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OPENSEQ.org

Above-500 synthetase

ID: 1485740703 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 656 (617)
Sequences: 699 (567.5)
Seq/Len: 1.133
Nf(neff/√len): 22.8

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: 1.133).

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
130_I140_I3.5631.00
242_A531_A3.1241.00
258_S371_S3.0671.00
242_A528_V2.6261.00
381_D565_R2.4760.99
166_P191_R2.4670.99
250_H525_D2.3820.99
223_W530_E2.3100.99
269_V550_L2.2430.99
381_D568_K2.2070.98
383_I532_T2.1560.98
245_A249_A2.1420.98
168_D187_R2.1200.98
552_E555_R2.0710.97
302_R561_A2.0680.97
565_R568_K2.0070.97
196_T202_L1.9870.96
269_V554_M1.8900.95
261_L303_A1.8760.94
134_A526_D1.8430.94
594_R637_E1.8380.94
83_L87_D1.8350.94
384_F532_T1.8280.93
301_R325_V1.8030.93
284_L321_L1.8010.93
301_R305_E1.7830.92
556_G560_D1.7690.92
592_G597_E1.7630.92
171_A189_V1.7370.91
365_R368_A1.7370.91
347_D510_D1.7150.90
259_C271_A1.7050.90
528_V531_A1.6980.89
144_R194_H1.6830.89
268_T303_A1.6810.89
168_D191_R1.6610.88
272_F558_V1.6550.88
197_G200_Y1.6520.88
381_D632_W1.6080.86
270_L376_T1.5910.85
270_L523_F1.5860.85
286_T300_A1.5740.84
246_S528_V1.5660.84
376_T521_A1.5660.84
601_V606_L1.5640.84
547_K568_K1.5510.83
630_E634_R1.5480.83
594_R630_E1.5320.82
232_L539_E1.5080.80
555_R560_D1.4740.78
258_S374_H1.4720.78
587_T611_A1.4690.78
568_K632_W1.4490.77
246_S250_H1.4480.77
121_V529_L1.4400.76
239_A384_F1.4350.76
242_A246_S1.4230.75
523_F550_L1.4220.75
273_A554_M1.4160.74
139_R154_D1.3960.73
381_D571_M1.3830.72
83_L90_P1.3820.72
553_A568_K1.3800.72
118_Y133_T1.3760.71
169_E598_H1.3690.71
265_L551_V1.3650.70
526_D530_E1.3620.70
121_V130_I1.3540.69
128_S204_L1.3520.69
300_A323_H1.3490.69
379_G565_R1.3460.69
486_D512_G1.3380.68
560_D563_P1.3370.68
266_D381_D1.3310.68
289_A571_M1.3310.68
379_G524_Y1.3250.67
406_L529_L1.3240.67
102_R106_G1.3160.66
142_H557_V1.3150.66
418_L422_K1.3120.66
266_D568_K1.3060.65
582_H585_E1.2920.64
174_L477_T1.2880.64
596_A601_V1.2810.63
97_I163_I1.2760.63
587_T610_A1.2720.62
87_D114_L1.2670.62
196_T265_L1.2660.62
134_A199_G1.2610.61
119_H140_I1.2600.61
304_V323_H1.2570.61
243_I273_A1.2510.60
355_G571_M1.2500.60
266_D547_K1.2490.60
565_R632_W1.2490.60
594_R597_E1.2450.60
243_I269_V1.2450.60
259_C534_A1.2440.60
390_A405_H1.2350.59
185_S447_R1.2310.59
381_D547_K1.2300.59
286_T294_S1.2300.59
311_A332_P1.2260.58
84_I473_G1.2250.58
81_L122_A1.2240.58
558_V563_P1.2190.58
61_W66_P1.2190.58
560_D564_A1.2150.57
433_W454_G1.2090.57
255_D372_R1.2050.56
382_E575_E1.2050.56
263_G379_G1.2020.56
108_E131_R1.2000.56
347_D525_D1.1980.56
281_S322_D1.1980.56
183_P462_W1.1970.55
202_L627_V1.1910.55
90_P237_R1.1900.55
274_A375_L1.1900.55
55_H58_G1.1880.55
394_L398_N1.1870.54
133_T136_G1.1870.54
53_V209_P1.1860.54
274_A282_L1.1850.54
272_F303_A1.1830.54
594_R598_H1.1710.53
289_A355_G1.1690.53
133_T139_R1.1670.53
90_P117_L1.1670.53
364_G601_V1.1660.52
266_D565_R1.1660.52
322_D369_T1.1630.52
498_V575_E1.1610.52
590_W607_L1.1590.52
154_D190_W1.1570.52
87_D90_P1.1540.51
527_R530_E1.1530.51
443_Q487_P1.1510.51
550_L578_G1.1500.51
168_D272_F1.1500.51
129_W201_G1.1500.51
244_A556_G1.1490.51
146_P305_E1.1470.51
299_W562_L1.1460.51
