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OPENSEQ.org

pista4

ID: 1440492895 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 461 (433)
Sequences: 570 (311.3)
Seq/Len: 1.316
Nf(neff/√len): 15.0

HHblits Results: (2015_06)
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: 1.316).

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
256_I325_L2.9931.00
233_A238_F2.6071.00
87_F91_Y2.2940.99
264_T269_V2.1780.99
292_Q331_V2.1460.99
255_S334_I2.0860.98
88_W91_Y1.9000.96
108_C128_C1.8990.96
119_C125_G1.8370.95
405_D411_S1.8330.95
97_C125_G1.7620.93
119_C128_C1.7600.93
106_G119_C1.7430.93
141_C145_C1.7070.92
163_L166_N1.6880.91
106_G125_G1.6870.91
240_W252_C1.6780.91
145_C170_C1.6560.90
430_S444_Y1.6420.90
252_C268_C1.6340.90
119_C123_F1.6180.89
115_Y127_N1.6000.88
405_D413_G1.5910.88
313_N393_N1.5690.87
410_D442_G1.5650.87
253_G265_A1.5490.86
361_H434_E1.5460.86
431_W444_Y1.5420.86
161_Y170_C1.5380.85
31_F37_A1.5080.84
414_P435_C1.5070.84
134_C155_C1.5070.84
157_C161_Y1.5060.84
143_Q158_T1.5000.83
157_C170_C1.4990.83
117_C125_G1.4670.82
256_I261_W1.4610.81
244_L269_V1.4560.81
428_I445_T1.4500.80
94_G110_D1.4360.80
97_C108_C1.4340.79
166_N170_C1.4300.79
361_H437_M1.4280.79
409_G444_Y1.4260.79
117_C128_C1.4260.79
230_G240_W1.4250.79
255_S428_I1.4160.78
67_E76_E1.4120.78
407_C414_P1.4120.78
405_D410_D1.4030.77
411_S430_S1.3970.77
97_C101_P1.3840.76
117_C123_F1.3800.76
253_G267_H1.3740.75
157_C160_G1.3620.74
418_E421_G1.3580.74
97_C115_Y1.3500.73
145_C161_Y1.3470.73
357_G410_D1.3410.73
353_V429_I1.3360.72
125_G128_C1.3330.72
410_D413_G1.3330.72
261_W356_W1.3310.72
97_C119_C1.3240.71
115_Y128_C1.3180.71
227_V230_G1.3140.71
413_G442_G1.3070.70
63_E76_E1.3050.70
240_W268_C1.2990.69
243_V250_A1.2980.69
228_V436_A1.2960.69
157_C163_L1.2900.69
398_G410_D1.2870.68
71_F85_T1.2830.68
397_A410_D1.2780.67
144_F158_T1.2700.67
155_C160_G1.2680.67
63_E67_E1.2670.67
134_C163_L1.2580.66
53_E67_E1.2540.65
108_C115_Y1.2500.65
430_S435_C1.2500.65
53_E76_E1.2440.64
230_G239_P1.2430.64
108_C119_C1.2370.64
71_F82_E1.2360.64
53_E63_E1.2350.64
155_C163_L1.2330.63
261_W318_L1.2260.63
160_G163_L1.2250.63
316_I405_D1.2250.63
43_R46_R1.2230.62
414_P430_S1.2230.62
405_D442_G1.2230.62
106_G117_C1.2220.62
163_L170_C1.2200.62
143_Q160_G1.2170.62
297_I322_D1.2130.62
410_D432_G1.2130.62
432_G442_G1.2120.61
141_C157_C1.2120.61
115_Y125_G1.2080.61
432_G435_C1.2080.61
410_D444_Y1.2070.61
409_G431_W1.2060.61
102_C108_C1.1950.60
407_C410_D1.1930.60
97_C106_G1.1920.60
405_D430_S1.1910.59
407_C411_S1.1880.59
263_V425_L1.1880.59
145_C157_C1.1850.59
409_G442_G1.1830.59
414_P432_G1.1800.58
407_C435_C1.1730.58
62_R67_E1.1730.58
230_G267_H1.1650.57
265_A268_C1.1610.57
375_P398_G1.1520.56
254_G268_C1.1500.55
