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T0848 172-354 Tp848

ID: 1407101906 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 183 (180)
Sequences: 470 (429.3)
Seq/Len: 2.611
Nf(neff/√len): 32.0

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: 2.611).

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
98_K149_E2.9081.00
82_K94_E2.2631.00
159_N163_Q2.2261.00
124_S127_E2.2211.00
94_E151_T2.1641.00
96_T149_E2.1421.00
91_A164_W2.0010.99
86_I91_A1.9650.99
96_T151_T1.9130.99
78_S98_K1.8080.99
5_K8_S1.7910.99
108_R112_K1.7600.98
80_Q96_T1.7060.98
27_T93_V1.6560.97
156_M164_W1.6450.97
97_V152_V1.6200.97
89_D158_K1.6100.97
157_K167_D1.6010.96
92_I153_E1.5920.96
28_G32_N1.5900.96
6_A11_V1.5380.95
123_A127_E1.5330.95
4_A7_L1.5210.95
156_M166_L1.4890.94
4_A10_Y1.4580.93
82_K96_T1.4530.93
8_S12_D1.4470.93
6_A18_K1.4320.92
38_F41_S1.4240.92
91_A156_M1.4190.92
7_L156_M1.3890.91
5_K9_A1.3690.90
32_N36_N1.3670.90
131_Y134_Q1.3640.90
160_D163_Q1.3560.89
23_F30_N1.2950.86
6_A91_A1.2890.86
159_N165_Q1.2780.85
141_K144_G1.2720.85
9_A14_L1.2340.82
127_E130_K1.2190.81
87_S90_E1.2020.80
32_N41_S1.1990.80
154_V166_L1.1880.79
86_I89_D1.1840.79
28_G57_A1.1750.78
99_P179_A1.1740.78
107_D115_D1.1720.78
6_A9_A1.1650.77
30_N33_E1.1630.77
84_T91_A1.1610.77
59_S76_N1.1420.75
32_N35_V1.1180.73
98_K147_S1.1170.73
77_S99_P1.1150.73
117_Y128_A1.1130.72
112_K138_E1.1120.72
108_R138_E1.1000.71
40_E44_D1.0930.70
109_I113_V1.0840.70
76_N100_V1.0810.69
77_S93_V1.0780.69
172_R175_E1.0770.69
108_R139_E1.0750.69
31_K35_V1.0690.68
149_E154_V1.0650.68
55_T69_I1.0630.67
140_F143_L1.0560.67
28_G58_D1.0530.66
19_D22_D1.0520.66
31_K97_V1.0490.66
6_A164_W1.0410.65
23_F91_A1.0370.65
172_R176_L1.0370.65
69_I73_L1.0330.64
23_F27_T1.0290.64
27_T95_A1.0240.63
139_E142_K1.0220.63
81_A84_T1.0200.63
44_D162_D1.0190.63
113_V132_A1.0180.62
77_S100_V1.0140.62
89_D114_K1.0100.62
6_A16_F1.0020.61
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  
3k7cA40.546492.90.82Contact Map
4hz9B20.639346.80.884Contact Map
1vqqA20.62332.70.894Contact Map
3robA40.694130.912Contact Map
3blzA120.6393130.912Contact Map
3hx8A40.67768.20.92Contact Map
2gxfA40.601180.92Contact Map
3fkaA40.62845.90.925Contact Map
3dukA60.65575.10.927Contact Map
3ehcA40.63394.60.928Contact 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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