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OPENSEQ.org

PhyB

ID: 1434397691 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 531 (492)
Sequences: 561 (383.5)
Seq/Len: 1.140
Nf(neff/√len): 17.3

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: 1.140).

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
175_V189_V4.1911.00
230_F286_A3.2621.00
391_D469_S3.2331.00
403_P413_I3.0051.00
49_E247_L2.9201.00
179_R204_S2.8661.00
193_H197_H2.6851.00
274_Q492_R2.5181.00
276_M315_V2.5010.99
276_M281_S2.4180.99
287_M336_M2.2500.99
238_I268_P2.1670.98
394_A467_F2.1520.98
278_N498_S2.0840.97
453_M465_F2.0390.97
433_D509_R1.9940.96
184_Y285_L1.9870.96
476_K501_A1.9610.96
250_Q255_T1.9440.96
36_A219_A1.9240.95
174_V339_F1.8890.95
30_P243_A1.8410.94
171_C201_V1.8280.93
451_C469_S1.7870.92
495_P498_S1.7170.90
32_G265_L1.7150.90
409_S412_Q1.6930.89
225_A230_F1.6930.89
243_A267_A1.6880.89
274_Q497_S1.6820.89
273_S277_A1.6750.89
46_G250_Q1.6640.88
443_A446_L1.6480.88
215_L475_I1.6380.87
225_A269_H1.6340.87
188_M276_M1.6230.87
225_A288_A1.6100.86
495_P499_F1.5910.85
188_M281_S1.5780.84
260_L263_S1.5410.82
38_D41_S1.5340.82
26_G269_H1.5270.82
403_P407_A1.5040.80
479_G499_F1.4990.80
392_G408_P1.4950.80
238_I279_M1.4920.80
199_E216_H1.4890.79
230_F288_A1.4860.79
225_A286_A1.4500.77
272_H284_S1.4480.77
278_N495_P1.4420.76
278_N499_F1.4210.75
230_F268_P1.4160.74
211_P217_Y1.4100.74
272_H288_A1.4070.74
36_A258_M1.4040.74
39_E121_R1.4030.73
117_A130_L1.4030.73
29_Q32_G1.3940.73
221_D275_Y1.3910.73
420_L453_M1.3890.72
123_D256_Q1.3870.72
233_N316_C1.3860.72
450_V469_S1.3690.71
241_C276_M1.3630.70
385_M390_C1.3590.70
278_N496_R1.3510.69
35_I51_A1.3480.69
231_K290_I1.3400.68
436_G440_Y1.3310.68
222_I226_S1.3300.68
185_D209_L1.3300.68
332_C451_C1.3260.67
80_L416_V1.3230.67
221_D498_S1.3220.67
188_M217_Y1.3170.67
222_I278_N1.3150.66
205_K208_D1.3100.66
209_L217_Y1.3010.65
188_M315_V1.2980.65
416_V440_Y1.2900.64
182_T478_G1.2880.64
217_Y388_V1.2840.64
393_A404_L1.2810.63
37_V128_I1.2800.63
248_V289_V1.2780.63
181_L201_V1.2720.63
435_L443_A1.2710.63
432_T435_L1.2670.62
55_L524_L1.2670.62
131_E329_R1.2660.62
121_R331_A1.2610.62
236_R275_Y1.2590.61
31_F267_A1.2500.61
28_I246_V1.2480.60
225_A272_H1.2460.60
24_R225_A1.2450.60
22_I288_A1.2430.60
496_R499_F1.2400.60
392_G467_F1.2360.59
364_L368_M1.2320.59
321_S512_P1.2320.59
241_C388_V1.2310.59
275_Y499_F1.2280.59
160_Q337_Q1.2270.58
228_F231_K1.2260.58
272_H275_Y1.2250.58
250_Q254_L1.2230.58
480_A484_P1.2230.58
171_C204_S1.2210.58
171_C189_V1.2120.57
179_R206_R1.2080.57
281_S315_V1.2050.56
226_S272_H1.2050.56
31_F243_A1.2030.56
132_P480_A1.1960.56
181_L258_M1.1910.55
479_G498_S1.1900.55
116_Y315_V1.1900.55
222_I498_S1.1860.55
37_V189_V1.1830.54
22_I226_S1.1810.54
155_A174_V1.1780.54
382_P386_D1.1760.54
25_G285_L1.1750.54
269_H483_H1.1740.53
