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OPENSEQ.org

RelA Pass 1

ID: 1429544385 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 701 (679)
Sequences: 1702 (1088.6)
Seq/Len: 2.507
Nf(neff/√len): 41.8

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: 2.507).

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
92_I97_L4.7071.00
338_G341_A4.6511.00
404_Y412_N3.8651.00
338_G342_P3.7961.00
420_D434_Q3.7731.00
419_V424_K3.1971.00
81_I88_K3.1801.00
31_A94_K3.1611.00
339_E342_P3.0381.00
67_L138_I3.0301.00
272_S275_D3.0111.00
227_L230_N2.9961.00
673_I685_I2.9381.00
454_I463_L2.8901.00
400_V453_F2.8701.00
149_T185_N2.7341.00
236_R325_E2.6621.00
624_I676_L2.6571.00
629_N635_D2.5941.00
29_V72_L2.5851.00
271_Q325_E2.5771.00
483_L521_I2.5641.00
476_R519_E2.5301.00
234_Q271_Q2.4971.00
269_V325_E2.4851.00
410_L440_T2.4361.00
224_L283_L2.3541.00
28_K73_M2.3471.00
70_E98_T2.3071.00
156_P159_R2.2811.00
430_L436_I2.1961.00
205_A257_L1.9690.99
255_M260_L1.9620.99
81_I91_I1.9600.99
456_T459_A1.9440.99
225_A229_H1.9230.99
17_I29_V1.9180.99
216_Y313_G1.8900.99
626_M632_Q1.8880.99
511_I520_Q1.8780.99
238_K328_R1.8760.99
35_F86_Y1.8700.99
385_T391_H1.8550.99
622_L673_I1.8270.99
46_K154_L1.8000.98
195_D198_M1.7770.98
650_V659_V1.7570.98
151_L193_N1.7460.98
621_Y660_N1.7350.98
62_L71_T1.7340.98
151_L162_I1.7340.98
428_T431_V1.7330.98
399_V417_A1.7310.98
429_P455_N1.7270.98
164_Q168_D1.6890.97
88_K104_D1.6650.97
578_T583_I1.6610.97
202_V244_I1.6610.97
513_N516_T1.6530.97
67_L71_T1.6160.96
661_I672_V1.6100.96
629_N632_Q1.6050.96
83_D147_N1.6030.96
90_D93_E1.6030.96
79_D83_D1.5870.96
274_A278_R1.5810.96
156_P160_A1.5760.96
147_N150_T1.5690.96
565_C589_C1.5670.96
338_G343_Q1.5580.95
418_K437_E1.5500.95
217_Q239_K1.5390.95
472_I516_T1.5320.95
640_C647_V1.5290.95
28_K70_E1.5200.94
214_C218_S1.5010.94
59_S72_L1.4980.94
206_L244_I1.4830.93
79_D82_E1.4780.93
645_A668_H1.4760.93
159_R193_N1.4720.93
408_L412_N1.4700.93
82_E147_N1.4570.93
72_L75_A1.4520.93
148_M186_L1.4480.92
271_Q275_D1.4360.92
101_E132_Q1.4340.92
151_L163_A1.4340.92
242_N249_H1.4340.92
565_C585_H1.4240.92
585_H589_C1.4180.91
102_L139_I1.4170.91
270_L279_L1.4120.91
291_Q310_K1.4080.91
16_I64_N1.4030.91
357_N360_I1.4010.91
632_Q679_H1.4000.91
79_D147_N1.3960.90
83_D150_T1.3950.90
419_V428_T1.3840.90
83_D108_K1.3780.90
163_A190_C1.3770.90
564_C589_C1.3760.90
36_A52_I1.3760.90
86_Y90_D1.3740.90
441_D444_A1.3700.89
