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T0825

ID: 1404799818 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 205 (203)
Sequences: 1170 (1116.7)
Seq/Len: 5.764
Nf(neff/√len): 78.4

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: 5.764).

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_L116_L2.1121.00
116_L157_L1.9781.00
77_Q118_Q1.9701.00
75_L157_L1.8911.00
115_Q156_Q1.8691.00
50_F91_F1.8001.00
118_Q159_Q1.8001.00
74_Q115_Q1.7091.00
49_A90_A1.6841.00
71_R112_R1.6501.00
116_L198_L1.6290.99
97_T138_T1.6260.99
56_T138_T1.6110.99
132_F173_F1.6090.99
157_L198_L1.6080.99
96_Q137_Q1.6010.99
149_K160_T1.5920.99
76_L158_L1.5840.99
72_N113_N1.5830.99
55_Q96_Q1.5800.99
67_K78_T1.5640.99
56_T97_T1.5460.99
91_F132_F1.5350.99
124_S165_S1.5290.99
121_T162_T1.5250.99
83_S124_S1.5250.99
9_F50_F1.5220.99
50_F132_F1.5080.99
112_R153_R1.5070.99
66_V100_S1.5040.99
148_V182_S1.4970.99
190_K201_T1.4870.99
90_A131_A1.4830.99
34_L75_L1.4580.99
117_L158_L1.4370.98
113_N154_N1.4350.98
108_K119_T1.4320.98
156_Q197_Q1.4210.98
123_H141_S1.4090.98
29_N70_N1.3850.98
76_L117_L1.3790.98
8_A172_A1.3740.98
71_R153_R1.3710.98
154_N195_N1.3580.98
140_A173_F1.3550.97
33_Q74_Q1.3440.97
80_T121_T1.3440.97
36_Q77_Q1.3330.97
131_A172_A1.3230.97
55_Q178_Q1.3170.97
17_A57_I1.3040.97
152_N193_N1.3030.97
80_T162_T1.2960.96
68_L109_L1.2950.96
14_Q55_Q1.2940.96
55_Q137_Q1.2930.96
31_N72_N1.2920.96
137_Q178_Q1.2820.96
42_S83_S1.2790.96
97_T179_T1.2780.96
14_Q137_Q1.2730.96
72_N154_N1.2710.96
11_P54_G1.2660.96
15_T97_T1.2660.96
30_R71_R1.2610.96
82_H104_D1.2560.96
96_Q178_Q1.2550.96
25_V59_S1.2360.95
66_V107_V1.2230.95
105_K146_K1.2200.95
58_A98_I1.2100.94
64_K105_K1.2080.94
83_S165_S1.2040.94
50_F173_F1.2030.94
74_Q156_Q1.1990.94
57_I98_I1.1980.94
31_N154_N1.1940.94
15_T56_T1.1900.94
150_L191_L1.1880.94
140_A180_I1.1810.93
75_L198_L1.1750.93
26_K37_T1.1750.93
164_H186_D1.1730.93
56_T179_T1.1630.93
39_T80_T1.1590.92
164_H182_S1.1590.92
93_P134_P1.1560.92
18_S22_D1.1540.92
139_I180_I1.1440.92
134_P177_G1.1420.92
77_Q159_Q1.1390.91
15_T138_T1.1380.91
39_T121_T1.1360.91
109_L150_L1.1340.91
153_R194_R1.1220.91
70_N111_N1.1170.90
74_Q197_Q1.1140.90
34_L116_L1.1140.90
138_T179_T1.1050.90
112_R194_R1.0990.89
184_S188_T1.0950.89
14_Q178_Q1.0920.89
36_Q159_Q1.0920.89
35_L76_L1.0890.89
90_A172_A1.0880.89
31_N113_N1.0850.89
41_H63_D1.0810.88
78_T119_T1.0730.88
8_A131_A1.0710.88
98_I139_I1.0700.88
41_H59_S1.0660.87
109_L191_L1.0590.87
72_N195_N1.0570.87
33_Q115_Q1.0560.87
119_T160_T1.0560.87
8_A49_A1.0520.87
125_S166_S1.0500.86
71_R194_R1.0450.86
91_F173_F1.0430.86
42_S124_S1.0300.85
52_P93_P1.0290.85
67_K149_K1.0260.85
16_I98_I1.0240.84
61_S65_T1.0220.84
39_T162_T1.0180.84
23_K64_K1.0170.84
111_N152_N1.0140.84
113_N195_N1.0140.84
67_K108_K1.0090.83
41_H61_S1.0030.83
16_I139_I1.0000.83
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  
1nr0A10.99511000.31Contact Map
2ymuA211000.314Contact Map
1vyhC1011000.319Contact Map
3sfzA10.97561000.322Contact Map
3w15A10.98541000.328Contact Map
3f3fA40.99511000.331Contact Map
4lg9A111000.351Contact Map
3mkqA311000.357Contact Map
3j65q10.99511000.361Contact Map
3zwlB20.99511000.362Contact 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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