232_L542_S1.1460.51
244_A557_V1.1450.50
260_E376_T1.1450.50
378_Y382_E1.1450.50
135_T524_Y1.1400.50
64_A563_P1.1370.50
441_E479_A1.1340.49
88_R551_V1.1340.49
373_Y520_A1.1290.49
131_R222_W1.1260.49
553_A565_R1.1220.48
644_R648_T1.1180.48
376_T579_L1.1170.48
118_Y134_A1.1160.48
133_T190_W1.1150.48
269_V523_F1.1150.48
238_R241_D1.1150.48
379_G382_E1.1140.48
447_R512_G1.1120.47
70_R252_G1.1120.47
644_R647_P1.1110.47
7_D136_G1.1090.47
92_A106_G1.1070.47
197_G219_E1.1040.47
58_G223_W1.1040.47
382_E501_G1.1020.46
365_R608_R1.1020.46
164_G479_A1.1020.46
490_G537_L1.0990.46
241_D403_W1.0980.46
163_I335_Y1.0980.46
381_D540_R1.0980.46
179_F507_A1.0970.46
2_P19_A1.0960.46
642_T646_T1.0960.46
225_P530_E1.0930.45
386_G540_R1.0920.45
263_G553_A1.0920.45
461_P602_D1.0920.45
595_L632_W1.0910.45
381_D523_F1.0900.45
232_L552_E1.0900.45
246_S525_D1.0890.45
419_P608_R1.0880.45
199_G338_L1.0880.45
383_I632_W1.0870.45
542_S606_L1.0860.45
243_I528_V1.0860.45
268_T558_V1.0830.45
535_V549_L1.0820.44
52_T55_H1.0780.44
54_A104_R1.0770.44
565_R630_E1.0770.44
142_H194_H1.0760.44
140_I152_A1.0760.44
203_A233_A1.0760.44
415_W420_T1.0740.44
172_L601_V1.0720.44
17_A20_A1.0720.44
333_Y562_L1.0710.43
324_H606_L1.0700.43
385_L540_R1.0690.43
415_W449_P1.0680.43
446_A486_D1.0670.43
268_T383_I1.0660.43
347_D631_T1.0660.43
547_K571_M1.0650.43
294_S571_M1.0630.43
569_D574_D1.0600.42
15_S99_E1.0600.42
322_D421_L1.0600.42
494_D571_M1.0590.42
358_R381_D1.0580.42
50_T56_P1.0560.42
505_F521_A1.0560.42
379_G568_K1.0540.42
200_Y221_R1.0540.42
17_A23_G1.0540.42
296_D547_K1.0530.42
115_P602_D1.0510.42
565_R599_G1.0500.41
418_L436_G1.0480.41
250_H375_L1.0460.41
643_P646_T1.0460.41
373_Y436_G1.0440.41
247_V250_H1.0440.41
377_G381_D1.0440.41
498_V529_L1.0440.41
268_T547_K1.0440.41
391_Y519_V1.0380.40
235_G539_E1.0380.40
117_L250_H1.0370.40
13_P18_G1.0360.40
51_L56_P1.0350.40
337_D340_S1.0340.40
82_V91_E1.0320.40
97_I108_E1.0300.40
382_E571_M1.0300.40
163_I448_T1.0300.40
466_H469_T1.0290.40
283_S324_H1.0280.39
316_N512_G1.0280.39
49_D443_Q1.0280.39
153_S602_D1.0270.39
284_L390_A1.0270.39
164_G487_P1.0260.39
77_G599_G1.0260.39
263_G381_D1.0250.39
166_P604_R1.0240.39
12_L24_Q1.0230.39
12_L193_V1.0210.39
121_V128_S1.0200.39
239_A250_H1.0190.39
643_P647_P1.0190.39
262_S267_S1.0180.38
263_G568_K1.0170.38
70_R200_Y1.0150.38
233_A640_W1.0140.38
127_E588_E1.0140.38
643_P648_T1.0140.38
192_G492_H1.0130.38
443_Q448_T1.0120.38
236_A607_L1.0120.38
205_P400_F1.0110.38
14_D59_R1.0100.38
390_A394_L1.0090.38
53_V108_E1.0090.38
235_G535_V1.0070.38
494_D547_K1.0070.38
527_R547_K1.0060.37
245_A469_T1.0050.37
153_S502_A1.0050.37
463_L626_T1.0020.37
491_R494_D1.0010.37
103_D252_G1.0000.37
237_R425_L1.0000.37
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: (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  
1jgtA20.70121000.617Contact Map
1q15A40.70431000.628Contact Map
1ct9A40.69821000.66Contact Map
3p52A20.338498.80.915Contact Map
3bl5A60.28298.70.918Contact Map
3fiuA40.338498.60.92Contact Map
1surA10.309598.50.923Contact Map
1xngA20.37898.40.925Contact Map
1wxiA10.361398.20.929Contact Map
1te5A20.275998.10.931Contact 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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