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OPENSEQ.org

spok1b n-terminal -force run

ID: 1490873308 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 50% gaps before running GREMLIN.
Length: 540 (489)
Sequences: 428 (351.6)
Seq/Len: 0.875
Nf(neff/√len): 15.9

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: 0.875).

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 > 50% 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
357_Q361_F3.0761.00
250_V316_L3.0151.00
219_D240_K2.6970.99
308_Y358_L2.3910.99
493_C497_C1.9980.94
291_A309_V1.9600.93
294_Q298_Y1.9490.93
240_K244_K1.9420.93
259_L289_A1.9260.93
112_T115_N1.9250.93
517_H525_H1.8760.91
76_P82_W1.8610.91
240_K243_H1.8470.90
513_N517_H1.8440.90
129_K132_D1.8420.90
357_Q360_S1.8260.90
511_C517_H1.8130.89
123_H141_R1.7330.86
495_Q498_L1.7230.86
43_Y142_P1.7020.85
251_R334_L1.6860.84
512_P517_H1.6800.84
307_G317_L1.6570.83
494_T498_L1.6520.82
36_R42_E1.6510.82
52_Y336_A1.6450.82
527_V535_M1.6280.81
493_C498_L1.6130.80
402_L406_E1.6090.80
508_D511_C1.5800.78
497_C501_L1.5620.77
387_L390_W1.5600.77
303_G494_T1.5600.77
289_A298_Y1.5500.76
292_L328_L1.5490.76
33_L36_R1.5410.76
128_E240_K1.5320.75
495_Q499_L1.5300.75
39_T42_E1.5220.75
528_N535_M1.5170.74
498_L501_L1.5140.74
316_L330_C1.5000.73
508_D513_N1.4950.73
305_S319_Y1.4920.72
296_F326_Q1.4890.72
468_R471_G1.4870.72
146_I150_L1.4690.71
497_C500_G1.4670.71
240_K298_Y1.4560.70
237_Y308_Y1.4510.69
219_D244_K1.4400.69
508_D512_P1.4350.68
217_Q220_G1.4270.68
86_T331_H1.4230.67
247_I314_C1.4200.67
219_D298_Y1.4160.67
375_S379_A1.4100.66
303_G312_G1.4090.66
147_L159_A1.4080.66
84_N88_V1.4050.66
401_G405_A1.3990.65
362_C370_A1.3950.65
149_V152_T1.3930.65
219_D243_H1.3920.65
219_D294_Q1.3870.64
491_Q514_V1.3820.64
315_L358_L1.3790.64
398_A401_G1.3750.63
494_T497_C1.3730.63
493_C501_L1.3650.63
310_A315_L1.3630.62
66_G244_K1.3620.62
296_F300_I1.3570.62
305_S320_V1.3570.62
55_L63_S1.3550.62
70_V75_Y1.3500.61
167_F170_N1.3500.61
168_S172_R1.3480.61
493_C500_G1.3460.61
310_A358_L1.3450.61
335_P338_D1.3440.61
109_S112_T1.3280.59
94_F101_C1.3260.59
223_I356_A1.3250.59
40_F43_Y1.3200.59
289_A294_Q1.3100.58
68_T298_Y1.3090.58
82_W85_F1.3080.58
318_L330_C1.3070.58
355_V361_F1.2910.56
322_R379_A1.2900.56
527_V532_F1.2900.56
135_E308_Y1.2890.56
428_T431_K1.2760.55
221_V242_A1.2740.55
250_V332_P1.2730.55
292_L358_L1.2710.54
508_D517_H1.2670.54
497_C508_D1.2650.54
303_G306_Y1.2630.54
499_L527_V1.2600.53
167_F219_D1.2570.53
75_Y260_F1.2540.53
317_L333_C1.2510.53
317_L357_Q1.2490.52
219_D238_D1.2470.52
495_Q501_L1.2460.52
291_A316_L1.2450.52
245_V253_A1.2450.52
307_G313_R1.2440.52
292_L309_V1.2340.51
88_V92_H1.2340.51
428_T464_R1.2320.51
237_Y358_L1.2290.51
321_D379_A1.2240.50
317_L361_F1.2240.50
441_A514_V1.2170.50
76_P85_F1.2120.49
304_V307_G1.2070.49
