.84
75_V84_L1.3420.83
14_S55_G1.2930.79
27_G39_Y1.2640.77
23_Y81_R1.2440.76
8_L40_L1.2230.74
66_M70_L1.2050.72
9_T20_L1.2000.72
9_T13_C1.2000.72
39_Y50_L1.1920.71
84_L89_R1.1520.67
9_T48_Q1.1300.65
12_V71_L1.1230.64
5_L76_L1.1170.64
15_A73_L1.1160.64
23_Y40_L1.1110.63
12_V67_L1.1060.63
72_V84_L1.1060.63
80_A90_L1.1000.62
18_M78_L1.0950.62
41_L72_V1.0950.62
48_Q70_L1.0820.60
30_F36_L1.0790.60
46_G50_L1.0610.58
3_D39_Y1.0370.55
71_L87_V1.0350.55
17_C23_Y1.0250.54
8_L58_R1.0230.54
68_G75_V1.0220.54
43_L50_L1.0200.53
50_L87_V1.0190.53
41_L44_C1.0120.53
29_R85_A1.0100.52
73_L78_L1.0040.52
54_A73_L1.0020.51
42_A69_V1.0000.51
62_L67_L1.0000.51
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  
3rceA10.94513.80.929Contact Map
2jafA10.9783.40.931Contact Map
3wajA10.94513.20.932Contact Map
4p02B10.29673.20.932Contact Map
3qapA10.9672.50.936Contact Map
4rngA60.29672.40.936Contact Map
5a63B102.40.936Contact Map
3giaA10.94512.20.937Contact Map
2mn6B20.35162.10.938Contact Map
3lb6C102.10.938Contact 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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