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OPENSEQ.org

prova646

ID: 1447867633 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 644 (567)
Sequences: 897 (656.4)
Seq/Len: 1.582
Nf(neff/√len): 27.6

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: 1.582).

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_F3.4491.00
303_A306_K3.2371.00
508_R514_P3.0941.00
154_T214_E2.9251.00
150_N153_N2.7831.00
136_F245_I2.6321.00
240_A460_L2.5661.00
277_L358_I2.5651.00
293_I361_F2.5031.00
235_I240_A2.4991.00
589_R596_P2.4541.00
267_F271_F2.4031.00
402_A405_F2.3131.00
458_V461_A2.3051.00
283_G365_S2.2690.99
287_P372_H2.2120.99
472_H552_Y2.2070.99
498_Y506_D2.1020.99
294_Q298_T2.0940.99
324_G487_V2.0920.99
270_L274_A2.0720.99
466_G470_F2.0700.99
222_E236_K2.0310.98
252_F255_W2.0270.98
244_L456_F1.9870.98
282_R285_T1.9490.98
241_L244_L1.9480.98
280_L284_L1.9390.98
90_H509_D1.9290.98
133_R219_Y1.9270.98
228_G550_Y1.9080.97
42_G420_D1.8900.97
229_I556_A1.8790.97
86_A503_F1.8680.97
90_H506_D1.8610.97
227_E231_D1.8280.96
153_N214_E1.8020.96
291_L294_Q1.7860.96
423_F427_E1.7580.95
137_A215_Y1.7340.95
297_L357_F1.6950.94
339_N344_D1.6950.94
39_S400_M1.6870.94
41_I351_I1.6850.94
244_L248_L1.6690.93
50_V417_L1.6680.93
554_S558_A1.6520.93
507_I511_I1.6270.92
91_N98_C1.6240.92
369_Y399_T1.6230.92
131_S415_L1.6180.92
280_L358_I1.6150.92
107_K436_E1.6150.92
505_E514_P1.6040.91
494_V503_F1.5830.91
64_A68_P1.5680.90
119_Y566_S1.5660.90
287_P369_Y1.5630.90
219_Y238_D1.5450.89
79_P104_P1.5360.89
106_F493_A1.5290.88
38_L42_G1.5230.88
506_D509_D1.5170.88
59_K312_D1.5140.88
138_S143_L1.5010.87
145_W148_C1.4960.87
282_R286_L1.4960.87
126_V463_C1.4950.87
49_N52_R1.4880.87
468_F547_Y1.4850.86
468_F472_H1.4740.86
291_L372_H1.4710.86
46_D52_R1.4700.86
148_C153_N1.4570.85
32_G35_D1.4530.85
135_F408_L1.4490.85
112_A486_A1.4480.85
209_Q214_E1.4460.84
271_F275_V1.4450.84
251_Y449_A1.4360.84
501_N524_R1.4350.84
82_Y86_A1.4310.84
116_I486_A1.4300.84
251_Y445_E1.4230.83
322_G327_V1.4190.83
405_F409_I1.4180.83
240_A244_L1.4140.83
147_S150_N1.4140.83
267_F412_M1.4130.83
150_N154_T1.4120.82
136_F241_L1.4110.82
79_P88_G1.3970.82
234_A465_Q1.3790.80
41_I45_V1.3790.80
132_L415_L1.3740.80
371_A376_V1.3710.80
144_P148_C1.3700.80
106_F575_A1.3680.80
49_N53_F1.3610.79
138_S145_W1.3590.79
241_L245_I1.3570.79
352_N359_A1.3520.79
277_L281_I1.3460.78
54_P61_G1.3400.78
47_L52_R1.3390.78
273_Y355_T1.3330.77
48_A52_R1.3290.77
461_A470_F1.3260.77
288_G368_G1.3240.76
249_I415_L1.3230.76
149_N153_N1.3210.76
27_R30_W1.3200.76
521_V526_V1.3190.76
488_F492_I1.3170.76
501_N525_F1.3120.76
59_K308_E1.3090.75
153_N157_C1.3080.75
143_L146_T1.3070.75
41_I421_S1.3000.75
88_G104_P1.3000.75
65_F79_P1.2990.75
284_L293_I1.2800.73
590_F596_P1.2760.73
350_F354_A1.2730.72
555_W559_L1.2720.72
90_H337_Y1.2700.72
50_V359_A1.2600.71
449_A453_S1.2590.71
321_L332_A1.2590.71
