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T0848 165-354 -force run

ID: 1405064903 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 190 (184)
Sequences: 128 (116.8)
Seq/Len: 0.696
Nf(neff/√len): 8.6

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: 0.696).

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
14_L163_M1.8490.86
13_A25_K1.7850.84
39_N43_N1.7380.81
104_V159_V1.6790.78
87_Q103_T1.6460.76
89_K101_E1.6230.75
34_T161_V1.5980.73
131_S134_E1.5310.69
7_L10_S1.4950.66
23_F35_G1.4490.62
12_K16_A1.4420.62
162_K174_D1.4120.59
163_M173_L1.4000.58
115_R162_K1.3900.58
68_A81_S1.3890.58
161_V169_D1.3870.57
20_V23_F1.3810.57
39_N48_S1.3620.55
131_S158_T1.3490.54
96_D140_L1.3300.53
85_S105_K1.3280.52
109_A143_Y1.3140.51
144_P153_A1.2950.50
101_E158_T1.2840.49
13_A23_F1.2730.48
44_D51_D1.2530.46
117_E161_V1.2360.45
13_A30_F1.2320.44
67_K162_K1.2310.44
85_S107_V1.2220.44
112_L163_M1.2210.43
26_D94_S1.2180.43
31_E69_L1.2130.43
45_F105_K1.1990.42
46_N131_S1.1750.40
24_G112_L1.1740.40
106_P156_E1.1730.40
53_Y132_Y1.1680.39
40_E70_D1.1680.39
69_L102_A1.1640.39
71_N87_Q1.1640.39
154_S183_L1.1620.39
61_S129_S1.1600.39
49_A90_T1.1590.38
9_D16_A1.1520.38
51_D100_V1.1320.36
67_K134_E1.1290.36
86_I135_A1.1230.36
36_A64_A1.1200.35
37_N40_E1.1170.35
24_G169_D1.1170.35
106_P154_S1.1160.35
69_L126_K1.1140.35
116_I120_V1.1130.35
57_S102_A1.1100.35
66_S120_V1.1030.34
83_N155_S1.0980.34
43_N97_E1.0960.34
13_A24_G1.0940.33
134_E137_K1.0930.33
54_L78_E1.0930.33
36_A80_L1.0840.33
28_A40_E1.0840.33
7_L14_L1.0810.32
70_D83_N1.0750.32
48_S124_Y1.0750.32
63_Y165_K1.0750.32
76_I147_F1.0730.32
154_S159_V1.0690.32
71_N138_Y1.0690.32
32_K100_V1.0650.31
26_D47_E1.0630.31
147_F150_L1.0600.31
11_A15_S1.0580.31
181_A184_V1.0570.31
13_A16_A1.0560.31
57_S145_E1.0510.30
17_Y20_V1.0500.30
4_A7_L1.0480.30
122_D126_K1.0480.30
88_A179_R1.0440.30
167_D172_Q1.0440.30
46_N73_V1.0420.30
24_G33_I1.0410.30
67_K183_L1.0400.29
170_Q173_L1.0390.29
53_Y182_E1.0370.29
49_A84_S1.0360.29
153_A161_V1.0350.29
117_E121_K1.0320.29
96_D114_D1.0280.29
11_A16_A1.0220.28
167_D184_V1.0220.28
60_S82_K1.0220.28
95_K182_E1.0120.28
95_K128_S1.0080.27
46_N94_S1.0060.27
121_K125_S1.0040.27
33_I47_E1.0030.27
89_K148_K1.0030.27
67_K109_A1.0020.27
23_F29_D1.0000.27
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: (05Jul14)
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  
3k7cA40.531690.10.875Contact Map
4hz9B20.631659.60.907Contact Map
4fczB20.77896.40.943Contact Map
3fkaA40.61585.60.944Contact Map
2qguA10.76325.50.944Contact Map
3fwcB40.28425.40.945Contact Map
3robA40.67894.80.946Contact Map
1s94A20.294730.951Contact Map
4orlA10.57892.70.952Contact Map
1vqqA20.62.60.952Contact 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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