OPENSEQ.org
CcmE-01

ID: 1517605976 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 159 (145)
Sequences: 1320 (731.3)
Seq/Len: 9.103
Nf(neff/√len): 60.7

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: 9.103).

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
42_E47_K3.6571.00
67_M90_S3.6201.00
67_M83_T2.8731.00
3_I6_K2.7921.00
79_K96_E2.5781.00
84_I109_V2.5271.00
140_E144_E2.5001.00
65_M87_A2.2641.00
112_Q125_E2.2541.00
104_R107_Q2.1821.00
72_Q81_T2.1811.00
30_L34_I1.9811.00
116_E122_L1.9741.00
59_R124_K1.9571.00
43_I60_L1.8691.00
141_K145_A1.8501.00
104_R109_V1.8201.00
83_T90_S1.8111.00
20_A24_G1.8041.00
65_M143_M1.8001.00
114_E124_K1.7891.00
30_L35_D1.7591.00
80_V99_L1.6591.00
144_E149_R1.6441.00
24_G28_Y1.5831.00
139_V142_A1.5511.00
116_E120_H1.5331.00
41_G89_G1.5151.00
99_L126_V1.4891.00
28_Y32_S1.4410.99
94_S120_H1.4370.99
43_I62_V1.4330.99
71_V80_V1.4210.99
57_G114_E1.3950.99
41_G88_E1.3870.99
71_V106_G1.3700.99
88_E146_N1.3430.99
141_K144_E1.3210.99
59_R114_E1.2950.99
27_L34_I1.2840.99
83_T92_D1.2580.98
41_G45_Y1.1890.97
143_M147_H1.1700.97
81_T94_S1.1530.97
32_S36_L1.1450.96
139_V143_M1.1430.96
74_D77_S1.1400.96
17_A21_L1.1400.96
93_V109_V1.1160.96
60_L121_I1.1080.95
68_P106_G1.1070.95
27_L31_R1.1070.95
39_T104_R1.1000.95
37_F110_V1.0990.95
23_I28_Y1.0910.95
107_Q139_V1.0830.95
142_A146_N1.0590.94
79_K94_S1.0220.92
67_M111_V1.0110.92
67_M109_V1.0000.91
38_Y60_L1.0000.91
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  
1sr3A10.7171000.315Contact Map
1j6qA10.62261000.32Contact Map
2kctA10.52831000.572Contact Map
3wtsA20.4528370.95Contact Map
3ne5B20.47830.20.953Contact Map
3vmaA10.842829.40.953Contact Map
2g3rA10.2516240.955Contact Map
4r9fA10.610123.50.955Contact Map
3ucpA10.484319.70.957Contact Map
3pmqA10.408816.50.958Contact 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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