May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org

Mcd

ID: 1485516475 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 548 (537)
Sequences: 567 (254.1)
Seq/Len: 1.056
Nf(neff/√len): 11.0

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: 1.056).

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
329_A344_F4.7701.00
342_S392_L4.6501.00
332_D398_G3.8701.00
310_H384_G3.1451.00
309_V327_L2.8801.00
309_V329_A2.6771.00
263_D266_K2.6701.00
309_V344_F2.2610.98
349_V359_T2.1930.98
225_S228_S2.0540.97
306_E386_R1.9590.95
143_R452_G1.8830.94
262_T265_Q1.8330.93
307_W389_A1.7740.91
263_D267_A1.7690.91
332_D335_T1.7550.90
324_V345_L1.7430.90
359_T362_M1.6730.87
11_L273_L1.6560.87
145_R149_L1.6480.86
310_H383_D1.6480.86
235_E238_R1.6210.85
369_V376_K1.5810.83
176_R235_E1.5740.83
308_V386_R1.5700.82
294_G337_D1.5610.82
101_Q490_L1.5580.82
65_E68_R1.5330.80
52_F537_I1.5100.79
494_R539_A1.5080.79
323_H350_P1.4680.76
307_W344_F1.4670.76
341_L398_G1.4400.74
54_A544_R1.4390.74
483_L545_R1.4340.74
189_G193_R1.4300.73
194_D319_A1.4120.72
284_F407_T1.4040.71
106_I118_D1.4030.71
535_A539_A1.4000.71
362_M383_D1.3970.71
264_A390_E1.3920.70
429_V521_I1.3740.69
307_W397_E1.3730.69
147_V151_R1.3540.67
395_G399_Q1.3510.67
12_T23_A1.3310.65
264_A267_A1.3300.65
302_K342_S1.3300.65
536_E542_I1.3280.65
176_R210_V1.3280.65
327_L346_A1.3250.65
268_A347_E1.3090.64
300_A344_F1.3040.63
22_E117_Q1.3030.63
269_W278_I1.3020.63
146_L537_I1.2980.63
219_F541_V1.2910.62
490_L535_A1.2880.62
261_G265_Q1.2820.61
453_K505_Q1.2710.60
12_T19_P1.2710.60
18_L71_R1.2680.60
59_W494_R1.2640.60
375_M525_A1.2620.59
63_Y488_A1.2580.59
19_P30_S1.2550.59
327_L387_V1.2540.59
293_L296_L1.2520.58
215_I539_A1.2500.58
196_L319_A1.2470.58
59_W539_A1.2420.58
42_V354_A1.2400.57
16_D117_Q1.2360.57
47_L396_V1.2280.56
13_L360_P1.2250.56
19_P26_E1.2210.56
16_D26_E1.2200.55
90_I459_V1.2110.55
70_M94_A1.2040.54
137_G145_R1.2020.54
301_V310_H1.2020.54
253_A494_R1.1980.53
309_V346_A1.1940.53
218_E266_K1.1920.53
113_T117_Q1.1830.52
18_L117_Q1.1800.52
30_S44_S1.1800.52
56_A536_E1.1790.52
147_V537_I1.1780.52
528_L531_F1.1770.51
21_V116_V1.1680.51
257_I393_L1.1670.50
101_Q526_R1.1640.50
12_T32_L1.1640.50
21_V26_E1.1630.50
264_A336_T1.1590.50
27_T117_Q1.1550.49
319_A378_Y1.1540.49
283_V325_M1.1500.49
526_R529_N1.1500.49
22_E30_S1.1490.49
11_L396_V1.1480.49
26_E41_K1.1470.49
216_P258_L1.1400.48
18_L25_F1.1390.48
12_T30_S1.1300.47
9_D23_A1.1260.47
15_S44_S1.1240.46
172_R235_E1.1240.46
15_S117_Q1.1230.46
20_E116_V1.1230.46
13_L117_Q1.1200.46
27_T30_S1.1200.46
23_A27_T1.1190.46
246_L541_V1.1170.46
24_L116_V1.1160.46
206_A328_L1.1140.46
172_R234_E1.1110.45
94_A459_V1.1090.45
12_T24_L1.1090.45
17_A20_E1.1050.45
234_E465_R1.1050.45
496_A524_D1.1040.45
