OPENSEQ.org
6a4

ID: 1516584567 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 543 (536)
Sequences: 3013 (1821.4)
Seq/Len: 5.621
Nf(neff/√len): 78.7

HHblits Results: (2016_02)
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: 5.621).

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
185_M399_F3.9611.00
232_R235_L2.9621.00
344_A347_F2.8861.00
235_L239_K2.8541.00
331_L356_L2.7081.00
68_H75_I2.6781.00
192_Y395_V2.6111.00
181_A403_L2.5941.00
127_N130_N2.5281.00
181_A399_F2.5091.00
58_F269_L2.4751.00
234_V302_F2.4751.00
223_R226_T2.4481.00
244_K247_E2.4411.00
29_R257_Q2.4161.00
241_N244_K2.3851.00
114_S156_F2.3671.00
112_L350_I2.3661.00
176_I181_A2.3241.00
182_L186_L2.2431.00
184_I402_S2.2041.00
451_K457_S2.1341.00
181_A406_L2.0981.00
108_A357_I2.0721.00
112_L354_L2.0391.00
55_I290_S2.0281.00
4_R274_S2.0201.00
180_L406_L2.0121.00
418_E422_T1.9801.00
77_R84_K1.9741.00
70_N78_K1.9601.00
54_G262_L1.9381.00
214_Y296_T1.8931.00
4_R377_D1.8871.00
208_V212_F1.8811.00
403_L407_T1.8461.00
401_G404_V1.8331.00
110_Y114_S1.7771.00
223_R227_L1.7731.00
26_N293_N1.7721.00
45_P245_L1.7461.00
265_G430_A1.7371.00
18_I292_V1.7101.00
405_T413_V1.6911.00
97_I266_F1.6891.00
271_A370_G1.6861.00
67_Y449_D1.6651.00
115_S349_A1.6591.00
110_Y179_Q1.6561.00
218_S222_V1.6561.00
464_I468_A1.6561.00
191_I364_T1.6551.00
441_Y449_D1.6541.00
20_Y366_A1.6541.00
442_G445_Q1.6390.99
497_Y501_I1.6330.99
109_L357_I1.6280.99
223_R348_F1.6070.99
105_M360_G1.6000.99
192_Y392_L1.5940.99
102_N184_I1.5890.99
331_L334_T1.5780.99
238_L302_F1.5650.99
131_T155_E1.5570.99
218_S299_V1.5560.99
193_F196_W1.5530.99
116_F350_I1.5510.99
231_W234_V1.5500.99
228_P313_E1.5490.99
185_M189_T1.5470.99
431_L478_I1.5360.99
113_I186_L1.5020.99
465_C469_I1.5010.99
339_I349_A1.4970.99
163_Q177_S1.4960.99
225_A230_A1.4940.99
18_I22_V1.4900.99
517_Y521_R1.4810.99
354_L358_T1.4800.99
197_K204_K1.4800.99
444_T467_V1.4780.99
67_Y452_E1.4780.99
7_W16_S1.4740.99
183_C186_L1.4690.99
74_S378_E1.4680.99
415_K495_Y1.4670.99
113_I183_C1.4600.99
227_L230_A1.4510.98
69_R278_F1.4480.98
373_T377_D1.4470.98
318_D324_K1.4420.98
209_T358_T1.4400.98
19_G362_D1.4390.98
219_V222_V1.4290.98
64_L75_I1.4290.98
28_W32_Y1.4270.98
6_T69_R1.4260.98
405_T417_L1.4170.98
112_L357_I1.4160.98
184_I188_F1.4110.98
254_A257_Q1.4000.98
188_F398_C1.3960.98
431_L435_V1.3930.98
258_I294_C1.3890.98
414_V418_E1.3880.98
83_F436_A1.3880.98
194_S361_L1.3760.98
435_V440_F1.3750.98
127_N131_T1.3700.98
160_H179_Q1.3640.97
251_W254_A1.3620.97
71_G377_D1.3600.97
431_L475_L1.3590.97
89_A429_V1.3590.97
258_I293_N1.3580.97
449_D452_E1.3400.97
228_P233_G1.3400.97
211_T215_I1.3390.97
181_A185_M1.3340.97
287_L291_V1.3330.97
263_G268_V1.3280.97
365_F369_E1.3240.97
225_A234_V1.3230.97
272_F366_A1.3230.97
27_V356_L1.3190.97
110_Y183_C1.3180.97
33_I257_Q1.3170.97
362_D365_F1.3130.97
237_Y302_F1.3100.97
217_L303_V1.3060.96
20_Y263_G1.2950.96
461_F465_C1.2930.96
448_R457_S1.2880.96
