GREMLIN.BAKERLAB.org
Powered by OPENSEQ.org
2

ID: 1501762574 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 212 (208)
Sequences: 449 (296.1)
Seq/Len: 2.159
Nf(neff/√len): 20.5

HHblits Results: (2016_02)
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: 2.159).

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
194_P202_D2.4541.00
112_R115_E2.0460.99
29_Q32_D1.9560.99
35_Q40_Y1.7410.97
85_I117_I1.7340.97
2_A6_K1.7100.97
15_P19_K1.6250.95
195_D202_D1.5880.95
2_A5_D1.5660.94
15_P25_A1.5600.94
186_Y189_Q1.5080.92
112_R121_K1.5060.92
150_N160_T1.4980.92
3_Q6_K1.4960.92
17_M21_F1.4890.92
67_L75_L1.4860.92
15_P20_E1.4820.92
146_S151_G1.4700.91
118_E121_K1.4680.91
69_P145_L1.4610.91
26_I29_Q1.4590.91
32_D36_W1.4000.88
198_I203_F1.3760.87
22_A29_Q1.3730.87
193_G202_D1.3270.84
72_L75_L1.3250.84
2_A154_P1.3070.83
15_P26_I1.3020.83
14_L29_Q1.2970.82
64_R145_L1.2950.82
25_A28_V1.2880.82
143_E156_I1.2850.82
21_F29_Q1.2670.80
11_P14_L1.2640.80
25_A30_P1.2550.79
196_G202_D1.2470.79
3_Q7_P1.2320.78
10_I14_L1.2270.77
5_D170_K1.2230.77
31_Q34_I1.2230.77
9_C12_P1.2220.77
11_P40_Y1.2150.76
11_P22_A1.2010.75
4_T7_P1.1970.75
11_P21_F1.1920.74
21_F25_A1.1860.74
11_P15_P1.1850.74
87_A159_S1.1700.72
160_T202_D1.1590.71
11_P29_Q1.1580.71
36_W40_Y1.1570.71
36_W161_F1.1570.71
25_A29_Q1.1560.71
198_I205_Q1.1560.71
3_Q8_T1.1470.70
115_E121_K1.1460.70
22_A32_D1.1440.70
21_F37_A1.1430.70
132_V138_L1.1430.70
92_Q185_N1.1380.69
139_K165_Y1.1280.68
32_D38_A1.1270.68
191_V207_P1.1270.68
41_F90_L1.1230.68
107_V180_V1.1170.67
121_K163_F1.1150.67
17_M26_I1.1110.67
11_P26_I1.1060.66
17_M29_Q1.0990.65
170_K188_E1.0980.65
182_R203_F1.0900.64
5_D89_E1.0840.64
45_S80_A1.0820.64
5_D189_Q1.0820.64
69_P117_I1.0770.63
104_F108_M1.0760.63
10_I33_L1.0710.62
39_D153_S1.0710.62
3_Q121_K1.0700.62
50_P97_V1.0680.62
200_V209_V1.0630.62
39_D101_T1.0580.61
182_R190_E1.0550.61
20_E25_A1.0420.59
12_P15_P1.0420.59
112_R148_D1.0410.59
21_F26_I1.0410.59
134_I137_T1.0330.58
29_Q125_L1.0320.58
2_A90_L1.0310.58
26_I30_P1.0250.57
29_Q36_W1.0210.57
89_E138_L1.0210.57
28_V36_W1.0200.57
25_A36_W1.0180.57
2_A117_I1.0170.57
153_S188_E1.0170.57
121_K160_T1.0140.56
143_E154_P1.0140.56
101_T107_V1.0130.56
16_K145_L1.0100.56
22_A25_A1.0060.55
107_V144_V1.0050.55
193_G198_I1.0020.55
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: (06Aug15)
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  
4mvfA10.929299.90.468Contact Map
3mwuA10.863299.90.472Contact Map
4qoxA10.924599.90.475Contact Map
3q5iA10.943499.90.476Contact Map
3lijA10.943499.90.485Contact Map
3nyvA10.910499.90.491Contact Map
2julA10.712399.90.524Contact Map
4ik8A10.886899.80.589Contact Map
3sjsA10.78399.80.6Contact Map
4i2yA20.924599.80.6Contact 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.

Page generated in 0.018 seconds.