239_P268_C1.1460.55
357_G442_G1.1450.55
60_L77_V1.1440.55
267_H444_Y1.1380.54
253_G268_C1.1380.54
425_L450_Y1.1360.54
385_S440_K1.1360.54
230_G265_A1.1330.54
269_V301_P1.1300.53
398_G444_Y1.1290.53
366_A370_Q1.1290.53
29_T33_D1.1270.53
314_H450_Y1.1260.53
36_N39_K1.1250.53
359_V370_Q1.1230.53
174_V177_P1.1220.53
434_E437_M1.1200.52
244_L264_T1.1170.52
37_A46_R1.1170.52
303_H457_K1.1160.52
257_V262_I1.1150.52
357_G431_W1.1150.52
357_G435_C1.1140.52
240_W253_G1.1140.52
318_L450_Y1.1140.52
73_E76_E1.1080.51
252_C266_A1.1070.51
356_W423_S1.1050.51
91_Y97_C1.1040.51
58_G62_R1.1030.51
250_A284_I1.1030.51
336_I435_C1.1030.51
134_C139_G1.1010.51
241_Q253_G1.1000.50
66_E76_E1.0980.50
410_D414_P1.0980.50
337_A434_E1.0970.50
87_F97_C1.0960.50
62_R76_E1.0950.50
410_D431_W1.0940.50
435_C444_Y1.0930.50
141_C144_F1.0910.50
186_T194_T1.0910.50
61_E66_E1.0900.49
37_A41_L1.0880.49
226_R230_G1.0880.49
241_Q252_C1.0880.49
397_A409_G1.0830.49
411_S431_W1.0810.49
30_V37_A1.0810.49
405_D409_G1.0810.49
81_T85_T1.0790.48
405_D444_Y1.0790.48
155_C158_T1.0760.48
54_E63_E1.0740.48
409_G430_S1.0710.48
385_S408_Q1.0630.47
239_P266_A1.0620.47
139_G155_C1.0620.47
357_G413_G1.0620.47
72_E76_E1.0610.47
36_N40_I1.0600.46
54_E76_E1.0570.46
181_V184_S1.0540.46
257_V261_W1.0530.46
398_G442_G1.0530.46
114_S126_K1.0520.46
263_V302_H1.0510.46
357_G444_Y1.0500.45
410_D435_C1.0490.45
54_E67_E1.0480.45
414_P442_G1.0480.45
414_P444_Y1.0470.45
160_G166_N1.0460.45
256_I262_I1.0440.45
255_S305_Y1.0430.45
409_G432_G1.0420.45
155_C161_Y1.0410.45
127_N436_A1.0390.44
407_C430_S1.0380.44
64_C67_E1.0330.44
73_E84_T1.0330.44
357_G397_A1.0300.44
36_N68_K1.0300.44
261_W267_H1.0280.43
407_C432_G1.0270.43
57_Q79_E1.0220.43
398_G405_D1.0220.43
357_G398_G1.0210.43
281_E291_E1.0210.43
426_T436_A1.0200.43
398_G409_G1.0200.43
351_G417_T1.0200.43
108_C117_C1.0200.43
186_T193_E1.0190.42
257_V263_V1.0190.42
334_I425_L1.0180.42
93_D96_Q1.0170.42
267_H431_W1.0140.42
141_C170_C1.0140.42
286_E322_D1.0140.42
322_D325_L1.0120.42
187_S194_T1.0120.42
75_R80_N1.0100.42
85_T88_W1.0100.42
157_C166_N1.0100.42
262_I421_G1.0090.41
315_D444_Y1.0080.41
316_I320_E1.0070.41
380_A446_K1.0070.41
357_G409_G1.0050.41
135_N142_E1.0040.41
63_E73_E1.0030.41
31_F41_L1.0010.41
431_W442_G1.0000.41
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  
4nzqA10.80911000.407Contact Map
4bxwA20.59871000.447Contact Map
3nxpA10.7051000.558Contact Map
3h5cB10.66811000.579Contact Map
4durA20.89591000.581Contact Map
3f1sB10.55531000.618Contact Map
4kkdA20.76361000.628Contact Map
1zjkA10.78091000.632Contact Map
2bdyA10.56181000.635Contact Map
2f83A10.78521000.636Contact 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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