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T0826 11-211

ID: 1406428352 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 201 (193)
Sequences: 556 (455.9)
Seq/Len: 2.881
Nf(neff/√len): 32.8

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: 2.881).

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
121_G125_A3.0231.00
52_N152_S2.8241.00
72_L128_Y2.6831.00
42_T167_Y2.3001.00
69_P129_I2.2101.00
81_Q108_L2.1851.00
163_Q167_Y2.1791.00
69_P125_A2.1381.00
39_F167_Y2.0541.00
49_F155_C2.0041.00
81_Q89_F1.9831.00
82_E89_F1.9230.99
5_L128_Y1.9210.99
12_Y17_L1.9170.99
77_A117_I1.9120.99
69_P128_Y1.9050.99
94_L193_K1.8450.99
93_M96_N1.8160.99
13_S55_F1.7800.99
98_L193_K1.7700.99
141_E145_R1.6960.98
178_T188_G1.6830.98
84_F128_Y1.5570.96
53_F153_F1.5550.96
14_S48_F1.5440.96
61_P65_K1.4710.95
52_N148_L1.4580.94
9_L68_I1.4230.93
21_F188_G1.4040.93
142_L150_A1.4030.93
151_V154_L1.3910.92
126_L130_A1.3560.91
53_F156_A1.3500.91
164_Y168_A1.3320.90
39_F163_Q1.3270.90
21_F175_K1.3200.89
66_V69_P1.3200.89
90_N93_M1.3070.89
10_S17_L1.2970.88
21_F182_V1.2960.88
65_K69_P1.2860.88
85_F143_L1.2850.88
21_F47_L1.2660.87
12_Y16_V1.2570.86
76_A151_V1.2520.86
6_I153_F1.2430.85
160_A173_N1.2410.85
70_L74_I1.2130.83
118_V122_V1.2100.83
146_L150_A1.1970.82
83_I182_V1.1840.81
13_S71_I1.1820.81
58_I67_L1.1790.81
49_F159_I1.1640.80
117_I122_V1.1560.79
21_F25_V1.1560.79
20_A83_I1.1560.79
11_L48_F1.1390.77
53_F149_A1.1350.77
119_C126_L1.1300.77
153_F157_L1.1300.77
93_M172_R1.1260.76
95_N99_Q1.1210.76
50_L87_I1.1140.75
135_Y141_E1.1100.75
180_L185_N1.0960.74
154_L157_L1.0750.71
116_W120_L1.0750.71
76_A121_G1.0750.71
89_F108_L1.0630.70
5_L68_I1.0510.69
130_A134_K1.0460.68
170_F185_N1.0440.68
22_F182_V1.0410.68
169_S173_N1.0350.67
84_F112_G1.0350.67
38_I41_Y1.0320.67
134_K140_K1.0200.66
109_I114_V1.0150.65
62_F66_V1.0140.65
169_S172_R1.0090.64
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: (12Jul14)
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  
4o6yA20.63684.50.963Contact Map
3j1zP20.94533.20.965Contact Map
1fmeA10.11442.30.967Contact Map
2m3eA10.24382.20.968Contact Map
1oqwA20.288620.969Contact Map
3qrxB10.09951.70.97Contact Map
4httA20.27861.60.97Contact Map
2m7gA10.28861.60.97Contact Map
2k1aA10.2091.60.971Contact Map
1q90M10.16421.40.972Contact 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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