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

A1_main

ID: 1438523844 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 1000 (610)
Sequences: 2118 (1734.9)
Seq/Len: 3.472
Nf(neff/√len): 70.2

HHblits Results: (2013_03)
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: 3.472).

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
517_N545_N2.6781.00
498_M531_A2.2901.00
382_C411_S2.1401.00
361_R364_F2.0051.00
430_C465_V1.9611.00
67_N96_N1.9461.00
311_R340_D1.9231.00
386_H455_H1.9191.00
483_W513_D1.9021.00
47_M81_S1.8881.00
278_E307_D1.8390.99
451_M479_D1.8270.99
134_N163_N1.7600.99
360_L364_F1.7230.99
370_I373_L1.7190.99
315_I487_H1.6840.99
447_D451_M1.6830.99
453_P519_A1.6690.99
521_H551_F1.6680.99
82_V114_V1.6550.99
466_V497_T1.6540.99
218_G252_A1.6480.98
502_L534_L1.6060.98
246_F316_L1.5870.98
364_F368_Q1.5750.98
385_L397_V1.5650.98
487_H553_H1.5590.98
282_H487_H1.5580.98
419_H487_H1.5520.97
11_S14_G1.5450.97
493_G528_H1.5330.97
318_T422_A1.5050.97
455_H487_H1.4990.97
136_A243_A1.4920.97
245_H315_I1.4900.97
553_H556_L1.4880.97
356_G359_N1.4880.97
293_A325_I1.4860.97
307_D316_L1.4810.96
455_H521_H1.4770.96
280_M346_F1.4750.96
457_A466_V1.4720.96
167_C204_N1.4680.96
136_A313_P1.4670.96
418_L430_C1.4610.96
364_F367_M1.4590.96
212_H455_H1.4580.96
32_T63_D1.4540.96
490_S531_A1.4530.96
71_H521_H1.4490.96
270_V336_V1.4420.96
365_M368_Q1.4400.96
386_H419_H1.4280.95
532_V563_V1.4280.95
83_K150_Q1.4260.95
138_I315_I1.4250.95
77_N111_N1.4200.95
212_H419_H1.4050.95
71_H104_H1.4030.95
282_H386_H1.4000.95
400_L405_V1.3990.95
100_M130_G1.3950.95
105_I172_Q1.3940.94
42_G78_Q1.3830.94
360_L363_E1.3800.94
87_S154_K1.3780.94
369_Q373_L1.3740.94
141_C215_V1.3690.94
43_Q46_L1.3630.94
479_D483_W1.3490.93
71_H138_I1.3470.93
475_L541_D1.3410.93
104_H245_H1.3390.93
386_H417_P1.3320.93
208_A237_E1.3320.93
171_H210_P1.3280.92
386_H521_H1.3240.92
315_I346_F1.3220.92
499_K565_L1.3190.92
158_K232_Q1.3140.92
84_F295_Y1.3110.92
104_H282_H1.3100.92
248_A251_G1.3050.92
232_Q302_D1.3040.91
411_S415_K1.3040.91
282_H313_P1.3000.91
306_I410_K1.2970.91
39_A107_V1.2970.91
189_G198_L1.2960.91
369_Q372_E1.2920.91
368_Q372_E1.2870.91
318_T389_C1.2830.91
167_C241_C1.2810.91
521_H553_H1.2760.90
248_A256_V1.2700.90
163_N167_C1.2690.90
115_M148_A1.2680.90
49_K53_D1.2670.90
85_L90_A1.2660.90
278_E344_R1.2630.90
368_Q371_K1.2600.90
524_A527_G1.2580.89
169_P280_M1.2560.89
204_N274_D1.2560.89
415_K447_D1.2520.89
378_D382_C1.2510.89
398_N467_Q1.2510.89
104_H171_H1.2480.89
241_C274_D1.2470.89
