OPENSEQ.org
3M0Z

ID: 1516284707 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 249 (231)
Sequences: 708 (496.9)
Seq/Len: 3.065
Nf(neff/√len): 32.7

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: 3.065).

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
201_Y216_I3.2821.00
33_A237_V3.1111.00
141_A176_F2.3701.00
29_E33_A2.3371.00
205_L216_I2.0681.00
192_P213_V1.9200.99
26_N232_T1.8310.99
220_I240_L1.8300.99
27_A53_A1.8280.99
192_P196_I1.7970.99
196_I201_Y1.7260.99
110_G116_V1.6880.98
67_A160_S1.6680.98
155_K188_F1.6550.98
55_V85_E1.6440.98
81_A131_I1.6190.98
239_Q243_M1.6010.97
234_P238_R1.5910.97
19_V56_D1.5860.97
110_G114_T1.5820.97
232_T237_V1.5800.97
189_W215_K1.5610.97
32_D234_P1.5600.97
75_G221_Y1.5340.96
32_D63_L1.5160.96
97_Q100_T1.5080.96
190_L213_V1.4900.96
202_S243_M1.4840.96
180_A186_H1.4590.95
30_I35_E1.4510.95
100_T105_S1.4370.94
174_A178_A1.4190.94
161_S191_E1.3910.93
59_D63_L1.3690.92
170_L204_I1.3660.92
58_R62_K1.3620.92
123_T127_G1.3480.91
238_R242_E1.3440.91
161_S215_K1.3410.91
82_M86_I1.3340.91
198_L239_Q1.3240.90
235_A239_Q1.3190.90
148_E185_A1.3030.90
61_A74_A1.2990.89
147_L151_I1.2690.88
191_E215_K1.2610.87
35_E237_V1.2600.87
241_L244_T1.2550.87
227_K230_G1.2280.85
202_S246_Q1.2270.85
28_R32_D1.2010.84
108_L124_G1.1980.84
59_D87_S1.1960.83
35_E224_I1.1890.83
42_V238_R1.1720.82
39_L210_D1.1710.82
21_A26_N1.1660.81
59_D62_K1.1630.81
199_E239_Q1.1590.81
54_V88_R1.1490.80
52_S134_G1.1490.80
163_K219_H1.1440.79
196_I224_I1.1400.79
45_K219_H1.1390.79
28_R238_R1.1380.79
141_A144_I1.1260.78
235_A238_R1.1160.77
16_C36_G1.1150.77
58_R61_A1.1090.76
22_G38_V1.1050.76
192_P204_I1.0970.75
202_S206_K1.0960.75
36_G214_S1.0930.75
197_D212_G1.0930.75
92_P95_V1.0910.75
235_A242_E1.0900.75
33_A234_P1.0860.74
243_M246_Q1.0840.74
176_F196_I1.0830.74
39_L143_G1.0810.74
137_S160_S1.0750.73
85_E203_E1.0740.73
84_S162_I1.0700.73
97_Q105_S1.0700.73
36_G244_T1.0700.73
126_P148_E1.0670.72
27_A31_Y1.0590.72
201_Y244_T1.0580.72
241_L245_K1.0570.71
104_T109_L1.0560.71
199_E243_M1.0560.71
27_A34_A1.0560.71
239_Q242_E1.0540.71
99_F105_S1.0470.70
149_T206_K1.0460.70
115_V154_L1.0430.70
130_K240_L1.0390.70
22_G26_N1.0360.69
19_V213_V1.0350.69
171_K175_E1.0350.69
115_V159_G1.0320.69
77_P127_G1.0310.69
151_I179_V1.0180.67
38_V73_G1.0120.67
102_V140_A1.0050.66
45_K163_K1.0010.65
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  
3m0zA411000.348Contact Map
3m6yA40.9921000.361Contact Map
1twdA20.799299.90.56Contact Map
3iwpA120.819399.90.582Contact Map
4r9xA20.791299.90.605Contact Map
2bdqA20.726999.80.641Contact Map
4aajA10.75199.80.657Contact Map
1v5xA20.763199.80.66Contact Map
1nsjA10.775199.70.679Contact Map
4wuiA10.775199.70.696Contact 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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