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OPENSEQ.org

RelA Pass 1

ID: 1429544503 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 739 (726)
Sequences: 1694 (1101.6)
Seq/Len: 2.333
Nf(neff/√len): 40.9

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: 2.333).

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
91_E96_K4.7371.00
418_Y426_E3.9271.00
434_N448_D3.8031.00
433_V438_V3.2331.00
80_V87_L3.1871.00
66_L139_L3.1281.00
722_V734_V3.0771.00
30_K93_D3.0641.00
274_T277_D3.0171.00
150_R186_E2.9151.00
228_Y231_E2.9101.00
469_V478_I2.8711.00
414_I468_L2.8471.00
667_I725_I2.6911.00
273_E329_K2.6691.00
237_D329_K2.6541.00
28_V71_V2.6261.00
672_R678_D2.6161.00
235_F273_E2.5401.00
498_L537_V2.5261.00
491_V535_A2.5151.00
271_V329_K2.4871.00
157_K160_Q2.4711.00
225_I285_I2.4351.00
27_F72_A2.4341.00
424_V454_T2.4051.00
69_V97_D2.3101.00
444_L450_V2.1951.00
80_V90_I2.1381.00
257_K262_I2.0220.99
527_V536_A1.9950.99
217_L317_G1.9880.99
471_T474_A1.9370.99
399_T405_Q1.9250.99
206_M259_F1.9250.99
239_Y332_H1.9130.99
203_I245_I1.8950.99
226_K230_T1.8790.99
665_I722_V1.8750.99
165_R169_E1.8550.99
16_A28_V1.8540.99
669_G675_L1.8360.98
87_L103_D1.8070.98
34_Y85_I1.8000.98
196_N199_E1.8000.98
45_K155_L1.7900.98
61_L70_T1.7740.98
152_L163_I1.7720.98
664_E709_S1.7640.98
622_T628_A1.7400.98
443_K470_K1.7290.98
89_N92_F1.7260.97
152_L194_Y1.7200.97
66_L70_T1.7130.97
413_P431_A1.7130.97
442_A445_K1.7010.97
693_V708_V1.6930.97
220_D319_K1.6510.96
82_D148_N1.6510.96
215_E219_D1.6370.96
672_R675_L1.6340.96
78_D82_D1.6240.96
207_M245_I1.6230.96
148_N151_T1.6140.96
529_S532_S1.6030.96
455_N458_S1.5930.95
276_S280_A1.5920.95
710_F721_V1.5920.95
218_V240_G1.5650.95
157_K161_E1.5640.95
27_F69_V1.5360.94
422_T426_E1.5350.94
432_K451_E1.5310.94
683_L690_I1.5260.94
58_A71_V1.5240.94
487_K532_S1.5160.94
78_D81_E1.5100.93
688_K717_H1.5000.93
54_P148_N1.4900.93
78_D148_N1.4790.92
100_D133_K1.4770.92
81_E148_N1.4730.92
272_M281_M1.4730.92
152_L164_S1.4730.92
609_C634_C1.4610.92
35_A51_I1.4420.91
82_D151_T1.4320.91
15_L63_D1.4290.91
149_M187_L1.4250.91
273_E277_D1.4180.90
160_Q194_Y1.4170.90
243_K251_K1.4160.90
168_M246_Y1.4160.90
147_H151_T1.4160.90
71_V74_G1.4080.90
675_L728_V1.4030.90
82_D107_K1.4010.90
107_K148_N1.4000.89
44_R50_Y1.3990.89
101_I140_V1.3960.89
204_S245_I1.3940.89
44_R82_D1.3920.89
342_H345_Y1.3900.89
295_R314_T1.3850.89
81_E151_T1.3830.89
29_K33_D1.3790.89
39_H78_D1.3780.88
39_H148_N1.3750.88
227_S231_E1.3720.88
221_I322_I1.3720.88
44_R151_T1.3690.88
228_Y288_L1.3690.88
217_L318_P1.3660.88
144_D148_N1.3650.88
223_T227_S1.3540.87
277_D280_A1.3450.87
411_S725_I1.3430.87
286_H313_T1.3420.87
13_V25_A1.3410.87
44_R148_N1.3380.86
44_R47_G1.3380.86
53_H147_H1.3380.86
202_K206_M1.3380.86
