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

3j5p

ID: 1491407535 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 586 (573)
Sequences: 710 (493.8)
Seq/Len: 1.239
Nf(neff/√len): 20.6

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: 1.239).

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
110_L115_A2.3930.99
140_L143_S2.1810.99
227_L230_A2.1540.98
549_M552_T2.0290.97
548_L553_V1.9910.97
547_A552_T1.9840.97
312_L315_K1.9300.96
171_D175_N1.9230.96
111_V156_F1.9000.96
142_L145_A1.8890.95
392_S400_S1.8790.95
364_R368_E1.8740.95
569_A572_I1.8690.95
141_P145_A1.8490.95
175_N220_N1.8300.94
466_D552_T1.8120.94
466_D470_F1.8040.94
339_T439_W1.7980.94
466_D547_A1.7640.93
98_A110_L1.7490.92
177_V181_L1.7370.92
304_L308_L1.6770.90
331_Y339_T1.6760.90
93_T96_H1.6590.90
551_E554_N1.6450.89
466_D549_M1.6240.88
448_G459_I1.6170.88
143_S177_V1.5790.86
453_G546_I1.5730.86
547_A553_V1.5650.86
43_T47_C1.5610.85
95_L107_V1.5500.85
572_I576_E1.5480.85
539_I545_L1.5440.84
272_Y286_L1.5430.84
227_L231_A1.5360.84
543_N547_A1.5220.83
542_L547_A1.5200.83
338_F434_S1.5180.83
572_I578_S1.5080.83
456_A459_I1.5010.82
549_M564_W1.4940.82
550_G553_V1.4920.82
220_N224_L1.4890.81
573_L576_E1.4790.81
303_L307_P1.4790.81
540_L546_I1.4640.80
175_N179_H1.4570.79
225_T229_L1.4330.78
509_I512_G1.4280.78
454_I466_D1.4280.78
539_I543_N1.4210.77
98_A107_V1.4160.77
141_P146_A1.4140.77
168_S176_T1.4140.77
506_K512_G1.4110.76
500_T504_L1.3990.75
556_I568_R1.3980.75
436_A480_G1.3970.75
130_K133_P1.3890.75
382_G385_Y1.3860.75
509_I549_M1.3830.74
564_W567_Q1.3820.74
91_G96_H1.3820.74
565_K573_L1.3800.74
432_V439_W1.3690.73
311_L319_F1.3670.73
455_Y469_R1.3640.73
543_N549_M1.3570.72
315_K319_F1.3530.72
123_G126_F1.3470.71
313_Q328_F1.3460.71
139_E175_N1.3400.71
335_M438_G1.3390.71
549_M553_V1.3390.71
312_L316_W1.3380.71
47_C64_A1.3350.71
94_A98_A1.3340.70
553_V566_L1.3250.70
381_R384_Q1.3190.69
575_T579_F1.3110.69
95_L98_A1.2940.67
553_V564_W1.2830.66
51_A66_L1.2790.66
505_F510_G1.2760.65
311_L315_K1.2700.65
45_K50_K1.2660.65
230_A234_G1.2650.65
536_L541_L1.2630.64
403_E406_F1.2630.64
174_G178_L1.2630.64
450_Q459_I1.2600.64
547_A550_G1.2580.64
470_F477_F1.2560.64
332_C339_T1.2540.64
459_I549_M1.2520.63
562_N570_I1.2450.63
95_L110_L1.2440.63
146_A149_N1.2430.62
315_K331_Y1.2420.62
569_A576_E1.2400.62
332_C412_F1.2340.62
478_L482_S1.2260.61
563_I567_Q1.2250.61
572_I579_F1.2200.60
453_G535_I1.2200.60
485_V533_Y1.2180.60
202_I207_A1.2170.60
103_N106_L1.2150.60
49_L66_L1.2130.60
509_I556_I1.2120.60
449_F457_V1.2080.59
530_L533_Y1.2070.59
455_Y459_I1.2060.59
455_Y553_V1.2050.59
176_T179_H1.2040.59
107_V111_V1.2000.58
466_D477_F1.1980.58
179_H229_L1.1970.58
443_L466_D1.1910.58
467_L471_M1.1890.57
543_N546_I1.1890.57
563_I566_L1.1860.57
333_L340_A1.1830.57
51_A63_I1.1810.57
304_L307_P1.1780.56
46_T51_A1.1770.56
433_F528_I1.1730.56
140_L145_A1.1720.56
311_L314_D1.1700.56
560_S566_L1.1630.55
459_I466_D1.1620.55
50_K54_N1.1610.55
494_Y500_T1.1600.55
553_V563_I1.1570.54
478_L481_F1.1540.54
332_C336_I1.1540.54
89_Y125_F1.1530.54
415_V528_I1.1530.54
