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OPENSEQ.org

PhyB_AT

ID: 1434653884 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 517 (494)
Sequences: 632 (387)
Seq/Len: 1.279
Nf(neff/√len): 17.4

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: 1.279).

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
161_V175_V4.2631.00
216_F272_A3.3131.00
377_D455_S3.2141.00
389_P399_I2.9811.00
35_E233_L2.9221.00
165_R190_S2.8931.00
179_H183_H2.7971.00
260_Q478_R2.5591.00
262_M301_V2.4441.00
262_M267_S2.3620.99
224_I254_P2.2100.99
273_M322_M2.1850.99
380_A453_F2.0970.98
264_N484_S2.0760.98
439_M451_F1.9860.97
419_D495_R1.9820.97
22_A205_A1.9760.97
170_Y271_L1.9410.97
236_Q241_T1.9310.96
462_K487_A1.9300.96
160_V325_F1.9110.96
16_P229_A1.9060.96
157_C187_V1.8130.94
481_P484_S1.7970.94
211_A216_F1.7340.92
437_C455_S1.7300.92
18_G251_L1.6960.91
32_G236_Q1.6900.91
260_Q483_S1.6810.91
259_S263_A1.6720.90
211_A255_H1.6700.90
481_P485_F1.6570.90
395_S398_Q1.6520.90
201_L461_I1.6500.90
229_A253_A1.6440.89
465_G485_F1.6230.89
211_A274_A1.6190.89
174_M262_M1.5670.86
389_P393_A1.5600.86
174_M267_S1.5530.86
12_G255_H1.5400.85
429_A432_L1.5360.85
22_A244_M1.5180.84
24_D27_S1.5170.84
224_I265_M1.5160.84
246_L249_S1.5090.83
216_F274_A1.4980.83
258_H270_S1.4920.82
378_G394_P1.4910.82
15_Q18_G1.4810.82
211_A272_A1.4780.82
185_E202_H1.4700.81
197_P203_Y1.4370.79
264_N481_P1.4150.77
216_F254_P1.4130.77
25_E107_R1.4080.77
406_L439_M1.4050.77
217_K276_I1.3970.76
264_N485_F1.3910.76
219_N302_C1.3740.74
422_G426_Y1.3520.73
318_C437_C1.3520.73
109_D242_Q1.3500.73
21_I37_A1.3490.73
264_N482_R1.3480.72
171_D195_L1.3480.72
103_A116_L1.3460.72
258_H274_A1.3430.72
207_D261_Y1.3360.72
371_M376_C1.3330.71
465_G484_S1.3310.71
482_R485_F1.3300.71
41_L510_L1.3270.71
195_L203_Y1.3150.70
227_C262_M1.3130.70
107_R317_A1.3110.69
66_L402_V1.3100.69
207_D484_S1.3090.69
436_V455_S1.3030.69
117_E315_R1.2950.68
157_C175_V1.2940.68
174_M301_V1.2940.68
402_V426_Y1.2930.68
167_L244_M1.2910.68
208_I264_N1.2860.67
256_G274_A1.2850.67
227_C374_V1.2810.67
191_K194_D1.2810.67
174_M203_Y1.2730.66
157_C190_S1.2640.65
211_A258_H1.2630.65
146_Q323_Q1.2620.65
208_I212_S1.2590.65
14_I232_V1.2560.65
203_Y374_V1.2490.64
17_F253_A1.2480.64
378_G453_F1.2480.64
214_F217_K1.2450.64
168_T464_G1.2400.63
466_A470_P1.2380.63
212_S258_H1.2340.63
207_D264_N1.2260.62
102_Y301_V1.2250.62
236_Q240_L1.2180.61
379_A390_L1.2170.61
421_L429_A1.2150.61
118_P466_A1.2080.60
153_I370_I1.2070.60
17_F229_A1.2010.60
234_V275_V1.1990.59
350_L354_M1.1980.59
8_I212_S1.1970.59
465_G481_P1.1950.59
294_M459_K1.1940.59
222_R261_Y1.1920.59
254_P271_L1.1850.58
167_L187_V1.1840.58
229_A254_P1.1840.58
47_S427_P1.1830.58
30_I58_A1.1820.58
212_S481_P1.1810.58
