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ldtmabCovariance

ID: 1507825811 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 334 (327)
Sequences: 1012 (541)
Seq/Len: 3.095
Nf(neff/√len): 29.9

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: 3.095).

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
264_A286_T3.5141.00
290_K294_E3.2801.00
191_D209_N3.2141.00
207_E212_I3.1701.00
34_M67_I3.0581.00
205_N212_I2.8721.00
163_D186_H2.7871.00
47_G52_T2.7331.00
324_P327_Q2.5961.00
203_I215_T2.5851.00
107_G301_V2.4681.00
192_A210_G2.4621.00
137_E153_E2.4501.00
191_D297_K2.2561.00
47_G51_V2.2441.00
204_L218_T2.1831.00
268_S272_Q2.1381.00
128_I148_V2.1221.00
162_V187_F2.1051.00
193_V208_R2.0781.00
136_V157_D1.9891.00
262_V292_F1.9591.00
46_I50_G1.9381.00
212_I215_T1.9080.99
29_L32_V1.8810.99
196_R207_E1.8430.99
271_A275_T1.8280.99
232_Y260_I1.8210.99
161_S188_T1.7930.99
242_I246_R1.7740.99
106_V192_A1.7540.99
238_F261_Y1.7380.99
155_F303_I1.7200.99
234_I253_T1.7130.99
57_E60_G1.6950.98
222_K225_A1.6830.98
141_Y331_G1.6770.98
28_V50_G1.6680.98
269_V272_Q1.6550.98
144_N147_E1.6530.98
22_V29_L1.6500.98
22_V32_V1.6500.98
31_S70_D1.6440.98
195_S296_T1.6240.98
36_N60_G1.5980.97
218_T284_V1.5790.97
251_Y290_K1.5750.97
195_S292_F1.5630.97
325_W328_W1.5620.97
110_V164_V1.5400.97
214_K291_W1.5310.96
239_K251_Y1.5080.96
122_A126_K1.4890.96
229_N307_T1.4890.96
249_V267_W1.4880.96
236_E261_Y1.4860.96
60_G169_Y1.4820.96
149_R320_D1.4810.96
134_P159_G1.4790.95
98_P104_V1.4790.95
134_P160_T1.4620.95
120_N123_A1.4500.95
165_K184_A1.4420.95
133_N161_S1.4360.94
272_Q277_T1.4350.94
219_S283_N1.4290.94
107_G194_I1.4130.94
198_D306_N1.4080.94
128_I140_F1.3970.93
196_R305_S1.3880.93
199_D220_M1.3820.93
42_I59_L1.3630.92
254_Q261_Y1.3630.92
117_N146_R1.3580.92
110_V187_F1.3520.92
197_V220_M1.3520.92
124_A173_L1.3330.91
228_N232_Y1.3210.91
250_Q264_A1.2950.89
49_D52_T1.2940.89
249_V265_A1.2910.89
208_R213_I1.2910.89
19_P55_T1.2840.89
208_R295_N1.2750.88
204_L284_V1.2730.88
264_A285_S1.2630.88
218_T282_L1.2630.88
258_S317_G1.2570.87
112_I128_I1.2560.87
155_F231_T1.2530.87
241_L261_Y1.2460.87
45_E56_T1.2410.86
199_D307_T1.2390.86
258_S322_N1.2360.86
238_F241_L1.2310.86
162_V189_I1.2280.86
128_I166_V1.2270.86
216_M284_V1.2200.85
32_V67_I1.2170.85
68_N80_N1.2150.85
219_S277_T1.1910.83
161_S186_H1.1860.83
199_D202_K1.1850.83
268_S277_T1.1820.83
213_I295_N1.1800.82
264_A267_W1.1790.82
239_K250_Q1.1690.82
262_V284_V1.1680.82
317_G322_N1.1550.81
312_L315_T1.1520.80
94_P112_I1.1460.80
235_G254_Q1.1460.80
125_E139_A1.1440.80
43_A56_T1.1390.79
150_W162_V1.1370.79
291_W295_N1.1320.79
228_N260_I1.1310.79
124_A168_T1.1290.78
232_Y255_M1.1260.78
24_A71_A1.1190.78
192_A301_V1.1050.76
326_A329_K1.1050.76
29_L69_A1.1040.76
141_Y323_I1.1020.76
36_N169_Y1.0970.76
24_A52_T1.0950.75
256_S311_V1.0910.75
220_M282_L1.0860.75
104_V189_I1.0860.75
66_T80_N1.0760.74
271_A274_R1.0710.73
61_Y169_Y1.0590.72
33_T41_E1.0580.72
192_A207_E1.0550.72
266_P286_T1.0540.71
15_A121_R1.0530.71
101_G125_E1.0480.71
251_Y294_E1.0450.70
172_N175_D1.0430.70
140_F332_N1.0390.70
268_S271_A1.0380.70
154_S157_D1.0370.70
193_V297_K1.0360.70
73_G77_A1.0350.69
204_L262_V1.0350.69
198_D201_N1.0330.69
112_I166_V1.0300.69
37_S63_K1.0230.68
223_D226_P1.0210.68
234_I255_M1.0170.67
111_A149_R1.0160.67
194_I210_G1.0160.67
24_A27_G1.0160.67
43_A57_E1.0110.67
196_R303_I1.0100.67
195_S262_V1.0100.67
93_M180_Q1.0080.66
194_I237_R1.0060.66
92_T180_Q1.0050.66
246_R283_N1.0050.66
110_V130_I1.0040.66
226_P308_V1.0030.66
153_E326_A1.0020.66
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  
4qtfA101000.264Contact Map
3vypA20.76051000.387Contact Map
4jmnA10.60781000.555Contact Map
4xvoA30.61081000.555Contact Map
4k73A10.61381000.562Contact Map
4hu2A10.56591000.623Contact Map
1zatA10.66771000.761Contact Map
5bmqA101000.786Contact Map
4xxtA10.610899.90.817Contact Map
4lzhA10.604899.90.82Contact 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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