61_L74_G1.3370.86
229_T281_M1.3350.86
433_V442_A1.3320.86
82_D106_T1.3280.86
210_K213_E1.3270.86
495_R534_Y1.3260.86
81_E106_T1.3260.86
39_H50_Y1.3240.86
39_H42_Q1.3180.85
60_I150_R1.3170.85
630_H634_C1.3150.85
44_R81_E1.3110.85
77_H81_E1.3100.85
463_R482_F1.3080.85
309_Q334_V1.3050.85
27_F98_V1.3030.84
608_C634_C1.3030.84
37_A40_F1.3020.84
164_S191_A1.3020.84
675_L678_D1.3010.84
519_E523_P1.3010.84
39_H81_E1.2970.84
676_L693_V1.2960.84
39_H53_H1.2930.84
185_W244_H1.2890.84
54_P78_D1.2870.83
39_H44_R1.2850.83
413_P433_V1.2840.83
68_A72_A1.2830.83
107_K144_D1.2810.83
211_R242_P1.2800.83
609_C630_H1.2800.83
39_H77_H1.2800.83
104_G137_V1.2790.83
53_H77_H1.2780.83
618_E637_I1.2780.83
61_L71_V1.2770.83
85_I89_N1.2710.82
73_C101_I1.2620.82
39_H82_D1.2580.81
44_R107_K1.2570.81
251_K323_E1.2570.81
82_D147_H1.2550.81
87_L100_D1.2530.81
78_D83_T1.2530.81
44_R78_D1.2500.81
54_P82_D1.2460.81
536_A542_I1.2440.80
104_G126_K1.2400.80
486_D489_L1.2390.80
596_Q651_E1.2380.80
629_I650_V1.2380.80
149_M152_L1.2360.80
155_L159_K1.2320.80
611_P634_C1.2310.79
332_H336_E1.2290.79
199_E202_K1.2280.79
44_R77_H1.2270.79
77_H148_N1.2270.79
44_R147_H1.2260.79
455_N459_F1.2250.79
91_E99_R1.2250.79
53_H148_N1.2180.78
53_H78_D1.2180.78
58_A74_G1.2110.78
54_P107_K1.2100.78
222_V226_K1.2100.78
185_W211_R1.2060.78
44_R54_P1.2050.77
620_Y646_R1.2020.77
155_L163_I1.2020.77
31_A35_A1.2010.77
54_P81_E1.2000.77
83_T148_N1.2000.77
82_D144_D1.1990.77
48_E53_H1.1980.77
106_T148_N1.1980.77
683_L708_V1.1970.77
281_M284_Y1.1970.77
27_F30_K1.1930.76
57_V144_D1.1900.76
87_L99_R1.1900.76
491_V531_E1.1890.76
77_H151_T1.1890.76
593_V617_I1.1850.76
78_D151_T1.1840.76
77_H82_D1.1800.75
78_D147_H1.1740.75
243_K342_H1.1740.75
616_P632_A1.1730.75
156_R159_K1.1730.75
69_V98_V1.1680.74
251_K342_H1.1670.74
78_D106_T1.1650.74
394_R406_E1.1640.74
80_V103_D1.1640.74
78_D107_K1.1630.74
619_G648_I1.1610.74
329_K333_Q1.1600.74
410_D443_K1.1580.73
395_I442_A1.1570.73
39_H151_T1.1570.73
428_A440_L1.1560.73
88_D92_F1.1550.73
279_Y286_H1.1550.73
87_L91_E1.1510.73
282_V326_I1.1510.73
33_D36_T1.1500.73
81_E144_D1.1490.73
44_R49_P1.1480.72
39_H106_T1.1470.72
608_C630_H1.1460.72
672_R704_A1.1460.72
72_A98_V1.1460.72
226_K237_D1.1440.72
419_A473_K1.1430.72
77_H147_H1.1430.72
34_Y93_D1.1430.72
54_P147_H1.1430.72
50_Y148_N1.1420.72
44_R144_D1.1390.72
50_Y78_D1.1390.72
50_Y77_H1.1380.72
54_P77_H1.1370.71
671_N704_A1.1360.71
39_H54_P1.1360.71
665_I708_V1.1340.71
81_E147_H1.1340.71
422_T477_K1.1330.71
39_H147_H1.1310.71
683_L710_F1.1290.71
60_I186_E1.1250.70
674_G689_S1.1250.70
83_T151_T1.1230.70
53_H82_D1.1220.70
397_V444_L1.1210.70
432_K437_M1.1180.70
192_F199_E1.1170.70
522_L530_E1.1170.70
251_K264_D1.1160.69
47_G53_H1.1150.69
21_N24_D1.1140.69
