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T0818 -force run

ID: 1402702917 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 166 (156)
Sequences: 79 (73.4)
Seq/Len: 0.506
Nf(neff/√len): 5.9

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: 0.506).

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
54_F69_S1.8830.81
77_F88_N1.8130.77
80_I84_I1.7990.77
20_F23_C1.7840.76
133_W139_Y1.7720.75
46_V80_I1.6900.70
49_D54_F1.6160.65
69_S73_I1.5680.62
88_N142_I1.5390.60
45_I69_S1.4970.56
53_L102_G1.4850.55
45_I149_K1.4500.53
136_H139_Y1.4420.52
139_Y145_I1.4350.52
133_W136_H1.4230.51
74_R139_Y1.4030.49
82_G117_T1.3810.47
45_I76_L1.3670.46
82_G118_E1.3660.46
134_N145_I1.3640.46
78_E81_D1.3430.45
45_I73_I1.3300.44
118_E123_Y1.3230.43
41_M83_A1.2950.41
64_N127_F1.2900.41
133_W142_I1.2690.39
50_S74_R1.2690.39
44_C52_K1.2510.38
87_Y93_G1.2510.38
53_L97_E1.2480.37
44_C53_L1.2430.37
77_F93_G1.2180.35
50_S63_D1.2170.35
20_F79_Y1.2030.34
41_M145_I1.1990.34
135_E152_N1.1890.33
8_M16_L1.1780.33
41_M122_E1.1750.32
81_D87_Y1.1730.32
72_E143_N1.1730.32
98_A123_Y1.1610.31
42_M76_L1.1570.31
16_L140_E1.1480.31
45_I48_K1.1260.29
134_N149_K1.1140.28
14_L20_F1.1010.28
13_A18_M1.1000.27
7_I133_W1.0980.27
87_Y147_I1.0960.27
79_Y138_E1.0960.27
22_S120_G1.0950.27
76_L125_I1.0920.27
106_Y115_F1.0880.27
58_N113_F1.0850.27
45_I106_Y1.0820.26
41_M103_I1.0700.26
137_P140_E1.0660.25
46_V115_F1.0660.25
73_I147_I1.0540.25
30_D61_M1.0530.25
11_F28_H1.0520.25
46_V84_I1.0440.24
100_N138_E1.0380.24
66_K127_F1.0320.23
14_L91_G1.0300.23
69_S93_G1.0290.23
28_H120_G1.0260.23
44_C72_E1.0240.23
50_S139_Y1.0190.23
10_S137_P1.0140.22
73_I77_F1.0140.22
150_D160_G1.0130.22
41_M130_H1.0100.22
46_V113_F1.0050.22
37_N115_F1.0020.22
30_D36_E1.0020.22
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  
2mc8A10.668764.20.907Contact Map
3k7cA40.584350.40.914Contact Map
3gzbA80.843448.20.915Contact Map
3zbiC140.144639.10.92Contact Map
3hx8A40.74734.20.922Contact Map
3cu3A10.825329.40.925Contact Map
4n4rB20.6205270.926Contact Map
2geyA40.686723.60.928Contact Map
3f14A10.668719.50.931Contact Map
3bb9A60.692819.20.931Contact 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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