212_H245_H1.2420.89
128_L338_I1.2420.89
47_M50_I1.2380.88
88_R155_K1.2370.88
104_H521_H1.2330.88
325_I465_V1.2320.88
139_I213_L1.2320.88
138_I212_H1.2300.88
74_V174_A1.2240.88
174_A285_S1.2210.87
458_A497_T1.2200.87
110_M145_N1.2200.87
134_N208_A1.2180.87
501_I506_L1.2180.87
280_M384_P1.2150.87
246_F456_L1.2110.87
357_L361_R1.2090.87
119_L297_I1.2080.87
402_G471_K1.2060.87
316_L349_L1.2050.87
329_L334_A1.2040.86
138_I282_H1.1980.86
470_L536_L1.1960.86
107_V174_A1.1950.86
357_L360_L1.1930.86
455_H485_A1.1910.86
96_N105_I1.1880.86
339_K410_K1.1850.85
104_H212_H1.1820.85
285_S288_D1.1810.85
458_A466_V1.1810.85
527_G560_R1.1770.85
149_L256_V1.1770.85
422_A425_G1.1770.85
102_P346_F1.1750.85
272_T409_S1.1720.84
126_V407_I1.1710.84
106_A115_M1.1700.84
556_L559_K1.1680.84
74_V77_N1.1680.84
451_M517_N1.1670.84
316_L387_Y1.1660.84
225_M399_N1.1650.84
81_S148_A1.1640.84
138_I141_C1.1610.84
358_K362_P1.1600.84
387_Y456_L1.1590.84
211_L223_I1.1590.84
223_I255_I1.1560.83
389_C422_A1.1560.83
403_F472_K1.1500.83
288_D322_S1.1450.83
36_H69_P1.1450.83
149_L181_C1.1430.82
155_K262_S1.1420.82
111_N114_V1.1390.82
282_H455_H1.1390.82
120_E187_R1.1380.82
432_R500_V1.1360.82
412_K480_H1.1360.82
237_E307_D1.1360.82
487_H521_H1.1350.82
138_I171_H1.1350.82
356_G361_R1.1350.82
171_H386_H1.1350.82
434_L502_L1.1340.82
299_V332_K1.1340.82
213_L420_F1.1340.82
454_L466_V1.1320.82
485_A519_A1.1300.81
357_L364_F1.1280.81
513_D517_N1.1280.81
86_L153_L1.1270.81
243_A313_P1.1260.81
153_L159_P1.1250.81
470_L500_V1.1230.81
524_A556_L1.1220.81
214_A317_A1.1220.81
107_V285_S1.1190.80
285_S325_I1.1190.80
399_N403_F1.1190.80
401_L536_L1.1180.80
39_A42_G1.1170.80
351_V422_A1.1160.80
386_H487_H1.1150.80
315_I455_H1.1150.80
520_L535_L1.1130.80
88_R121_H1.1120.80
298_S471_K1.1120.80
325_I429_T1.1100.80
282_H419_H1.1090.80
437_I440_T1.1080.80
161_K272_T1.1070.79
359_N364_F1.1070.79
454_L469_L1.1050.79
144_N218_G1.1030.79
490_S493_G1.1010.79
560_R563_V1.1000.79
216_Q286_L1.1000.79
92_P270_V1.0980.79
486_L498_M1.0960.79
261_S331_S1.0960.79
318_T321_A1.0940.78
174_A215_V1.0940.78
535_L540_A1.0910.78
227_L258_L1.0900.78
274_D340_D1.0890.78
233_I303_I1.0890.78
128_L235_P1.0860.78
86_L117_V1.0860.78
70_L82_V1.0840.77
92_P303_I1.0840.77
506_L509_T1.0820.77
169_P346_F1.0800.77
235_P305_K1.0800.77
63_D67_N1.0800.77
174_A182_M1.0780.77
212_H521_H1.0760.77
524_A532_V1.0750.77
496_Q562_E1.0750.77
215_V218_G1.0750.77
182_M222_M1.0730.76
567_I572_R1.0730.76
458_A461_G1.0720.76
38_A47_M1.0710.76
490_S519_A1.0710.76
63_D204_N1.0700.76
