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OPENSEQ.org

testdDAT

ID: 1447866967 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 631 (567)
Sequences: 986 (718.7)
Seq/Len: 1.739
Nf(neff/√len): 30.2

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: 1.739).

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
240_A456_F3.4911.00
154_T214_E3.2431.00
508_R514_P3.0791.00
303_A306_K3.0221.00
150_N153_N2.7821.00
136_F245_I2.7241.00
589_R596_P2.7101.00
235_I240_A2.6931.00
293_I361_F2.6821.00
267_F271_F2.6341.00
277_L358_I2.5221.00
240_A460_L2.5191.00
472_H552_Y2.3221.00
402_A405_F2.2701.00
283_G365_S2.2531.00
458_V461_A2.2521.00
270_L274_A2.2140.99
241_L244_L2.1780.99
244_L456_F2.1350.99
287_P372_H2.1190.99
133_R219_Y2.0620.99
86_A503_F2.0530.99
282_R285_T2.0380.99
324_G487_V2.0360.99
42_G420_D2.0180.99
294_Q298_T2.0010.99
498_Y506_D2.0010.99
280_L284_L1.9770.98
252_F255_W1.9720.98
228_G550_Y1.9560.98
466_G470_F1.9490.98
291_L294_Q1.9110.98
222_E236_K1.8790.98
229_I556_A1.8580.97
90_H509_D1.8550.97
90_H506_D1.8000.97
423_F427_E1.7850.96
50_V417_L1.7710.96
137_A215_Y1.7470.96
64_A68_P1.7470.96
227_E231_D1.7460.96
131_S415_L1.7100.95
153_N214_E1.7090.95
280_L358_I1.7050.95
505_E514_P1.6790.95
507_I511_I1.6770.94
339_N344_D1.6750.94
297_L357_F1.6680.94
209_Q214_E1.6480.94
240_A244_L1.6310.93
136_F241_L1.6230.93
91_N98_C1.6200.93
107_K436_E1.6180.93
554_S558_A1.5930.92
148_C153_N1.5880.92
291_L372_H1.5700.92
494_V503_F1.5700.92
126_V463_C1.5680.91
590_F596_P1.5600.91
468_F547_Y1.5450.91
38_L42_G1.5440.91
282_R286_L1.5380.90
41_I351_I1.5290.90
112_A486_A1.5190.90
116_I486_A1.5190.90
39_S400_M1.5180.90
267_F412_M1.5100.89
468_F472_H1.5050.89
506_D509_D1.5030.89
59_K312_D1.4950.89
106_F493_A1.4900.88
287_P369_Y1.4810.88
138_S143_L1.4810.88
461_A470_F1.4760.88
132_L415_L1.4760.88
79_P104_P1.4650.87
501_N524_R1.4640.87
251_Y449_A1.4600.87
521_V526_V1.4500.87
249_I415_L1.4470.86
369_Y399_T1.4420.86
271_F275_V1.4280.85
106_F575_A1.4280.85
288_G368_G1.4270.85
251_Y445_E1.4260.85
79_P88_G1.4250.85
48_A52_R1.4190.85
310_W313_A1.4110.85
135_F408_L1.4110.85
46_D52_R1.4080.84
244_L248_L1.4020.84
82_Y86_A1.3990.84
234_A465_Q1.3920.83
405_F409_I1.3900.83
352_N359_A1.3780.83
32_G35_D1.3780.83
119_Y566_S1.3780.83
49_N52_R1.3710.82
49_N53_F1.3690.82
219_Y238_D1.3690.82
313_A316_Q1.3520.81
145_W148_C1.3520.81
291_L371_A1.3440.80
94_G431_T1.3420.80
241_L245_I1.3380.80
54_P61_G1.3350.80
350_F354_A1.3320.80
123_Y475_D1.3320.80
321_L332_A1.3290.79
27_R30_W1.3250.79
150_N154_T1.3240.79
147_S150_N1.3200.79
371_A376_V1.3120.78
593_L596_P1.3080.78
47_L52_R1.2970.77
149_N153_N1.2930.77
138_S145_W1.2890.76
385_G388_L1.2810.76
273_Y355_T1.2800.76
146_T398_A1.2790.76
449_A453_S1.2760.75
153_N157_C1.2720.75
143_L146_T1.2700.75
99_W104_P1.2700.75
574_V578_K1.2690.75
41_I45_V1.2680.75
431_T435_D1.2600.74
277_L281_I1.2570.74
41_I421_S1.2560.74
386_P471_F1.2460.73
112_A571_I1.2440.73
86_A507_I1.2430.73