111_S115_N1.2030.48
507_L514_V1.2000.48
309_V316_L1.1980.48
308_Y315_L1.1980.48
313_R317_L1.1960.48
245_V291_A1.1940.48
297_D310_A1.1930.47
241_A244_K1.1900.47
187_N190_D1.1880.47
339_V354_A1.1790.46
335_P339_V1.1780.46
309_V320_V1.1750.46
128_E219_D1.1740.46
73_K76_P1.1700.45
359_V377_E1.1680.45
90_H93_Y1.1600.45
246_A249_H1.1570.44
319_Y365_S1.1560.44
497_C507_L1.1550.44
305_S372_E1.1540.44
492_Y497_C1.1540.44
493_C511_C1.1510.44
64_S127_N1.1460.43
108_E112_T1.1440.43
131_I222_G1.1440.43
146_I359_V1.1380.43
293_T298_Y1.1370.42
240_K294_Q1.1360.42
297_D301_T1.1350.42
507_L525_H1.1340.42
441_A528_N1.1340.42
238_D244_K1.1330.42
466_A471_G1.1330.42
335_P354_A1.1320.42
220_G401_G1.1310.42
143_V290_M1.1280.42
51_L78_R1.1250.41
140_E495_Q1.1250.41
38_T42_E1.1220.41
297_D328_L1.1210.41
292_L333_C1.1210.41
355_V358_L1.1210.41
82_W90_H1.1200.41
127_N172_R1.1180.41
513_N525_H1.1150.41
497_C511_C1.1070.40
300_I308_Y1.1040.40
385_A440_A1.0960.39
94_F293_T1.0960.39
42_E105_Q1.0960.39
246_A371_L1.0950.39
58_T66_G1.0950.39
222_G231_Q1.0930.39
195_R198_Q1.0900.38
156_A307_G1.0900.38
235_F362_C1.0880.38
493_C508_D1.0850.38
70_V290_M1.0840.38
125_A131_I1.0780.37
52_Y134_F1.0780.37
72_G464_R1.0750.37
494_T500_G1.0710.37
59_D78_R1.0690.37
61_S66_G1.0680.37
253_A257_E1.0670.37
142_P146_I1.0670.37
161_I170_N1.0660.36
493_C513_N1.0620.36
112_T116_L1.0620.36
220_G288_I1.0610.36
150_L359_V1.0600.36
295_V360_S1.0600.36
190_D193_L1.0580.36
511_C525_H1.0560.36
93_Y97_V1.0550.36
468_R488_P1.0540.35
85_F90_H1.0510.35
167_F240_K1.0510.35
79_L97_V1.0500.35
52_Y139_V1.0490.35
80_R329_Y1.0480.35
263_V293_T1.0470.35
184_A187_N1.0450.35
310_A328_L1.0430.35
115_N266_R1.0410.34
507_L517_H1.0400.34
299_M303_G1.0350.34
238_D243_H1.0330.34
244_K294_Q1.0320.34
292_L297_D1.0310.34
353_T387_L1.0300.33
62_R70_V1.0300.33
493_C512_P1.0280.33
105_Q113_T1.0270.33
145_G223_I1.0240.33
184_A188_T1.0230.33
497_C513_N1.0220.33
128_E298_Y1.0210.33
281_R285_E1.0210.33
299_M312_G1.0210.33
108_E115_N1.0210.33
529_A533_T1.0200.33
241_A298_Y1.0190.33
468_R472_P1.0190.33
64_S199_A1.0180.33
305_S375_S1.0160.32
218_P392_E1.0150.32
165_F355_V1.0130.32
262_E266_R1.0130.32
398_A406_E1.0110.32
73_K82_W1.0090.32
161_I309_V1.0040.31
294_Q299_M1.0040.31
333_C356_A1.0040.31
359_V362_C1.0010.31
221_V338_D1.0010.31
501_L535_M1.0000.31
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  
3l9kW40.070426.40.981Contact Map
4lqsB10.190712.90.984Contact Map
2l58A10.059312.50.984Contact Map
3v1vA10.12597.50.985Contact Map
3j4sA10.05747.30.985Contact Map
4j1vA20.19447.30.985Contact Map
4l6yA20.04636.80.986Contact Map
1wcoN10.04446.40.986Contact Map
1gotG10.10376.10.986Contact Map
3nojA10.11855.90.986Contact 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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