519_A551_F1.0700.76
104_H138_I1.0690.76
292_L396_S1.0680.76
420_F488_H1.0680.76
356_G360_L1.0670.76
407_I542_I1.0650.76
104_H455_H1.0640.76
172_Q213_L1.0640.76
107_V215_V1.0610.75
403_F538_H1.0610.75
245_H386_H1.0610.75
318_T326_V1.0610.75
74_V107_V1.0610.75
212_H282_H1.0600.75
311_R382_C1.0580.75
271_N337_D1.0570.75
325_I396_S1.0550.75
71_H348_H1.0530.75
139_I246_F1.0520.74
174_A422_A1.0520.74
221_E291_E1.0510.74
313_P453_P1.0510.74
126_V200_I1.0500.74
418_L433_L1.0490.74
172_Q387_Y1.0490.74
28_D32_T1.0470.74
228_D298_S1.0470.74
468_L472_K1.0470.74
36_H212_H1.0450.74
154_K228_D1.0440.74
174_A248_A1.0430.74
213_L456_L1.0430.74
177_G251_G1.0420.73
245_H487_H1.0400.73
274_D278_E1.0390.73
169_P485_A1.0390.73
107_V248_A1.0380.73
94_L161_K1.0380.73
304_N375_M1.0370.73
392_G461_G1.0350.73
419_H453_P1.0330.73
169_P243_A1.0320.72
419_H521_H1.0320.72
136_A519_A1.0320.72
276_C342_F1.0310.72
35_L47_M1.0310.72
224_K294_D1.0310.72
171_H212_H1.0310.72
523_A532_V1.0300.72
36_H104_H1.0300.72
359_N362_P1.0290.72
108_Q249_T1.0280.72
185_I189_G1.0280.72
215_V422_A1.0270.72
185_I198_L1.0270.72
171_H553_H1.0260.72
249_T319_A1.0250.72
36_H39_A1.0250.72
488_H554_L1.0250.72
458_A490_S1.0240.72
11_S22_K1.0240.72
139_I172_Q1.0240.72
295_Y468_L1.0240.72
471_K503_D1.0230.72
86_L227_L1.0230.72
204_N208_A1.0220.71
205_N546_K1.0210.71
403_F504_T1.0210.71
144_N178_S1.0180.71
215_V223_I1.0180.71
386_H553_H1.0180.71
71_H245_H1.0170.71
340_D344_R1.0170.71
455_H553_H1.0170.71
348_H487_H1.0160.71
429_T497_T1.0160.71
422_A458_A1.0160.71
309_E380_D1.0130.70
328_L432_R1.0130.70
36_H138_I1.0120.70
296_L301_A1.0120.70
507_K510_D1.0120.70
489_A498_M1.0100.70
11_S17_N1.0090.70
235_P338_I1.0090.70
78_Q81_S1.0080.70
534_L538_H1.0080.70
291_E395_G1.0080.70
138_I386_H1.0070.70
316_L488_H1.0070.70
40_A108_Q1.0060.70
102_P210_P1.0060.70
126_V303_I1.0040.69
529_A533_A1.0040.69
179_K253_T1.0040.69
248_A422_A1.0040.69
245_H282_H1.0030.69
125_D302_D1.0020.69
138_I169_P1.0020.69
155_K229_N1.0000.69
476_F542_I1.0000.69
135_T209_T1.0000.69
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: (31Jan15)
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  
4rlvA10.5751000.571Contact Map
4cj9A20.6121000.588Contact Map
3j5pB40.5211000.686Contact Map
1n11A10.4041000.694Contact Map
3ljnA10.2721000.772Contact Map
3utmA20.3171000.775Contact Map
4oavB20.6161000.775Contact Map
4rlyA10.31000.781Contact Map
4ot9A10.2821000.793Contact Map
1wdyA10.2781000.802Contact 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 1.261 seconds.