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OPENSEQ.org

1a_48_380

ID: 1486796661 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 333 (326)
Sequences: 386 (279.7)
Seq/Len: 1.184
Nf(neff/√len): 15.5

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: 1.184).

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
192_F235_N2.2180.99
189_V203_I2.1350.98
225_Y241_I2.0630.97
217_V245_N1.9360.96
59_D62_G1.8670.95
134_G156_G1.8550.94
128_A151_V1.8460.94
142_L212_F1.6070.87
11_D15_D1.5710.85
62_G76_H1.5510.84
169_E180_Q1.4970.81
264_K286_K1.4760.80
136_D204_H1.4690.79
310_M314_A1.4620.79
52_P60_F1.4620.79
161_D164_M1.4610.79
119_Q141_G1.4590.78
142_L218_H1.4530.78
58_I149_H1.4140.75
227_L241_I1.4040.75
5_L9_E1.3920.74
291_E299_C1.3870.73
76_H114_C1.3850.73
292_V317_L1.3840.73
136_D228_E1.3810.73
23_L42_A1.3760.72
312_A327_N1.3760.72
112_N153_V1.3700.72
191_K201_S1.3660.72
141_G158_V1.3650.72
59_D80_P1.3310.69
311_K329_Q1.3240.68
8_E158_V1.3230.68
76_H80_P1.3220.68
128_A154_L1.3220.68
163_A295_I1.3170.68
190_I209_L1.3080.67
40_R62_G1.2960.66
181_R206_W1.2790.64
296_A313_V1.2670.63
80_P225_Y1.2600.63
116_N120_D1.2580.62
126_D152_R1.2510.62
183_G188_E1.2390.61
23_L264_K1.2350.60
199_T206_W1.2300.60
114_C121_C1.2260.60
80_P133_G1.2230.59
238_T248_C1.2220.59
96_R101_L1.2210.59
141_G225_Y1.2170.59
232_L237_M1.2170.59
279_W289_V1.2160.59
59_D67_H1.2100.58
140_Q224_T1.2090.58
190_I205_G1.2070.58
36_A204_H1.2040.57
204_H228_E1.2040.57
83_G136_D1.2020.57
122_D150_G1.1860.56
124_Q150_G1.1840.56
157_T298_R1.1800.55
158_V215_E1.1770.55
5_L42_A1.1760.55
180_Q198_S1.1740.55
33_H89_R1.1730.54
322_S328_G1.1710.54
179_W229_R1.1710.54
9_E216_S1.1620.53
63_S76_H1.1610.53
144_D148_S1.1570.53
15_D180_Q1.1570.53
150_G182_D1.1550.53
47_C131_I1.1510.52
64_W79_C1.1480.52
319_A325_I1.1480.52
80_P145_A1.1470.52
13_F38_A1.1460.52
149_H171_F1.1430.52
309_N317_L1.1420.51
237_M318_S1.1400.51
101_L104_S1.1390.51
272_E280_K1.1380.51
142_L213_F1.1330.51
135_Y233_K1.1300.50
6_S166_F1.1290.50
80_P131_I1.1280.50
23_L96_R1.1200.49
326_I331_I1.1200.49
164_M181_R1.1160.49
40_R59_D1.1160.49
309_N312_A1.1140.49
42_A162_G1.1140.49
72_D158_V1.1130.49
17_Y21_F1.1110.48
92_E287_T1.1110.48
6_S9_E1.1080.48
88_A92_E1.1080.48
267_G277_N1.1060.48
61_G76_H1.1060.48
312_A318_S1.1060.48
86_D89_R1.1030.48
110_V115_L1.1000.47
199_T204_H1.0990.47
79_C314_A1.0980.47
205_G288_T1.0960.47
329_Q332_M1.0920.47
4_K125_A1.0920.47
216_S287_T1.0880.46
154_L266_V1.0870.46
59_D83_G1.0830.46
131_I311_K1.0770.45
131_I204_H1.0740.45
295_I321_S1.0710.45
139_F212_F1.0710.45
13_F33_H1.0710.45
188_E205_G1.0710.45
130_C154_L1.0710.45
64_W330_A1.0690.44
318_S327_N1.0640.44
260_E329_Q1.0600.44
176_K257_V1.0590.43
147_H219_C1.0560.43
179_W289_V1.0560.43
158_V220_I1.0540.43
287_T292_V1.0480.42
19_G28_Q1.0470.42
308_E312_A1.0460.42
98_R326_I1.0460.42
214_T292_V1.0460.42
27_Q135_Y1.0450.42
138_G144_D1.0430.42
21_F209_L1.0420.42
23_L266_V1.0420.42
160_F208_D1.0410.42
119_Q221_D1.0400.42
228_E236_I1.0400.42
58_I288_T1.0400.42
78_C143_C1.0390.42
161_D235_N1.0390.42
169_E181_R1.0380.41
55_D283_R1.0380.41
61_G121_C1.0340.41
5_L278_R1.0340.41
188_E207_Q1.0340.41
8_E291_E1.0340.41
153_V292_V1.0300.41
58_I128_A1.0290.41
287_T291_E1.0280.41
99_K221_D1.0260.40
23_L249_P1.0240.40
37_G40_R1.0240.40
131_I179_W1.0230.40
136_D145_A1.0220.40
96_R168_R1.0220.40
132_H194_F1.0190.40
274_W288_T1.0180.40
161_D330_A1.0170.40
161_D295_I1.0170.40
16_R227_L1.0160.39
39_L160_F1.0140.39
36_A179_W1.0140.39
320_K323_T1.0080.39
37_G322_S1.0060.38
80_P136_D1.0060.38
105_D209_L1.0060.38
43_E157_T1.0030.38
68_F144_D1.0030.38
131_I298_R1.0010.38
195_E209_L1.0000.38
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  
2knjA10.090115.30.967Contact Map
3ld1A10.18927.20.971Contact Map
3cx5H20.20125.80.972Contact Map
4b8nA40.12015.70.972Contact Map
4m1aA20.16225.70.972Contact Map
4wikA20.22524.40.974Contact Map
1x3xA20.09313.70.975Contact Map
1whnA10.20723.70.975Contact Map
4n1vA10.24923.60.975Contact Map
2jojA10.23123.40.975Contact 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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