77_H144_D1.1100.69
249_Y253_R1.1040.68
159_K163_I1.0970.68
340_A345_Y1.0960.67
221_I268_I1.0960.67
251_K267_A1.0950.67
26_A30_K1.0930.67
246_Y250_R1.0930.67
225_I324_I1.0930.67
216_A220_D1.0920.67
324_I469_V1.0900.67
673_R689_S1.0900.67
81_E159_K1.0900.67
672_R728_V1.0890.67
527_V533_L1.0890.67
46_S82_D1.0880.67
53_H151_T1.0880.67
365_I395_I1.0870.66
106_T144_D1.0860.66
679_V683_L1.0860.66
340_A346_K1.0850.66
16_A62_A1.0830.66
88_D91_E1.0830.66
47_G148_N1.0820.66
149_M167_T1.0820.66
78_D167_T1.0800.66
69_V72_A1.0800.66
185_W242_P1.0800.66
39_H83_T1.0790.66
53_H57_V1.0790.66
283_G286_H1.0790.66
50_Y107_K1.0770.65
77_H106_T1.0740.65
243_K323_E1.0730.65
342_H346_K1.0720.65
39_H107_K1.0720.65
323_E342_H1.0690.65
50_Y147_H1.0660.64
677_N680_L1.0660.64
665_I734_V1.0640.64
691_S711_G1.0630.64
683_L688_K1.0590.64
81_E107_K1.0580.63
251_K340_A1.0570.63
279_Y282_V1.0560.63
279_Y283_G1.0540.63
131_M135_I1.0540.63
487_K491_V1.0540.63
50_Y82_D1.0530.63
267_A342_H1.0530.63
395_I410_D1.0500.63
50_Y53_H1.0480.62
61_L105_V1.0470.62
80_V106_T1.0470.62
18_K411_S1.0470.62
38_A89_N1.0450.62
170_I294_G1.0450.62
44_R53_H1.0430.62
106_T151_T1.0420.62
107_K147_H1.0420.62
144_D151_T1.0420.62
47_G77_H1.0420.62
722_V726_K1.0410.62
243_K340_A1.0400.61
236_G281_M1.0400.61
442_A448_D1.0390.61
53_H81_E1.0390.61
269_R340_A1.0380.61
285_I315_V1.0370.61
82_D159_K1.0370.61
343_W608_C1.0350.61
622_T636_N1.0340.61
230_T236_G1.0340.61
40_F43_V1.0330.61
224_K289_W1.0330.61
34_Y414_I1.0330.61
521_I547_V1.0310.60
695_A706_I1.0310.60
269_R325_Q1.0310.60
144_D147_H1.0300.60
193_R204_S1.0290.60
668_Y733_S1.0280.60
106_T147_H1.0280.60
618_E647_L1.0270.60
323_E340_A1.0260.60
251_K269_R1.0260.60
528_K532_S1.0250.60
54_P151_T1.0250.60
611_P630_H1.0250.60
325_Q342_H1.0250.60
498_L534_Y1.0240.60
479_R717_H1.0230.60
229_T236_G1.0230.60
127_M291_P1.0210.59
201_Y204_S1.0210.59
103_D126_K1.0210.59
366_K369_V1.0180.59
39_H159_K1.0170.59
80_V104_G1.0160.59
608_C611_P1.0150.59
269_R342_H1.0140.59
596_Q649_E1.0130.58
675_L730_D1.0130.58
44_R57_V1.0110.58
395_I472_N1.0100.58
598_A601_L1.0100.58
107_K151_T1.0090.58
269_R323_E1.0080.58
485_Q488_E1.0080.58
269_R346_K1.0060.58
207_M265_L1.0060.58
50_Y151_T1.0030.57
11_E15_L1.0020.57
83_T107_K1.0010.57
53_H106_T1.0000.57
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  
1vj7A20.45331000.511Contact Map
3l9dA20.25031000.77Contact Map
3nr1A20.23551000.833Contact Map
2be3A20.25851000.837Contact Map
3nqwA20.23141000.839Contact Map
2ekiA10.108399.80.923Contact Map
3hvzA60.086699.70.936Contact Map
1wwtA10.117799.40.948Contact Map
2kmmA10.098899.30.948Contact Map
1wxqA10.285599.30.948Contact 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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