GREMLIN.BAKERLAB.org
Powered by OPENSEQ.org
ToMV_full_aln

ID: 1500292846 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 441 (401)
Sequences: 1519 (1422.9)
Seq/Len: 3.788
Nf(neff/√len): 71.1

Jackhmmer Results: (2016_04)
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: 3.788).

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
307_L405_S3.3361.00
296_T299_C3.1401.00
378_A409_K3.0261.00
370_H399_H2.8941.00
379_D410_S2.6951.00
326_S329_M2.5871.00
239_L373_Q2.4061.00
344_K378_A2.3941.00
230_F233_L2.3801.00
173_I261_Y2.3551.00
240_M373_Q2.2341.00
231_K256_D2.1341.00
329_M332_G2.0881.00
382_L403_S2.0811.00
186_V191_A2.0761.00
323_K326_S1.9971.00
268_P373_Q1.9721.00
239_L268_P1.9631.00
378_A408_T1.9421.00
279_P282_F1.9371.00
143_R146_L1.9321.00
377_Y380_V1.8811.00
146_L149_G1.8781.00
346_K380_V1.8481.00
194_M198_R1.8130.99
240_M268_P1.7880.99
346_K350_F1.7860.99
267_I373_Q1.7740.99
185_L218_F1.7570.99
270_I373_Q1.7250.99
184_I195_I1.7200.99
211_N214_T1.7070.99
372_V377_Y1.6710.99
159_V291_E1.6590.99
166_G169_K1.6510.99
142_L146_L1.6360.99
303_V307_L1.6060.98
293_R298_R1.5930.98
328_E331_S1.5550.98
323_K327_Q1.5280.98
327_Q331_S1.5240.98
303_V411_L1.4900.97
346_K377_Y1.4780.97
189_R192_A1.4710.97
379_D412_K1.4380.96
240_M401_L1.4230.96
240_M270_I1.4230.96
157_K257_I1.4170.96
372_V380_V1.4120.96
270_I370_H1.4050.96
240_M307_L1.4010.95
240_M375_E1.4000.95
296_T370_H1.3880.95
349_T355_K1.3850.95
239_L401_L1.3680.95
239_L267_I1.3640.95
381_S414_Y1.3620.94
186_V192_A1.3620.94
422_V425_I1.3530.94
329_M333_A1.3430.94
212_V216_D1.3420.94
183_L230_F1.3330.94
167_C176_R1.3250.93
351_T354_D1.3210.93
352_Q368_T1.3170.93
326_S331_S1.3170.93
311_Y401_L1.3080.93
238_G241_L1.3060.93
240_M267_I1.3050.93
98_T336_I1.3000.93
299_C370_H1.2980.92
382_L413_Y1.2980.92
347_I358_L1.2970.92
213_R217_S1.2920.92
354_D383_V1.2900.92
188_G191_A1.2860.92
299_C304_T1.2840.92
252_M402_V1.2820.92
190_Q194_M1.2790.92
214_T217_S1.2740.91
186_V195_I1.2690.91
296_T304_T1.2620.91
189_R240_M1.2610.91
376_T407_H1.2420.90
299_C307_L1.2400.90
164_V167_C1.2380.90
240_M245_C1.2320.90
190_Q375_E1.2310.90
84_V87_S1.2290.89
98_T102_K1.2220.89
165_P265_Q1.2150.89
242_H245_C1.2140.89
234_F239_L1.2120.89
367_H401_L1.2100.88
367_H372_V1.2070.88
240_M296_T1.2000.88
323_K329_M1.1990.88
173_I195_I1.1910.87
211_N215_V1.1850.87
280_A283_A1.1850.87
239_L270_I1.1760.86
163_G166_G1.1690.86
379_D415_T1.1690.86
367_H371_E1.1680.86
345_G350_F1.1670.86
143_R149_G1.1660.86
375_E402_V1.1660.86
265_Q397_S1.1650.86
268_P375_E1.1650.86
150_E153_V1.1650.86
346_K351_T1.1630.86
345_G379_D1.1630.86
92_A95_V1.1620.86
242_H261_Y1.1570.85
382_L411_L1.1470.85
303_V310_R1.1470.85
239_L269_Y1.1470.85
350_F354_D1.1410.84
342_P346_K1.1390.84
269_Y373_Q1.1350.84
328_E332_G1.1340.84
212_V215_V1.1330.84
303_V407_H1.1310.83
76_D79_S1.1300.83
373_Q401_L1.1220.83
293_R303_V1.1190.83
240_M271_N1.1130.82
262_G373_Q1.1130.82
173_I234_F1.1110.82
171_K306_F1.1110.82
54_L57_I1.1070.82
188_G239_L1.1070.82
266_Q374_G1.1000.81
143_R297_L1.0990.81
327_Q330_V1.0990.81
104_H108_L1.0980.81
273_V276_F1.0950.81
232_R257_I1.0940.81
270_I371_E1.0930.80
163_G169_K1.0910.80
262_G402_V1.0910.80
212_V218_F1.0900.80
97_E101_R1.0890.80
164_V265_Q1.0870.80
163_G168_G1.0740.79
158_V258_A1.0690.78
304_T307_L1.0640.78
278_Y282_F1.0630.78
303_V399_H1.0620.78
205_I208_T1.0600.78
150_E154_S1.0560.77
211_N217_S1.0560.77
278_Y281_H1.0530.77
186_V299_C1.0530.77
234_F267_I1.0520.77
187_P240_M1.0500.77
176_R259_Y1.0480.76
369_V403_S1.0460.76
305_H309_Q1.0430.76
306_F310_R1.0340.75
368_T371_E1.0330.75
176_R373_Q1.0310.75
214_T218_F1.0280.74
263_D266_Q1.0250.74
422_V426_R1.0250.74
296_T415_T1.0250.74
267_I399_H1.0220.74
193_E199_A1.0210.74
240_M366_V1.0200.74
291_E295_T1.0190.74
61_T403_S1.0180.73
164_V401_L1.0180.73
97_E100_A1.0170.73
33_V37_K1.0160.73
240_M299_C1.0150.73
187_P405_S1.0140.73
346_K354_D1.0140.73
138_K141_T1.0120.73
240_M399_H1.0050.72
262_G368_T1.0050.72
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  
3vkwA10.99771000.274Contact Map
2xzlA10.93651000.485Contact Map
2wjyA10.90021000.494Contact Map
2gk6A20.87531000.496Contact Map
4b3fX10.95011000.499Contact Map
4pj3A10.95691000.499Contact Map
3upuA30.60771000.526Contact Map
3e1sA10.88441000.542Contact Map
1w36D20.85031000.547Contact Map
4n0nA10.76421000.57Contact 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 0.0257 seconds.