195_L305_T1.1780.57
30_I65_S1.1750.57
258_H261_Y1.1750.57
216_F219_N1.1740.57
23_V114_I1.1740.57
141_A160_V1.1730.57
257_C469_H1.1660.56
219_N272_A1.1650.56
255_H469_H1.1640.56
11_G271_L1.1610.56
261_Y485_F1.1600.56
104_I312_F1.1570.55
170_Y225_V1.1540.55
10_R211_A1.1500.55
267_S301_V1.1500.55
378_G393_A1.1480.54
216_F469_H1.1440.54
368_P372_D1.1430.54
19_C40_M1.1410.54
184_G264_N1.1390.54
8_I274_A1.1350.53
32_G238_D1.1320.53
61_T65_S1.1310.53
265_M479_M1.1270.52
11_G211_A1.1270.52
185_E301_V1.1250.52
278_N330_N1.1240.52
264_N465_G1.1200.52
339_M490_E1.1200.52
212_S264_N1.1200.52
335_L339_M1.1190.52
110_V431_A1.1190.52
418_T421_L1.1170.51
323_Q326_G1.1160.51
23_V175_V1.1140.51
224_I258_H1.1120.51
11_G17_F1.1090.51
207_D481_P1.1090.51
325_F329_L1.1080.50
207_D258_H1.1070.50
307_S498_P1.1060.50
275_V370_I1.1060.50
478_R483_S1.1040.50
154_K158_D1.1030.50
269_A446_K1.1000.50
224_I246_L1.1000.50
32_G241_T1.0980.49
16_P231_P1.0980.49
11_G229_A1.0960.49
211_A271_L1.0950.49
216_F257_C1.0940.49
183_H275_V1.0920.49
30_I33_Y1.0870.48
211_A257_C1.0870.48
165_R192_R1.0870.48
207_D485_F1.0850.48
394_P399_I1.0850.48
220_R326_G1.0850.48
261_Y481_P1.0840.48
398_Q431_A1.0820.48
184_G261_Y1.0810.48
500_E503_E1.0810.48
208_I484_S1.0800.48
218_Q248_G1.0790.48
458_A491_V1.0770.47
265_M485_F1.0710.47
156_L271_L1.0710.47
73_I77_R1.0700.47
142_I324_A1.0670.46
380_A451_F1.0670.46
210_Q214_F1.0660.46
417_S501_T1.0640.46
176_Y184_G1.0630.46
253_A274_A1.0630.46
258_H272_A1.0620.46
184_G224_I1.0620.46
12_G211_A1.0610.46
184_G484_S1.0600.46
464_G496_S1.0540.45
114_I157_C1.0540.45
207_D252_R1.0530.45
211_A215_L1.0530.45
269_A303_H1.0520.45
465_G482_R1.0480.45
429_A437_C1.0480.45
182_E295_R1.0470.44
360_P381_F1.0410.44
212_S484_S1.0390.44
216_F253_A1.0390.44
160_V276_I1.0380.44
479_M484_S1.0350.43
463_W481_P1.0340.43
455_S460_E1.0310.43
347_T450_L1.0300.43
184_G207_D1.0280.43
13_Y253_A1.0270.42
179_H182_E1.0270.42
118_P370_I1.0230.42
146_Q161_V1.0220.42
184_G209_P1.0220.42
88_N104_I1.0190.42
71_S103_A1.0170.41
258_H262_M1.0170.41
30_I268_I1.0120.41
213_R296_L1.0100.41
216_F271_L1.0090.41
117_E265_M1.0090.41
32_G234_V1.0080.41
255_H480_H1.0050.40
405_W426_Y1.0040.40
270_S470_P1.0040.40
216_F256_G1.0010.40
300_V326_G1.0000.40
453_F503_E1.0000.40
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  
4ourA10.86651000.216Contact Map
4q0jA10.90331000.344Contact Map
3zq5A10.93621000.381Contact Map
3nhqA80.89751000.412Contact Map
4gw9A40.91681000.455Contact Map
4bwiA20.69251000.571Contact Map
4cqhA10.55321000.609Contact Map
4e04A20.5881000.628Contact Map
2oolA20.57641000.634Contact Map
2k2nA10.326999.90.865Contact 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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