227_L286_N1.3690.89
108_K147_N1.3670.89
45_R83_D1.3620.89
45_R51_Y1.3540.89
40_H79_D1.3480.88
275_D278_R1.3390.88
55_P147_N1.3380.88
226_E230_N1.3370.88
38_L41_T1.3340.88
45_R150_T1.3340.88
40_H51_Y1.3330.88
82_E150_T1.3250.87
480_A518_F1.3250.87
61_I149_T1.3210.87
146_H150_T1.3150.87
567_P589_C1.3120.86
397_A676_L1.3120.86
30_L34_D1.3100.86
82_E107_T1.3070.86
78_H82_E1.2990.86
220_W318_L1.2980.86
284_R309_I1.2980.86
45_R82_E1.2970.86
201_N205_A1.2950.85
45_R48_G1.2930.85
40_H147_N1.2910.85
209_T212_E1.2880.85
574_Q592_L1.2850.85
45_R147_N1.2840.85
88_K101_E1.2840.85
143_D147_N1.2810.85
69_A73_M1.2770.84
228_L279_L1.2760.84
14_K26_V1.2750.84
62_L75_A1.2740.84
216_Y314_E1.2720.84
54_H146_H1.2720.84
503_L507_Q1.2720.84
632_Q635_D1.2680.84
210_K241_N1.2670.84
83_D107_T1.2670.84
448_P467_L1.2670.84
62_L72_L1.2660.84
305_Q330_A1.2660.84
564_C585_H1.2660.84
575_G604_M1.2600.83
249_H319_S1.2570.83
208_Q316_T1.2540.83
184_D243_N1.2450.82
640_C659_V1.2440.82
203_Q244_I1.2390.82
40_H43_I1.2360.82
34_D37_D1.2310.81
59_S75_A1.2300.81
633_V650_V1.2280.81
105_G136_V1.2270.81
154_L158_K1.2270.81
148_M151_L1.2260.81
476_R515_N1.2200.80
279_L282_A1.2200.80
55_P79_D1.2200.80
40_H78_H1.2190.80
40_H54_H1.2180.80
105_G125_K1.2180.80
54_H78_H1.2150.80
198_M201_N1.2140.80
40_H83_D1.2140.80
28_K99_V1.2140.80
399_V419_V1.2080.80
70_E99_V1.2070.79
584_V606_L1.2070.79
126_I289_V1.2060.79
45_R108_K1.2060.79
45_R79_D1.2050.79
88_K92_I1.2030.79
40_H82_E1.2010.79
552_Q607_Q1.2010.79
58_V143_D1.1960.79
83_D146_H1.1960.79
28_K31_A1.1950.79
32_A36_A1.1950.79
40_H45_R1.1930.78
549_R573_I1.1910.78
184_D210_K1.1910.78
222_Q226_E1.1890.78
576_H602_N1.1880.78
328_R332_R1.1870.78
154_L162_I1.1870.78
325_E329_K1.1870.78
418_K423_I1.1870.78
221_E225_A1.1840.78
79_D84_T1.1810.77
155_R158_K1.1790.77
108_K143_D1.1780.77
89_E92_I1.1770.77
35_F94_K1.1770.77
471_D474_E1.1750.77
54_H79_D1.1730.77
405_S458_K1.1680.76
74_A102_L1.1660.76
572_P587_I1.1620.76
83_D143_D1.1600.76
567_P585_H1.1580.75
380_K392_E1.1580.75
73_M99_V1.1560.75
55_P83_D1.1560.75
45_R146_H1.1550.75
51_Y79_D1.1490.75
17_I63_A1.1480.74
381_I428_T1.1470.74
81_I104_D1.1470.74
107_T147_N1.1430.74
61_I185_N1.1430.74
82_E143_D1.1390.74
45_R78_H1.1380.74
49_E54_H1.1380.74
229_H235_G1.1370.73
225_A236_R1.1340.73
39_A90_D1.1330.73
414_A426_L1.1330.73
408_L462_A1.1310.73
520_Q526_L1.1270.73
78_H147_N1.1260.72
84_T147_N1.1240.72
55_P108_K1.1220.72
247_L251_V1.1210.72
