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OPENSEQ.org

brae1

ID: 1420471610 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 666 (650)
Sequences: 923 (742.9)
Seq/Len: 1.420
Nf(neff/√len): 29.1

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: 1.420).

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
120_S128_G3.6371.00
116_I120_S2.9271.00
120_S129_A2.8531.00
215_Y608_H2.7281.00
116_I128_G2.5841.00
117_S128_G2.5071.00
6_L9_I2.4981.00
245_F604_V2.4711.00
117_S120_S2.3881.00
242_T608_H2.2680.99
210_A237_L2.2030.99
409_V413_N2.2020.99
275_G576_M2.1560.99
608_H612_S2.1390.99
236_G240_I2.0590.98
271_F581_L2.0340.98
269_Y592_N1.9300.97
426_S450_K1.9260.97
151_F156_M1.8790.96
301_L547_S1.8470.96
21_I24_F1.8410.96
6_L10_M1.7970.95
215_Y242_T1.7950.95
256_I260_V1.7680.94
242_T612_S1.7600.94
17_Q21_I1.7580.94
164_A168_G1.7550.94
561_K565_E1.7400.94
420_L428_G1.7270.93
238_V612_S1.7050.93
17_Q20_V1.6970.93
77_N174_N1.6960.93
646_Y653_T1.6820.92
245_F249_I1.6820.92
471_I474_D1.6750.92
157_F161_I1.6740.92
155_A159_T1.6520.91
422_L426_S1.6410.91
246_F291_T1.6370.91
215_Y241_G1.6210.90
546_V550_I1.6210.90
194_V198_W1.6180.90
214_G241_G1.6020.90
116_I129_A1.5950.89
160_L172_I1.5940.89
84_R87_E1.5870.89
574_D578_K1.5850.89
556_L560_Y1.5690.88
214_G238_V1.5640.88
295_T605_A1.5580.88
68_L72_F1.5570.88
113_F117_S1.5500.87
237_L241_G1.5300.87
215_Y612_S1.5280.86
112_Q128_G1.5250.86
94_L98_K1.5240.86
68_L76_A1.5200.86
17_Q24_F1.5070.85
295_T299_V1.5060.85
9_I16_T1.5010.85
561_K597_L1.4740.84
196_S199_L1.4650.83
79_F563_V1.4630.83
21_I31_L1.4570.83
646_Y660_V1.4510.82
79_F91_F1.4430.82
563_V573_Y1.4380.82
91_F288_A1.4360.81
231_I234_V1.4210.80
6_L12_R1.4180.80
561_K569_N1.4090.80
219_L611_I1.4070.80
21_I32_F1.4010.79
547_S608_H1.3990.79
194_V197_R1.3950.79
6_L11_R1.3950.79
207_G548_I1.3830.78
640_I648_A1.3800.78
562_Q646_Y1.3760.77
97_T100_S1.3700.77
9_I12_R1.3700.77
117_S129_A1.3670.77
204_I249_I1.3640.77
209_A213_L1.3630.77
238_V242_T1.3590.76
296_F299_V1.3550.76
553_G558_M1.3480.75
423_D427_I1.3480.75
108_E124_G1.3390.75
120_S324_D1.3350.74
471_I659_K1.3300.74
9_I20_V1.3240.74
542_V579_L1.3240.74
84_R108_E1.3210.73
25_I30_V1.3190.73
125_Y128_G1.3180.73
261_S265_Y1.3170.73
88_F105_V1.3100.72
204_I207_G1.3100.72
34_I38_L1.3090.72
254_I277_R1.3060.72
300_T303_M1.3040.72
96_M275_G1.3040.72
238_V279_R1.3030.72
135_I541_F1.2980.71
251_E254_I1.2970.71
265_Y557_M1.2950.71
409_V473_K1.2930.71
423_D426_S1.2770.70
113_F116_I1.2750.69
566_A661_I1.2740.69
113_F128_G1.2720.69
303_M307_T1.2700.69
72_F80_M1.2690.69
427_I451_V1.2620.68
87_E91_F1.2600.68
563_V646_Y1.2580.68
176_F180_F1.2570.68
297_L547_S1.2570.68
169_M498_F1.2540.68
75_Y87_E1.2500.67
543_G550_I1.2440.67
165_V169_M1.2390.66
410_Q474_D1.2350.66
253_I588_K1.2330.66
32_F36_Y1.2320.66
541_F561_K1.2310.66
20_V23_P1.2300.65
77_N562_Q1.2300.65
10_M194_V1.2300.65
283_N294_C1.2290.65
243_Y289_T1.2260.65
590_T657_Y1.2230.65
113_F120_S1.2180.64
246_F257_L1.2160.64
211_L215_Y1.2150.64
17_Q32_F1.2130.64
9_I17_Q1.2100.64
36_Y40_S1.2100.64
320_T641_I1.2080.63
79_F653_T1.2050.63
447_E473_K1.2020.63
271_F275_G1.2010.63
10_M13_Q1.2010.63
76_A112_Q1.2010.63
297_L306_T1.2000.63
254_I276_M1.2000.63
79_F564_S1.1990.63
327_F500_V1.1980.62
593_Q598_F1.1960.62
550_I575_I1.1930.62
205_V209_A1.1920.62
293_L554_I1.1890.62
167_M170_L1.1880.61
411_D414_R1.1830.61
562_Q602_M1.1790.61
