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OPENSEQ.org

VMAT2

ID: 1485210662 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 515 (455)
Sequences: 695 (405.8)
Seq/Len: 1.527
Nf(neff/√len): 19.0

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: 1.527).

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
365_G398_M2.5101.00
375_C378_F2.1470.99
12_L15_S2.1010.99
10_R13_R1.8590.97
155_N210_S1.8270.96
176_M192_L1.8210.96
177_F189_A1.8120.96
185_F436_I1.7420.95
236_G419_Y1.6670.93
182_S192_L1.5970.91
320_M326_S1.5960.91
374_L455_T1.5760.90
245_E327_R1.5720.90
184_A188_I1.5560.89
30_L34_N1.5560.89
154_T203_A1.5400.88
206_G210_S1.5400.88
23_L30_L1.4950.86
228_G309_I1.4940.86
33_D38_T1.4910.86
60_I63_T1.4700.85
458_G475_P1.4680.85
297_I470_F1.4490.84
328_K331_L1.4440.84
39_V256_L1.4230.82
339_S342_Y1.4120.82
153_L157_I1.4100.82
165_A262_L1.4000.81
196_G200_S1.3870.80
478_E481_M1.3800.80
140_A461_D1.3570.78
289_L295_I1.3490.77
344_I347_N1.3280.76
162_P166_G1.3190.75
217_E220_K1.3160.75
352_L398_M1.3080.74
267_Q271_L1.3080.74
239_F255_V1.3040.74
243_L255_V1.2990.74
479_E483_I1.2950.73
407_M422_V1.2940.73
180_S185_F1.2820.72
232_G453_L1.2820.72
132_V138_S1.2790.72
187_L243_L1.2790.72
39_V395_A1.2750.72
377_P388_P1.2740.72
9_L13_R1.2740.72
10_R271_L1.2690.71
230_A236_G1.2690.71
177_F183_Y1.2670.71
112_T120_S1.2640.71
54_E183_Y1.2610.70
414_R417_S1.2600.70
408_G466_P1.2530.70
222_M260_V1.2480.69
213_T217_E1.2480.69
111_N115_P1.2470.69
303_C306_N1.2470.69
160_P385_L1.2430.69
365_G399_V1.2400.69
344_I458_G1.2310.68
229_L316_L1.2240.67
140_A434_Y1.2200.67
26_V33_D1.2190.67
115_P120_S1.2160.66
240_G253_F1.2150.66
225_A228_G1.2100.66
194_G240_G1.2080.66
440_A456_I1.2040.65
319_W323_T1.2000.65
30_L292_D1.1960.64
234_L365_G1.1960.64
112_T115_P1.1930.64
19_R23_L1.1920.64
44_I132_V1.1910.64
186_L189_A1.1890.64
116_S446_K1.1870.64
418_V421_S1.1860.64
337_P390_F1.1860.64
480_K484_L1.1800.63
36_L39_V1.1790.63
441_G453_L1.1770.63
480_K483_I1.1770.63
349_F357_G1.1770.63
334_A402_S1.1750.62
115_P119_P1.1730.62
26_V163_M1.1680.62
202_V397_G1.1650.61
68_V75_I1.1640.61
178_A250_T1.1630.61
43_I252_P1.1620.61
208_L439_S1.1590.61
106_Q111_N1.1570.61
350_G357_G1.1560.61
311_M318_I1.1550.60
262_L456_I1.1530.60
113_T120_S1.1480.60
63_T68_V1.1470.60
481_M484_L1.1440.59
137_A411_V1.1420.59
39_V403_M1.1410.59
123_R126_L1.1410.59
159_Y210_S1.1390.59
36_L419_Y1.1380.59
203_A206_G1.1330.58
74_S175_V1.1320.58
479_E484_L1.1320.58
29_A38_T1.1320.58
226_L233_V1.1300.58
42_P155_N1.1290.58
62_T67_L1.1290.58
315_A441_G1.1290.58
278_P325_C1.1240.57
306_N427_D1.1190.57
143_Q420_G1.1180.57
58_T484_L1.1160.57
140_A435_A1.1140.56
189_A408_G1.1080.56
100_H107_H1.1070.56
12_L334_A1.1050.55
230_A401_S1.1030.55
115_P492_K1.1030.55
77_S82_S1.1030.55
61_Q64_R1.1020.55
