OPENSEQ.org
AllY-alignment

ID: 1517503575 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 377 (365)
Sequences: 1305 (890.1)
Seq/Len: 3.575
Nf(neff/√len): 46.6

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: 3.575).

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
162_L351_V4.7991.00
116_G333_I4.4341.00
218_V237_A4.3311.00
152_R156_E3.4501.00
206_L245_V3.1881.00
184_L219_V3.1391.00
204_V249_L2.6901.00
93_E97_E2.6431.00
116_G335_V2.5951.00
321_V332_V2.5621.00
206_L221_A2.5341.00
159_I320_L2.5021.00
186_V206_L2.3991.00
165_V354_A2.2811.00
14_F22_W2.2791.00
166_V216_V2.2171.00
115_E124_P2.2121.00
118_D331_K2.2111.00
221_A248_A2.2031.00
65_G74_S2.1841.00
206_L219_V2.1541.00
64_K254_Q2.1451.00
210_P213_V2.0651.00
158_V334_E2.0361.00
334_E349_V1.9471.00
162_L332_V1.9081.00
127_V350_R1.8841.00
238_S243_M1.8701.00
236_G247_R1.8410.99
115_E126_Y1.7500.99
64_K74_S1.7400.99
247_R250_L1.7230.99
15_L18_E1.7140.99
300_E303_D1.6770.99
85_A337_L1.6660.99
152_R250_L1.6600.99
118_D121_T1.6490.99
127_V333_I1.6390.98
155_E314_E1.6150.98
151_G156_E1.5880.98
223_T252_V1.5850.98
96_P108_T1.5740.98
150_A346_V1.5690.98
209_L220_G1.5650.98
203_R226_E1.5330.97
106_Y109_E1.5290.97
159_I163_L1.5290.97
146_N165_V1.4990.97
158_V349_V1.4990.97
158_V161_G1.4970.97
127_V335_V1.4640.96
114_V129_A1.4550.96
210_P217_Y1.4500.96
67_T70_Q1.4410.96
125_V333_I1.4340.96
148_L348_R1.4290.96
209_L218_V1.4220.95
85_A148_L1.4160.95
120_T331_K1.3950.95
74_S254_Q1.3910.95
165_V351_V1.3880.95
149_S161_G1.3830.94
243_M247_R1.3770.94
96_P107_R1.3600.94
17_K69_I1.3440.93
159_I317_T1.3380.93
18_E21_R1.3350.93
163_L239_P1.3330.93
152_R236_G1.3300.93
236_G250_L1.3240.93
314_E318_E1.2980.92
20_L73_V1.2970.92
117_V122_R1.2530.90
154_R158_V1.2490.89
129_A133_F1.2480.89
35_V38_F1.2390.89
36_E51_R1.2310.89
163_L237_A1.2270.88
322_E325_A1.2250.88
65_G247_R1.2200.88
161_G349_V1.2180.88
116_G124_P1.2170.88
116_G132_V1.1940.86
238_S244_A1.1920.86
13_A153_L1.1920.86
64_K236_G1.1910.86
208_L219_V1.1850.86
195_R199_R1.1840.86
332_V351_V1.1820.86
148_L337_L1.1810.86
185_E300_E1.1770.85
134_H145_T1.1760.85
19_T152_R1.1730.85
324_V354_A1.1730.85
183_E205_E1.1660.85
4_I11_F1.1630.84
309_T316_L1.1580.84
165_V349_V1.1570.84
221_A249_L1.1560.84
16_P19_T1.1480.83
164_E251_E1.1460.83
197_L252_V1.1450.83
157_A347_V1.1370.83
245_V297_G1.1350.82
309_T319_E1.1270.82
154_R347_V1.1240.82
319_E323_R1.1230.82
40_D45_I1.1230.82
184_L319_E1.1220.81
77_M344_V1.1190.81
167_E254_Q1.1190.81
339_L345_P1.1170.81
120_T321_V1.1090.80
64_K167_E1.1080.80
156_E236_G1.1080.80
65_G254_Q1.1050.80
236_G254_Q1.1020.80
198_E203_R1.1010.80
149_S347_V1.1000.80
219_V304_L1.0970.79
324_V332_V1.0920.79
91_I126_Y1.0900.79
211_S214_E1.0890.79
69_I73_V1.0860.78
114_V335_V1.0860.78
37_K48_E1.0850.78
161_G313_L1.0830.78
220_G235_F1.0820.78
210_P216_V1.0760.78
321_V325_A1.0750.77
321_V351_V1.0740.77
46_P68_R1.0740.77
84_A339_L1.0730.77
120_T325_A1.0670.77
73_V136_W1.0660.77
151_G238_S1.0650.77
65_G73_V1.0650.77
74_S151_G1.0610.76
173_I210_P1.0580.76
132_V350_R1.0550.76
181_P209_L1.0500.75
64_K247_R1.0490.75
215_G323_R1.0440.74
338_T346_V1.0440.74
4_I9_E1.0440.74
78_E251_E1.0430.74
35_V48_E1.0420.74
64_K160_Q1.0390.74
50_R86_E1.0380.74
194_R204_V1.0350.74
366_N369_E1.0340.73
17_K30_R1.0340.73
318_E322_E1.0320.73
339_L343_D1.0310.73
219_V241_P1.0290.73
121_T331_K1.0280.73
18_E22_W1.0260.73
366_N370_K1.0240.72
92_I112_E1.0240.72
36_E45_I1.0220.72
77_M148_L1.0170.72
202_G256_L1.0150.72
158_V347_V1.0150.72
30_R37_K1.0100.71
172_S355_S1.0100.71
107_R110_P1.0080.71
11_F16_P1.0060.71
36_E265_S1.0050.70
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  
4v1tA20.94431000.241Contact Map
4q86A80.9311000.28Contact Map
1ekzA10.185718.90.965Contact Map
1sp8A40.214914.10.967Contact Map
3adlA10.183140.967Contact Map
3llhA20.167112.90.967Contact Map
2mdrA10.209511.40.968Contact Map
1o0wA20.206910.80.969Contact Map
4wyqB20.196310.70.969Contact Map
1di2A20.164510.60.969Contact 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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