17_Q23_P1.1770.60
24_F31_L1.1760.60
81_M174_N1.1710.60
274_V559_Y1.1700.60
65_M546_V1.1660.59
278_V281_K1.1610.59
214_G279_R1.1590.59
560_Y569_N1.1580.59
268_R275_G1.1550.58
275_G563_V1.1530.58
563_V576_M1.1500.58
274_V561_K1.1500.58
427_I449_F1.1480.58
94_L105_V1.1480.58
298_I554_I1.1470.57
654_S658_A1.1450.57
543_G569_N1.1430.57
85_R189_H1.1420.57
10_M14_F1.1400.57
550_I554_I1.1390.57
547_S550_I1.1330.56
646_Y654_S1.1320.56
24_F109_T1.1320.56
163_I166_L1.1300.56
36_Y39_V1.1280.56
587_A658_A1.1260.55
218_A611_I1.1250.55
342_E345_K1.1250.55
23_P559_Y1.1240.55
255_S277_R1.1220.55
112_Q120_S1.1200.55
6_L16_T1.1190.55
290_I562_Q1.1170.54
302_T552_I1.1150.54
231_I235_I1.1140.54
562_Q593_Q1.1090.54
246_F608_H1.1070.53
16_T23_P1.1070.53
241_G245_F1.1020.53
606_L639_V1.1010.53
167_M171_L1.1010.53
8_H12_R1.1000.53
64_F652_I1.0950.52
34_I37_T1.0950.52
283_N569_N1.0940.52
541_F565_E1.0940.52
297_L576_M1.0920.52
566_A581_L1.0900.52
562_Q575_I1.0900.52
258_Q274_V1.0880.52
271_F573_Y1.0880.52
249_I252_I1.0870.51
19_L30_V1.0870.51
443_G472_V1.0830.51
13_Q194_V1.0810.51
24_F32_F1.0810.51
562_Q566_A1.0800.51
46_Y89_S1.0800.51
171_L175_L1.0780.50
215_Y246_F1.0780.50
211_L412_Y1.0770.50
20_V28_V1.0770.50
425_Q450_K1.0770.50
541_F550_I1.0760.50
88_F272_V1.0760.50
245_F251_E1.0760.50
544_G553_G1.0750.50
12_R16_T1.0720.50
443_G448_V1.0710.50
10_M16_T1.0700.50
263_V267_P1.0700.50
451_V470_L1.0690.50
120_S127_L1.0680.49
9_I13_Q1.0680.49
113_F549_V1.0650.49
13_Q16_T1.0650.49
5_L12_R1.0640.49
283_N657_Y1.0630.49
23_P72_F1.0630.49
287_L546_V1.0620.49
647_M651_K1.0620.49
276_M282_M1.0620.49
553_G560_Y1.0610.49
19_L24_F1.0610.49
550_I608_H1.0610.49
10_M25_I1.0600.49
650_Y654_S1.0560.48
152_D155_A1.0560.48
274_V280_L1.0540.48
20_V24_F1.0540.48
39_V44_N1.0520.48
633_T637_L1.0520.48
266_H305_L1.0500.48
542_V656_I1.0490.48
24_F28_V1.0480.47
264_Y273_V1.0470.47
21_I29_S1.0440.47
35_E72_F1.0440.47
19_L31_L1.0430.47
79_F94_L1.0430.47
206_I244_A1.0420.47
239_I296_F1.0420.47
131_F529_L1.0420.47
299_V616_V1.0370.46
208_S240_I1.0360.46
13_Q23_P1.0350.46
263_V269_Y1.0330.46
593_Q602_M1.0320.46
280_L602_M1.0320.46
287_L565_E1.0320.46
5_L9_I1.0310.46
275_G547_S1.0310.46
271_F559_Y1.0310.46
598_F601_P1.0300.46
579_L589_I1.0300.46
67_L614_N1.0300.46
569_N657_Y1.0290.45
106_V259_Q1.0270.45
275_G581_L1.0260.45
24_F30_V1.0250.45
252_I273_V1.0250.45
296_F558_M1.0250.45
23_P556_L1.0250.45
81_M246_F1.0210.45
32_F38_L1.0200.45
650_Y657_Y1.0200.45
284_A294_C1.0190.44
87_E593_Q1.0170.44
255_S281_K1.0170.44
571_H619_L1.0160.44
313_H627_N1.0140.44
197_R200_R1.0130.44
250_S291_T1.0120.44
294_C578_K1.0120.44
268_R581_L1.0100.44
104_I152_D1.0090.43
582_D585_R1.0080.43
424_N475_N1.0050.43
79_F646_Y1.0040.43
102_R146_L1.0040.43
215_Y547_S1.0030.43
299_V612_S1.0010.43
235_I295_T1.0010.43
238_V559_Y1.0010.43
104_I586_I1.0000.43
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: (06Sep14)
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  
2f95B10.07515.80.983Contact Map
1iijA10.05264.90.984Contact Map
2l2tA20.06614.40.984Contact Map
2rddB10.04954.20.984Contact Map
4nohA20.24474.10.984Contact Map
3rlfF10.10363.40.985Contact Map
3arcM20.05112.70.985Contact Map
2ls2A10.03752.60.986Contact Map
3hd7A20.06162.60.986Contact Map
2kogA10.06162.50.986Contact 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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