92_Q97_I1.1510.54
466_D469_R1.1490.54
168_S207_A1.1470.53
441_N445_Y1.1460.53
497_L503_E1.1390.53
143_S147_C1.1380.52
450_Q467_L1.1370.52
473_V563_I1.1320.52
439_W458_M1.1290.52
439_W455_Y1.1290.52
129_T132_R1.1280.51
373_S536_L1.1280.51
171_D179_H1.1270.51
546_I552_T1.1270.51
484_A542_L1.1240.51
439_W442_M1.1200.51
563_I572_I1.1200.51
43_T50_K1.1190.51
63_I67_L1.1190.51
508_T511_M1.1170.50
175_N224_L1.1170.50
453_G564_W1.1170.50
242_I246_E1.1150.50
199_Y202_I1.1120.50
40_D43_T1.1110.50
49_L52_M1.1110.50
138_G145_A1.1110.50
468_C476_V1.1100.50
16_C20_E1.1090.50
434_S458_M1.1080.50
61_D70_A1.1050.49
569_A573_L1.1040.49
554_N558_Q1.1040.49
435_L446_T1.1020.49
171_D220_N1.1010.49
48_L66_L1.0960.48
380_F384_Q1.0960.48
313_Q330_V1.0950.48
100_E144_L1.0940.48
226_P230_A1.0930.48
146_A223_G1.0920.48
15_N40_D1.0910.48
467_L540_L1.0900.48
23_L27_Q1.0900.48
574_D577_K1.0890.48
412_F430_S1.0860.47
441_N457_V1.0790.47
21_S24_P1.0780.47
467_L546_I1.0780.47
437_M488_L1.0750.46
335_M339_T1.0750.46
434_S438_G1.0750.46
102_R137_F1.0730.46
129_T133_P1.0710.46
542_L546_I1.0710.46
400_S403_E1.0700.46
8_F11_V1.0690.46
138_G147_C1.0690.46
107_V153_I1.0690.46
16_C64_A1.0680.46
227_L243_L1.0680.46
175_N182_V1.0670.45
50_K69_V1.0670.45
462_M466_D1.0660.45
442_M446_T1.0660.45
273_D287_E1.0630.45
546_I549_M1.0630.45
231_A234_G1.0620.45
17_Q20_E1.0620.45
527_I530_L1.0610.45
466_D510_G1.0610.45
315_K320_V1.0600.45
95_L111_V1.0600.45
225_T230_A1.0600.45
547_A564_W1.0600.45
48_L51_A1.0600.45
96_H99_I1.0600.45
15_N18_E1.0590.45
552_T564_W1.0590.45
466_D480_G1.0580.45
47_C50_K1.0570.45
43_T54_N1.0560.44
11_V23_L1.0560.44
512_G541_L1.0560.44
96_H146_A1.0540.44
181_L206_G1.0540.44
9_D21_S1.0530.44
13_Q18_E1.0510.44
139_E147_C1.0500.44
381_R385_Y1.0490.44
477_F537_T1.0470.44
84_Y134_G1.0470.44
13_Q24_P1.0450.43
103_N111_V1.0440.43
256_S259_F1.0430.43
470_F474_Y1.0410.43
477_F536_L1.0390.43
508_T516_F1.0370.43
230_A242_I1.0360.42
501_C513_D1.0360.42
338_F438_G1.0350.42
227_L242_I1.0350.42
501_C504_L1.0340.42
97_I109_L1.0340.42
63_I86_D1.0330.42
570_I574_D1.0330.42
567_Q573_L1.0300.42
550_G557_A1.0280.42
62_T66_L1.0250.41
548_L563_I1.0240.41
459_I550_G1.0230.41
38_F54_N1.0220.41
504_L510_G1.0210.41
58_G69_V1.0200.41
51_A67_L1.0200.41
506_K509_I1.0190.41
9_D36_S1.0190.41
315_K458_M1.0170.41
98_A102_R1.0160.41
11_V14_S1.0150.40
224_L232_S1.0130.40
225_T228_A1.0130.40
466_D478_L1.0130.40
324_F448_G1.0130.40
82_A85_T1.0100.40
250_P253_R1.0100.40
573_L578_S1.0090.40
9_D24_P1.0080.40
127_K132_R1.0080.40
474_Y504_L1.0070.40
555_K565_K1.0060.40
408_V442_M1.0050.40
490_E528_I1.0040.39
526_F530_L1.0030.39
9_D13_Q1.0030.39
104_M108_T1.0000.39
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  
3j5pB40.99151000.302Contact Map
3j9pD40.77131000.492Contact Map
2etbA10.42491000.711Contact Map
2pnnA10.42321000.713Contact Map
3w9fA40.43171000.717Contact Map
4n5qA20.41981000.733Contact Map
2rfaA10.37881000.751Contact Map
4rlvA10.37371000.757Contact Map
4rlyA10.34811000.76Contact Map
1oy3D10.35151000.762Contact 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 0.8705 seconds.