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T0848 172-354 Tp848

ID: 1407216776 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 183 (179)
Sequences: 291 (263)
Seq/Len: 1.626
Nf(neff/√len): 19.7

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: 1.626).

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
96_T149_E2.2210.99
159_N163_Q2.1440.99
124_S127_E2.0720.99
80_Q96_T2.0090.98
98_K149_E1.9890.98
86_I89_D1.8280.97
82_K94_E1.8070.96
5_K8_S1.7750.96
96_T151_T1.7610.96
94_E151_T1.7210.95
99_P179_A1.6890.94
69_I140_F1.5910.91
85_S93_V1.5880.91
157_K167_D1.5790.91
102_A136_Y1.5700.91
32_N36_N1.5620.90
131_Y134_Q1.5540.90
89_D158_K1.5300.89
23_F30_N1.4950.87
97_V152_V1.4800.87
27_T93_V1.4520.85
138_E141_K1.4470.85
98_K147_S1.4030.83
28_G32_N1.3840.81
123_A127_E1.3750.81
5_K9_A1.3410.78
77_S93_V1.3370.78
6_A18_K1.3130.76
79_I153_E1.3050.76
84_T91_A1.2990.75
117_Y151_T1.2930.75
23_F93_V1.2890.75
108_R112_K1.2860.74
150_K175_E1.2610.72
4_A7_L1.2600.72
95_A162_D1.2500.71
112_K138_E1.2480.71
85_S144_G1.2410.70
23_F31_K1.2310.70
80_Q114_K1.2190.69
159_N165_Q1.2170.68
155_K167_D1.2100.68
4_A9_A1.2040.67
6_A23_F1.2030.67
7_L156_M1.2000.67
156_M166_L1.2000.67
4_A8_S1.1960.66
110_E114_K1.1880.66
39_N169_D1.1870.66
84_T93_V1.1750.64
160_D163_Q1.1720.64
33_E102_A1.1660.63
4_A10_Y1.1570.63
42_A67_N1.1550.62
154_V166_L1.1520.62
56_Y155_K1.1420.61
34_I135_V1.1390.61
175_E179_A1.1380.61
41_S162_D1.1190.59
59_S76_N1.1110.58
99_P150_K1.1100.58
78_S98_K1.1060.57
91_A98_K1.1040.57
74_S140_F1.1020.57
95_A165_Q1.0970.56
113_V119_K1.0890.56
108_R138_E1.0800.55
172_R175_E1.0720.54
35_V78_S1.0690.54
52_L55_T1.0660.53
102_A143_L1.0610.53
31_K97_V1.0570.52
114_K118_S1.0550.52
44_D139_E1.0530.52
93_V149_E1.0520.52
67_N71_E1.0470.51
86_I142_K1.0460.51
141_K144_G1.0450.51
79_I125_Y1.0340.50
6_A9_A1.0310.50
117_Y128_A1.0310.50
71_E132_A1.0300.49
59_S154_V1.0240.49
53_S149_E1.0200.48
116_Y119_K1.0170.48
6_A16_F1.0080.47
94_E153_E1.0060.47
27_T35_V1.0040.47
34_I38_F1.0020.47
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: (17Jul14)
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  
3k7cA40.551995.90.816Contact Map
4hz9B20.655758.10.891Contact Map
1vqqA20.62337.10.904Contact Map
3robA40.69418.80.917Contact Map
2gxfA40.6175160.919Contact Map
3fkaA40.61212.60.923Contact Map
3hx8A40.67219.60.927Contact Map
3blzA120.63937.20.931Contact Map
3dukA60.65036.90.932Contact Map
3ehcA40.6124.20.938Contact 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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