26_V29_A1.1020.55
176_M355_K1.1000.55
253_F401_S1.0980.55
71_T75_I1.0970.55
46_S236_G1.0960.55
230_A349_F1.0940.54
133_G218_R1.0930.54
159_Y194_G1.0880.54
69_V73_E1.0860.53
214_D219_G1.0840.53
38_T236_G1.0830.53
482_A492_K1.0790.53
111_N120_S1.0780.53
111_N114_V1.0780.53
145_L195_I1.0770.53
68_V74_S1.0770.53
168_C175_V1.0770.53
226_L342_Y1.0770.53
69_V72_S1.0740.52
58_T64_R1.0700.52
199_C236_G1.0690.52
73_E76_F1.0680.52
339_S346_T1.0670.52
182_S364_L1.0670.52
82_S115_P1.0670.52
155_N206_G1.0660.51
49_Y324_M1.0640.51
259_L340_I1.0630.51
111_N119_P1.0630.51
259_L307_M1.0630.51
335_F393_G1.0610.51
458_G462_I1.0580.51
10_R14_D1.0570.50
59_E62_T1.0570.50
156_R460_I1.0560.50
219_G317_P1.0560.50
181_S255_V1.0550.50
145_L265_A1.0550.50
57_S119_P1.0540.50
70_S73_E1.0520.50
146_T188_I1.0510.50
46_S328_K1.0510.50
160_P203_A1.0500.50
218_R222_M1.0490.50
35_M38_T1.0480.50
264_G365_G1.0470.49
115_P118_C1.0460.49
33_D45_P1.0460.49
30_L33_D1.0440.49
228_G454_M1.0430.49
178_A257_A1.0420.49
57_S63_T1.0410.49
153_L458_G1.0410.49
310_A434_Y1.0410.49
119_P122_D1.0410.49
33_D37_L1.0410.49
238_P252_P1.0400.49
8_L12_L1.0390.49
246_F329_W1.0390.49
236_G318_I1.0390.49
483_I492_K1.0380.48
166_G244_Y1.0380.48
208_L431_C1.0370.48
67_L70_S1.0360.48
79_Y120_S1.0360.48
395_A423_Y1.0360.48
479_E482_A1.0360.48
478_E482_A1.0360.48
139_K426_A1.0350.48
484_L492_K1.0350.48
303_C341_S1.0330.48
218_R420_G1.0330.48
9_L14_D1.0320.48
291_K352_L1.0320.48
385_L403_M1.0310.48
320_M330_Q1.0310.48
13_R276_V1.0300.48
450_F454_M1.0300.48
76_F82_S1.0290.48
133_G420_G1.0280.47
231_M463_A1.0280.47
420_G432_M1.0270.47
280_S344_I1.0260.47
114_V120_S1.0260.47
67_L74_S1.0250.47
115_P484_L1.0250.47
67_L71_T1.0220.47
218_R313_E1.0220.47
153_L322_E1.0220.47
26_V34_N1.0210.47
377_P421_S1.0200.47
471_L475_P1.0190.47
225_A418_V1.0180.46
218_R334_A1.0170.46
206_G237_P1.0170.46
154_T264_G1.0160.46
151_G155_N1.0150.46
31_L241_S1.0150.46
264_G289_L1.0140.46
311_M441_G1.0140.46
441_G458_G1.0120.46
286_L395_A1.0120.46
38_T197_S1.0120.46
96_G106_Q1.0110.46
58_T122_D1.0110.46
344_I368_I1.0100.46
342_Y349_F1.0050.45
19_R217_E1.0050.45
166_G177_F1.0050.45
62_T68_V1.0040.45
25_I297_I1.0040.45
408_G457_I1.0020.45
256_L400_D1.0010.45
350_G355_K1.0010.45
33_D39_V1.0010.45
70_S75_I1.0010.45
115_P126_L1.0010.45
63_T123_R1.0000.45
184_A444_I1.0000.45
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  
3wdoA10.82331000.708Contact Map
1pw4A10.78061000.713Contact Map
4j05A20.74371000.721Contact Map
4pypA10.75921000.724Contact Map
2cfqA10.7671000.725Contact Map
2gfpA20.71841000.728Contact Map
4w6vA101000.728Contact Map
3o7qA10.7321000.729Contact Map
4xnjA101000.735Contact Map
4tphA20.70871000.738Contact 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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