564_C567_P1.1200.72
78_H83_D1.1190.72
19_P397_A1.1190.72
206_L263_S1.1170.72
356_L381_I1.1170.72
396_G429_P1.1160.72
92_I100_A1.1150.71
54_H147_N1.1150.71
383_V430_L1.1140.71
280_E322_I1.1110.71
277_D284_R1.1110.71
79_D107_T1.1100.71
88_K100_A1.1090.71
79_D146_H1.1060.71
79_D150_T1.1050.70
249_H262_H1.1040.70
622_L659_V1.1040.70
220_W266_F1.1000.70
55_P82_E1.1000.70
148_M166_T1.0980.70
45_R143_D1.0980.70
45_R55_P1.0980.70
45_R50_P1.0980.70
51_Y78_H1.0960.70
339_E343_Q1.0960.70
640_C645_A1.0920.69
629_N679_H1.0920.69
89_E93_E1.0910.69
249_H265_A1.0900.69
70_E73_M1.0890.69
631_E646_G1.0880.69
79_D108_K1.0880.69
78_H150_T1.0870.69
158_K162_I1.0800.68
78_H146_H1.0760.67
479_G522_A1.0760.67
51_Y147_N1.0760.67
281_E284_R1.0730.67
223_N287_F1.0730.67
630_D646_G1.0720.67
82_E146_H1.0710.67
81_I107_T1.0670.67
79_D166_T1.0650.66
47_S83_D1.0640.66
224_L320_L1.0620.66
40_H107_T1.0600.66
191_Y198_M1.0600.66
277_D281_E1.0600.66
652_S657_T1.0580.66
55_P146_H1.0560.65
54_H83_D1.0550.65
552_Q605_P1.0520.65
22_S25_E1.0520.65
381_I457_Q1.0520.65
78_H143_D1.0500.65
511_I517_L1.0500.65
51_Y83_D1.0500.65
40_H150_T1.0450.64
82_E108_K1.0450.64
84_T150_T1.0440.64
574_Q603_I1.0430.64
640_C661_I1.0430.64
634_S637_I1.0410.64
215_K219_I1.0380.63
648_E662_V1.0380.63
320_L454_I1.0360.63
40_H55_P1.0360.63
40_H146_H1.0350.63
283_L311_L1.0340.63
267_E321_T1.0300.63
48_G54_H1.0300.63
82_E158_K1.0290.62
78_H107_T1.0280.62
55_P78_H1.0250.62
192_Q203_Q1.0250.62
51_Y146_H1.0250.62
506_L514_K1.0240.62
249_H267_E1.0230.62
277_D280_E1.0220.62
518_F636_L1.0200.61
48_G147_N1.0180.61
228_L235_G1.0180.61
249_H336_V1.0170.61
400_V454_I1.0150.61
62_L106_V1.0140.61
632_Q681_G1.0130.61
625_Y684_R1.0100.60
54_H82_E1.0080.60
560_K580_R1.0080.60
624_I659_V1.0080.60
78_H166_T1.0070.60
200_D203_Q1.0070.60
242_N319_S1.0070.60
54_H58_V1.0050.60
107_T143_D1.0040.60
90_D94_K1.0030.59
122_S384_Y1.0030.59
428_T434_Q1.0010.59
319_S336_V1.0010.59
51_Y108_K1.0000.59
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  
1vj7A20.47361000.521Contact Map
3l9dA20.25391000.782Contact Map
3nr1A20.24541000.831Contact Map
3nqwA20.24111000.837Contact Map
2be3A20.26391000.844Contact Map
2ekiA10.114199.80.921Contact Map
3hvzA60.091399.60.937Contact Map
1wxqA10.292499.40.945Contact Map
3j7y710.353899.40.946Contact Map
2kmmA10.104199.40.947Contact 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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