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T0833 -force run

ID: 1403811297 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 136 (130)
Sequences: 88 (71.2)
Seq/Len: 0.677
Nf(neff/√len): 6.2

Jackhmmer Results: (2014_04_16)
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: 0.677).

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
75_K117_F2.0310.92
77_F88_P1.8850.87
75_K116_N1.6910.78
10_I83_N1.6660.77
77_F117_F1.6510.76
23_I39_N1.6300.75
80_D87_V1.6290.75
66_N70_K1.5470.69
76_A88_P1.5320.68
9_S60_R1.4350.60
22_A103_I1.4200.59
30_D60_R1.4140.59
22_A70_K1.4060.58
59_V92_I1.3920.57
22_A66_N1.3880.57
36_K46_V1.3680.55
49_L57_K1.3640.55
63_F94_Y1.3430.53
39_N53_G1.3170.51
11_L106_N1.2910.49
31_Y124_M1.2910.49
54_L113_K1.2460.45
44_S63_F1.2260.43
60_R92_I1.2090.42
36_K78_R1.2080.42
39_N117_F1.2050.41
5_V106_N1.2050.41
20_S115_K1.2010.41
63_F112_K1.1930.40
111_D118_S1.1710.39
32_L86_W1.1690.39
58_Q108_G1.1620.38
64_Q118_S1.1600.38
70_K111_D1.1570.38
63_F76_A1.1560.38
44_S60_R1.1470.37
79_W107_Y1.1320.36
74_K126_I1.1290.35
105_T124_M1.1230.35
108_G124_M1.1160.34
14_V20_S1.1140.34
63_F89_F1.1070.34
58_Q105_T1.1050.34
59_V71_V1.1050.34
22_A67_E1.1040.34
48_F98_D1.1040.34
108_G126_I1.1020.33
15_F20_S1.0990.33
76_A90_Y1.0980.33
43_I86_W1.0960.33
58_Q126_I1.0950.33
3_T14_V1.0950.33
70_K96_Y1.0860.32
11_L93_T1.0810.32
49_L58_Q1.0780.32
21_L87_V1.0740.31
29_K67_E1.0690.31
70_K129_T1.0590.30
16_T83_N1.0490.30
70_K75_K1.0440.29
78_R89_F1.0300.28
80_D101_G1.0290.28
17_F92_I1.0270.28
62_E120_N1.0210.28
57_K91_Q1.0180.27
104_K117_F1.0120.27
62_E88_P1.0030.26
53_G85_E1.0000.26
46_V78_R1.0000.26
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: (17Jul14)
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  
3mswA10.80881000.281Contact Map
4ghbA20.595687.60.898Contact Map
4iglB20.786830.80.933Contact Map
4o9xA10.933819.50.939Contact Map
4iglA20.72798.80.948Contact Map
4iwtA20.3753.80.956Contact Map
1hcxA20.3752.90.958Contact Map
2y69D20.55882.70.959Contact Map
1qleD10.16912.70.959Contact Map
1v54D20.55882.60.959Contact 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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