112_A571_I1.2510.71
130_W471_F1.2420.70
79_P89_Q1.2400.70
133_R220_I1.2360.69
104_P108_G1.2330.69
94_G431_T1.2280.69
121_D425_G1.2240.68
385_G388_L1.2220.68
574_V578_K1.2150.67
232_L466_G1.2150.67
397_I407_A1.2150.67
52_R61_G1.2080.67
373_T399_T1.2060.66
87_L98_C1.2050.66
331_Y424_G1.2020.66
86_A507_I1.1980.66
68_P73_L1.1960.66
485_V568_V1.1960.66
431_T435_D1.1940.65
102_L494_V1.1910.65
593_L596_P1.1900.65
296_Y360_G1.1830.64
378_I381_V1.1830.64
148_C152_W1.1820.64
420_D423_F1.1740.63
53_F61_G1.1730.63
40_V348_T1.1700.63
317_V353_S1.1680.63
330_A428_A1.1650.63
401_P406_W1.1650.63
49_N61_G1.1650.63
313_A316_Q1.1570.62
46_D53_F1.1560.62
87_L494_V1.1540.61
386_P471_F1.1530.61
84_E89_Q1.1520.61
589_R593_L1.1520.61
322_G325_F1.1490.61
242_C405_F1.1490.61
310_W313_A1.1440.60
51_W61_G1.1400.60
251_Y255_W1.1380.60
139_F408_L1.1360.60
51_W55_Y1.1360.60
109_I493_A1.1340.59
228_G231_D1.1320.59
65_F77_G1.1320.59
306_K309_V1.1300.59
103_V497_I1.1280.59
45_V273_Y1.1250.59
33_K339_N1.1250.59
591_T596_P1.1190.58
89_Q104_P1.1140.57
213_S217_N1.1130.57
590_F594_T1.1120.57
310_W316_Q1.1110.57
79_P84_E1.1100.57
574_V577_F1.1070.57
69_Y79_P1.1040.56
291_L371_A1.1000.56
317_V352_N1.0970.56
148_C157_C1.0950.55
474_L563_I1.0910.55
100_G107_K1.0900.55
389_V392_V1.0830.54
81_F85_L1.0810.54
75_V492_I1.0800.54
359_A389_V1.0780.54
235_I460_L1.0780.54
124_Y148_C1.0770.54
569_V573_A1.0750.53
371_A377_R1.0740.53
337_Y510_M1.0710.53
105_L575_A1.0700.53
584_G589_R1.0690.53
300_N303_A1.0660.52
51_W54_P1.0630.52
565_G568_V1.0620.52
51_W57_C1.0590.52
589_R595_T1.0590.52
98_C106_F1.0580.52
47_L51_W1.0540.51
453_S536_V1.0540.51
257_G262_G1.0530.51
99_W104_P1.0520.51
559_L563_I1.0510.51
130_W153_N1.0490.51
138_S148_C1.0470.50
413_M417_L1.0450.50
489_F492_I1.0440.50
65_F84_E1.0430.50
45_V48_A1.0420.50
146_T398_A1.0380.50
317_V358_I1.0370.49
463_C471_F1.0350.49
130_W134_F1.0340.49
150_N214_E1.0320.49
296_Y361_F1.0270.48
148_C154_T1.0270.48
241_L460_L1.0220.48
472_H475_D1.0200.48
80_L322_G1.0200.48
73_L321_L1.0180.47
134_F148_C1.0160.47
56_L126_V1.0140.47
89_Q108_G1.0130.47
422_S483_I1.0130.47
33_K344_D1.0130.47
486_A571_I1.0120.47
285_T366_V1.0090.46
48_A53_F1.0080.46
134_F138_S1.0070.46
45_V52_R1.0060.46
98_C400_M1.0060.46
592_I595_T1.0050.46
54_P62_G1.0030.46
79_P108_G1.0020.46
283_G362_V1.0020.46
497_I576_I1.0010.46
489_F571_I1.0010.46
451_L492_I1.0000.46
82_Y419_L1.0000.46
138_S144_P1.0000.46
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  
4xp4A101000.26Contact Map
2a65A10.76091000.417Contact Map
4us3A10.66461000.464Contact Map
3giaA10.655390.70.975Contact Map
4djkA20.666188.60.976Contact Map
3l1lA10.628965.50.981Contact Map
1bpvA10.06069.50.988Contact Map
2jlnA10.68177.40.988Contact Map
2ksdA10.10876.70.989Contact Map
2mdlA10.02645.30.989Contact 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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