13_L22_E1.1020.44
8_G43_S1.1000.44
118_D396_V1.1000.44
372_Y531_F1.0990.44
41_K381_G1.0970.44
33_K344_F1.0950.44
54_A543_A1.0930.44
12_T27_T1.0920.43
269_W345_L1.0890.43
62_T464_A1.0890.43
160_G213_L1.0880.43
298_T309_V1.0880.43
56_A538_Q1.0870.43
144_A452_G1.0870.43
453_K509_G1.0830.43
8_G30_S1.0830.43
145_R148_A1.0830.43
304_G350_P1.0810.42
182_R204_A1.0800.42
12_T42_V1.0800.42
137_G149_L1.0800.42
294_G335_T1.0790.42
508_G511_G1.0760.42
15_S18_L1.0750.42
48_E442_K1.0750.42
16_D23_A1.0730.42
11_L14_A1.0730.42
8_G27_T1.0720.42
511_G541_V1.0720.42
179_A392_L1.0710.42
253_A257_I1.0700.41
29_R43_S1.0700.41
293_L538_Q1.0670.41
358_P361_G1.0650.41
426_A511_G1.0650.41
347_E351_G1.0640.41
34_E43_S1.0620.41
18_L26_E1.0610.41
67_L95_F1.0600.41
314_T524_D1.0590.40
142_A539_A1.0580.40
12_T33_K1.0570.40
474_E484_E1.0530.40
493_A529_N1.0530.40
349_V548_D1.0530.40
19_P354_A1.0520.40
31_A41_K1.0510.40
44_S117_Q1.0510.40
329_A346_A1.0500.40
9_D30_S1.0490.40
350_P359_T1.0480.39
8_G19_P1.0480.39
10_L14_A1.0470.39
8_G11_L1.0470.39
16_D43_S1.0440.39
18_L31_A1.0440.39
18_L106_I1.0440.39
91_L109_S1.0430.39
27_T43_S1.0420.39
144_A451_A1.0410.39
13_L26_E1.0400.39
9_D32_L1.0400.39
414_Q494_R1.0390.39
16_D31_A1.0380.39
211_F528_L1.0380.39
8_G18_L1.0370.38
8_G548_D1.0370.38
21_V113_T1.0360.38
9_D15_S1.0340.38
32_L40_G1.0340.38
19_P29_R1.0340.38
430_G503_A1.0340.38
329_A390_E1.0320.38
13_L16_D1.0320.38
260_G406_Q1.0300.38
15_S27_T1.0290.38
372_Y501_D1.0290.38
26_E35_R1.0280.38
485_A515_E1.0280.38
255_E293_L1.0270.38
12_T117_Q1.0240.37
205_L264_A1.0230.37
146_L329_A1.0220.37
259_C406_Q1.0220.37
245_S536_E1.0200.37
65_E380_I1.0200.37
31_A35_R1.0190.37
21_V103_R1.0190.37
30_S548_D1.0190.37
30_S41_K1.0180.37
12_T22_E1.0180.37
34_E44_S1.0180.37
342_S506_I1.0180.37
180_D428_E1.0180.37
13_L44_S1.0170.37
362_M380_I1.0160.37
299_R333_L1.0160.37
497_W501_D1.0150.37
76_R149_L1.0140.36
255_E486_G1.0140.36
484_E540_Q1.0130.36
314_T465_R1.0130.36
263_D543_A1.0130.36
302_K307_W1.0120.36
282_A404_L1.0090.36
14_A461_I1.0090.36
13_L35_R1.0070.36
12_T16_D1.0050.36
16_D19_P1.0040.36
26_E43_S1.0040.36
16_D41_K1.0040.36
25_F29_R1.0030.35
9_D27_T1.0020.35
12_T15_S1.0010.35
31_A548_D1.0010.35
12_T43_S1.0010.35
12_T111_T1.0010.35
24_L43_S1.0010.35
23_A117_Q1.0010.35
24_L106_I1.0010.35
27_T34_E1.0000.35
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  
2z1qA20.7191000.56Contact Map
3owaA40.71721000.56Contact Map
2jifA40.68981000.561Contact Map
4hr3A10.68981000.562Contact Map
2d29A20.69341000.562Contact Map
4rm7A10.66971000.563Contact Map
4irnA80.68251000.564Contact Map
1bucA20.68981000.565Contact Map
1ukwA20.6881000.565Contact Map
3r7kA40.68611000.566Contact 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 0.3838 seconds.