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T0818 -force run

ID: 1405102356 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 166 (142)
Sequences: 1024 (893)
Seq/Len: 7.211
Nf(neff/√len): 74.9

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: 7.211).

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
49_D52_K5.9671.00
44_C49_D2.6841.00
41_M53_L2.5221.00
44_C52_K1.8891.00
52_K55_D1.7761.00
43_E47_N1.7541.00
15_S18_M1.7251.00
39_V43_E1.7191.00
86_S91_G1.6741.00
45_I50_S1.6541.00
45_I53_L1.6521.00
37_N40_R1.6501.00
78_E82_G1.6121.00
115_F119_T1.5871.00
127_F130_H1.5150.99
117_T123_Y1.5100.99
124_T127_F1.4850.99
50_S54_F1.4520.99
97_E102_G1.4090.99
54_F73_I1.4010.99
127_F131_Y1.3670.99
117_T120_G1.3580.98
52_K56_F1.3290.98
20_F23_C1.2980.98
110_H113_F1.2510.97
97_E101_D1.2430.97
102_G105_C1.2400.97
40_R52_K1.2330.97
76_L81_D1.2290.97
91_G95_G1.2170.96
48_K53_L1.2100.96
105_C108_S1.2100.96
38_A41_M1.2040.96
108_S111_P1.1850.96
14_L17_I1.1760.95
72_E75_Q1.1750.95
16_L19_I1.1600.95
54_F57_Y1.1540.95
12_L16_L1.1520.95
39_V46_V1.1100.93
44_C56_F1.1100.93
98_A102_G1.1090.93
99_K102_G1.1060.93
125_I129_Y1.1030.93
129_Y132_I1.0940.92
139_Y144_M1.0910.92
135_E138_E1.0850.92
107_Y110_H1.0800.92
139_Y145_I1.0760.92
126_S129_Y1.0610.91
42_M46_V1.0600.91
136_H139_Y1.0580.91
127_F133_W1.0330.89
37_N64_N1.0310.89
108_S112_E1.0280.89
123_Y127_F1.0260.89
133_W136_H1.0160.88
13_A16_L1.0150.88
68_S73_I1.0100.88
140_E144_M1.0070.88
129_Y134_N1.0020.87
115_F118_E1.0000.87
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  
3k7cA40.524196.30.771Contact Map
1vqqA20.75393.30.807Contact Map
2mc8A10.686792.60.812Contact Map
3zbiC140.144670.40.858Contact Map
3ombA10.554256.70.87Contact Map
3bb9A60.692848.90.875Contact Map
3gzbA80.819345.80.878Contact Map
2ap3A10.8133440.879Contact Map
4kysA20.686743.70.879Contact Map
4n4rB20.7289430.88Contact 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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