485_V568_V1.2420.73
59_K308_E1.2380.72
104_P108_G1.2340.72
373_T399_T1.2330.72
90_H337_Y1.2320.72
451_L492_I1.2300.71
79_P84_E1.2260.71
310_W316_Q1.2250.71
317_V353_S1.2240.71
133_R220_I1.2210.71
84_E89_Q1.2200.71
591_T596_P1.2190.70
232_L466_G1.2170.70
378_I381_V1.2080.69
121_D425_G1.2060.69
322_G327_V1.2060.69
144_P148_C1.2050.69
148_C152_W1.2010.69
65_F79_P1.2010.69
420_D423_F1.1990.69
324_G332_A1.1970.68
68_P73_L1.1950.68
371_A377_R1.1870.68
89_Q104_P1.1860.67
79_P89_Q1.1830.67
105_L575_A1.1790.67
296_Y360_G1.1790.67
88_G104_P1.1780.67
276_L283_G1.1770.67
138_S148_C1.1760.66
53_F61_G1.1760.66
228_G231_D1.1750.66
584_G589_R1.1700.66
501_N525_F1.1690.66
87_L98_C1.1690.66
40_V348_T1.1670.66
51_W61_G1.1670.66
251_Y255_W1.1660.66
247_Y452_F1.1650.65
257_G263_K1.1630.65
130_W471_F1.1600.65
579_L590_F1.1600.65
331_Y424_G1.1540.64
337_Y510_M1.1530.64
397_I407_A1.1520.64
103_V497_I1.1470.64
50_V359_A1.1400.63
242_C405_F1.1390.63
154_T157_C1.1380.63
590_F594_T1.1330.62
46_D53_F1.1310.62
241_L460_L1.1210.61
589_R593_L1.1190.61
472_H475_D1.1140.60
213_S217_N1.1130.60
257_G262_G1.1110.60
100_G107_K1.1100.60
51_W57_C1.1070.60
462_S470_F1.1060.59
276_L362_V1.1060.59
462_S474_L1.1060.59
573_A576_I1.1040.59
555_W559_L1.1040.59
488_F492_I1.1030.59
33_K339_N1.1020.59
89_Q108_G1.1000.59
302_S305_Y1.0980.59
109_I493_A1.0940.58
87_L494_V1.0910.58
130_W153_N1.0890.58
337_Y509_D1.0860.57
211_A214_E1.0850.57
285_T366_V1.0850.57
258_I261_S1.0850.57
574_V577_F1.0840.57
49_N61_G1.0830.57
266_W272_P1.0830.57
81_F85_L1.0820.57
48_A53_F1.0820.57
589_R595_T1.0800.57
52_R61_G1.0730.56
284_L293_I1.0720.56
474_L563_I1.0710.56
51_W54_P1.0690.56
489_F492_I1.0680.55
130_W134_F1.0670.55
102_L494_V1.0640.55
235_I460_L1.0610.55
359_A389_V1.0570.54
330_A428_A1.0560.54
559_L563_I1.0520.54
413_M417_L1.0510.54
297_L361_F1.0480.53
48_A51_W1.0480.53
69_Y79_P1.0400.53
567_S572_P1.0400.53
81_F328_L1.0390.52
45_V48_A1.0370.52
66_L69_Y1.0370.52
157_C214_E1.0330.52
289_S292_G1.0320.52
88_G108_G1.0320.52
79_P108_G1.0300.51
99_W102_L1.0280.51
463_C471_F1.0250.51
51_W60_N1.0250.51
105_L594_T1.0230.51
139_F408_L1.0220.51
54_P62_G1.0210.50
124_Y148_C1.0210.50
56_L126_V1.0200.50
150_N214_E1.0180.50
592_I595_T1.0150.50
51_W55_Y1.0150.50
300_N303_A1.0130.50
565_G569_V1.0110.49
65_F69_Y1.0090.49
80_L322_G1.0090.49
98_C106_F1.0080.49
389_V392_V1.0070.49
53_F62_G1.0070.49
421_S484_L1.0060.49
317_V352_N1.0050.49
385_G390_F1.0050.49
142_S146_T1.0040.49
148_C157_C1.0040.49
458_V477_Y1.0000.48
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  
4xp4A101000.221Contact Map
2a65A10.77811000.382Contact Map
4us3A10.67831000.43Contact Map
3giaA10.660989.40.973Contact Map
4djkA20.671986.50.975Contact Map
3l1lA10.638762.30.979Contact Map
3rlfF10.2187250.984Contact Map
2jlnA10.692622.50.984Contact Map
2gutA10.063480.987Contact Map
4tquN104.80.988Contact 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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