382_V393_A1.2860.96
9_K12_D1.2840.96
14_L18_I1.2830.96
43_L298_F1.2800.96
175_G408_F1.2770.96
389_R393_A1.2720.96
516_T519_A1.2670.96
428_T478_I1.2620.96
230_A233_G1.2570.95
520_Y524_I1.2430.95
159_R162_L1.2400.95
58_F264_P1.2350.95
110_Y161_V1.2320.95
308_L317_E1.2300.95
218_S221_L1.2260.94
47_T51_I1.2260.94
7_W13_F1.2140.94
497_Y500_I1.2120.94
409_G412_Y1.2090.94
126_K130_N1.2060.94
463_R467_V1.2050.94
307_V338_A1.2050.94
31_P39_G1.2050.94
291_V295_M1.2050.94
99_S401_G1.1970.94
409_G414_V1.1940.93
52_F56_P1.1900.93
49_M255_A1.1870.93
103_T406_L1.1860.93
450_V454_L1.1850.93
109_L186_L1.1820.93
66_Q81_P1.1800.93
33_I36_Q1.1770.93
532_R539_P1.1750.93
411_A415_K1.1720.93
207_W213_P1.1710.93
15_L19_G1.1680.92
392_L396_I1.1680.92
278_F452_E1.1670.92
59_Y63_A1.1640.92
8_G12_D1.1620.92
62_L273_A1.1610.92
223_R228_P1.1610.92
396_I400_F1.1570.92
170_L499_S1.1560.92
517_Y520_Y1.1540.92
100_Y418_E1.1530.92
40_G43_L1.1530.92
229_G233_G1.1530.92
310_Y341_N1.1430.91
41_A242_W1.1420.91
73_I87_G1.1390.91
219_V223_R1.1360.91
227_L233_G1.1340.91
257_Q261_S1.1320.91
441_Y445_Q1.1290.91
510_S513_C1.1220.90
59_Y282_C1.1220.90
27_V359_L1.1190.90
215_I219_V1.1150.90
228_P310_Y1.1110.90
237_Y298_F1.1070.89
108_A356_L1.1040.89
444_T468_A1.1030.89
165_H168_K1.1020.89
123_T340_A1.1010.89
309_G323_A1.0940.89
28_W38_G1.0930.89
400_F404_V1.0910.89
438_S467_V1.0890.88
11_V15_L1.0880.88
50_A258_I1.0870.88
60_M462_W1.0870.88
372_I391_V1.0840.88
56_P65_G1.0830.88
30_F38_G1.0820.88
464_I469_I1.0820.88
404_V413_V1.0810.88
409_G413_V1.0800.88
70_N74_S1.0790.88
33_I253_D1.0790.88
498_W502_L1.0770.88
350_I354_L1.0760.88
231_W235_L1.0720.87
36_Q249_G1.0710.87
29_R414_V1.0710.87
221_L299_V1.0700.87
13_F62_L1.0680.87
77_R87_G1.0650.87
33_I37_N1.0630.87
130_N155_E1.0610.87
110_Y160_H1.0600.87
154_E158_T1.0590.87
26_N30_F1.0550.86
223_R230_A1.0530.86
71_G81_P1.0530.86
190_V361_L1.0510.86
408_F414_V1.0490.86
124_S127_N1.0470.86
293_N297_S1.0470.86
105_M364_T1.0450.86
81_P85_G1.0450.86
13_F17_V1.0450.86
24_L28_W1.0370.85
162_L180_L1.0320.85
154_E333_I1.0310.84
332_F353_F1.0290.84
190_V357_I1.0290.84
502_L506_I1.0280.84
176_I408_F1.0280.84
516_T520_Y1.0250.84
72_C90_I1.0230.84
499_S502_L1.0230.84
126_K136_N1.0190.84
327_G330_L1.0180.83
212_F216_I1.0170.83
63_A450_V1.0160.83
472_L476_F1.0140.83
62_L286_A1.0120.83
89_A514_I1.0080.83
102_N187_I1.0080.83
512_I516_T1.0080.83
415_K418_E1.0030.82
206_V362_D1.0030.82
182_L185_M1.0010.82
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  
4xp4A10100-0.012Contact Map
2a65A10.90421000.164Contact Map
4us3A10.78821000.219Contact Map
3giaA10.771697.90.936Contact Map
4djkA20.7808970.946Contact Map
3l1lA10.755196.90.946Contact Map
2jlnA10.769891.40.96Contact Map
4wgvA20.683254.20.972Contact Map
3dh4A40.760643.80.974Contact Map
2xq2A10.768260.977Contact 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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