268_P285_L1.1730.53
199_E315_V1.1730.53
271_C483_H1.1720.53
230_F483_H1.1690.53
198_G278_N1.1680.53
221_D278_N1.1670.53
243_A268_P1.1640.52
289_V384_I1.1590.52
118_I326_F1.1590.52
44_I47_Y1.1560.52
209_L319_T1.1550.52
230_F233_N1.1540.52
279_M493_M1.1540.52
270_G288_A1.1510.51
275_Y495_P1.1500.51
278_N479_G1.1490.51
44_I79_S1.1460.51
168_K172_D1.1450.51
349_L353_M1.1450.51
279_M499_F1.1410.50
184_Y239_V1.1400.50
353_M504_E1.1390.50
128_I171_C1.1380.50
412_Q445_A1.1360.50
75_T79_S1.1350.50
25_G225_A1.1350.50
167_I384_I1.1340.50
226_S495_P1.1320.49
308_M473_K1.1310.49
221_D495_P1.1280.49
394_A465_F1.1210.48
46_G252_D1.1200.48
124_V445_A1.1190.48
230_F271_C1.1160.48
44_I72_A1.1140.48
233_N286_A1.1140.48
339_F343_L1.1130.48
361_T464_L1.1030.47
514_E517_E1.1030.47
221_D499_F1.1020.47
198_G223_P1.1010.46
198_G498_S1.1000.46
46_G255_T1.0980.46
225_A271_C1.0970.46
25_G243_A1.0960.46
392_G407_A1.0940.46
226_S278_N1.0910.45
324_I420_L1.0900.45
292_N344_N1.0870.45
225_A285_L1.0800.44
198_G221_D1.0780.44
283_A460_K1.0780.44
198_G275_Y1.0710.44
337_Q340_G1.0690.43
224_Q228_F1.0680.43
431_S515_T1.0670.43
479_G495_P1.0650.43
221_D272_H1.0650.43
188_M279_M1.0640.43
419_W440_Y1.0640.43
408_P413_I1.0630.43
25_G31_F1.0620.43
234_R340_G1.0580.42
26_G225_A1.0560.42
196_E309_R1.0550.42
492_R497_S1.0540.42
472_A505_V1.0530.42
198_G238_I1.0530.42
44_I515_T1.0500.42
190_Y198_G1.0480.41
408_P470_H1.0460.41
30_P245_P1.0440.41
232_Q262_G1.0430.41
275_Y477_W1.0400.41
225_A229_L1.0380.40
314_V340_G1.0380.40
238_I272_H1.0380.40
279_M496_R1.0370.40
160_Q175_V1.0370.40
198_G499_F1.0360.40
22_I225_A1.0360.40
27_Y267_A1.0330.40
374_P395_F1.0330.40
226_S498_S1.0300.40
39_E126_V1.0300.40
248_V441_P1.0280.40
443_A451_C1.0280.40
87_I91_R1.0280.40
314_V336_M1.0240.39
267_A288_A1.0210.39
275_Y498_S1.0190.39
230_F285_L1.0160.38
469_S474_E1.0150.38
436_G508_S1.0150.38
61_S441_P1.0150.38
394_A413_I1.0140.38
193_H196_E1.0120.38
28_I58_M1.0110.38
36_A343_L1.0100.38
197_H289_V1.0090.38
226_S481_K1.0090.38
170_L285_L1.0090.38
202_A248_V1.0080.38
119_L132_P1.0080.38
238_I260_L1.0070.38
174_V290_I1.0060.38
269_H494_H1.0060.38
166_D172_D1.0060.38
33_C54_M1.0060.38
132_P384_I1.0050.37
478_G510_S1.0050.37
102_N118_I1.0050.37
245_P267_A1.0050.37
52_R58_M1.0040.37
284_S484_P1.0030.37
332_C458_I1.0020.37
230_F270_G1.0020.37
230_F267_A1.0010.37
272_H276_M1.0010.37
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  
4ourA10.84371000.256Contact Map
4q0jA10.88511000.372Contact Map
3zq5A10.9191000.407Contact Map
3nhqA80.88321000.437Contact Map
4gw9A40.90021000.478Contact Map
4bwiA20.67421000.59Contact Map
4cqhA10.54611000.624Contact Map
4e04A20.57631000.642Contact Map
2oolA20.56121000.649Contact Map
2k2nA10.318399.90.87Contact 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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