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OPENSEQ.org

lptD

ID: 1437775871 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 918 (807)
Sequences: 1523 (1066.4)
Seq/Len: 1.887
Nf(neff/√len): 37.5

Jackhmmer Results: (2015_01_07)
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: 1.887).

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
317_S338_Y5.4471.00
342_L346_Y4.5391.00
461_L483_I3.9591.00
244_L258_D3.2421.00
319_F338_Y3.1671.00
214_D229_N3.0971.00
628_A676_L3.0861.00
335_V351_Y3.0441.00
185_D201_N2.9861.00
325_S333_T2.9551.00
560_V605_S2.9491.00
569_T596_R2.8991.00
333_T353_R2.7521.00
239_A261_Y2.6771.00
568_Y597_S2.6481.00
368_Y375_G2.5771.00
348_A364_G2.5641.00
782_N816_S2.5351.00
630_Y672_N2.5321.00
604_D627_R2.5321.00
346_Y366_F2.5261.00
156_K172_D2.4901.00
319_F336_T2.4891.00
264_C853_C2.4751.00
195_R217_Q2.4281.00
566_Y597_S2.4171.00
340_F350_L2.3941.00
594_Q641_L2.3881.00
276_N291_N2.3681.00
422_R446_Q2.3381.00
289_A309_F2.2631.00
364_G379_A2.2071.00
858_L882_I2.1720.99
674_L701_F2.1530.99
317_S340_F2.1390.99
272_T295_R2.1340.99
274_K295_R2.0960.99
368_Y406_N2.0550.99
190_H193_E2.0280.99
156_K171_G2.0160.99
417_E449_T1.9790.99
219_Q222_N1.9620.99
680_S693_I1.9520.99
166_I190_H1.9460.98
347_D367_R1.9440.98
173_V187_A1.9410.98
275_G278_V1.9280.98
377_V404_L1.9180.98
399_R425_D1.9090.98
350_L364_G1.9020.98
404_L418_V1.9020.98
834_D837_K1.8920.98
281_N284_T1.8860.98
256_L259_G1.8730.98
696_G700_Y1.8620.98
420_Y446_Q1.8390.98
338_Y342_L1.8340.98
850_D889_K1.8300.98
177_Q180_M1.8050.97
635_Y705_R1.7810.97
643_V646_T1.7760.97
559_Y606_G1.7650.97
304_T307_I1.7460.96
600_L633_V1.7150.96
184_G198_L1.7050.96
856_L884_L1.6910.96
174_V183_E1.6780.95
168_T188_N1.6450.95
155_A169_L1.6360.94
499_T548_G1.6290.94
343_A346_Y1.6160.94
215_H228_D1.6130.94
285_G314_R1.6090.94
464_Q479_R1.6070.94
286_F316_Q1.6040.94
273_L292_A1.6030.94
525_G529_D1.5980.93
375_G406_N1.5970.93
444_V469_A1.5930.93
814_D830_R1.5900.93
408_T416_A1.5850.93
186_E199_V1.5680.93
624_L678_V1.5640.92
157_A170_A1.5590.92
240_R262_T1.5580.92
232_Y260_T1.5530.92
185_D200_G1.5530.92
459_G485_F1.5520.92
544_H665_K1.5510.92
525_G528_P1.5440.92
170_A186_E1.5370.92
308_Y316_Q1.5360.92
563_T602_K1.5330.91
134_E139_G1.5290.91
524_R529_D1.5220.91
194_N221_D1.5130.91
524_R527_R1.5130.91
654_D657_W1.5090.91
370_T375_G1.5010.90
317_S341_N1.4940.90
340_F348_A1.4850.90
684_E690_R1.4790.89
544_H567_L1.4760.89
375_G634_P1.4660.89
245_Y257_K1.4630.89
628_A674_L1.4600.89
631_L673_Q1.4590.89
345_N368_Y1.4500.88
198_L216_A1.4500.88
415_L451_T1.4470.88
411_D414_W1.4370.87
242_S260_T1.4320.87
181_Q205_R1.4300.87
495_G551_L1.4290.87
546_E565_K1.4220.87
580_K583_L1.4190.87
697_Q700_Y1.4080.86
128_C132_Y1.4040.86
285_G312_D1.4010.86
400_W422_R1.4000.86
570_K595_D1.3930.85
633_V669_G1.3890.85
514_N519_D1.3760.84
515_I519_D1.3710.84
349_T365_E1.3690.84
524_R528_P1.3680.84
232_Y241_G1.3670.84
504_F541_D1.3650.84
828_L846_G1.3610.83
749_I767_A1.3580.83
697_Q704_R1.3560.83
363_E380_A1.3560.83
598_L636_K1.3520.83
330_T355_M1.3490.83
240_R269_N1.3480.83
381_Y398_D1.3450.82
519_D522_S1.3440.82
497_Q550_S1.3430.82
564_L601_V1.3410.82
632_Y672_N1.3410.82
857_R885_Q1.3380.82
154_S174_V1.3380.82
291_N303_Y1.3380.82
337_P352_P1.3310.81
413_R454_G1.3310.81
285_G311_I1.3310.81
342_L348_A1.3300.81
379_A402_Y1.3270.81
276_N293_T1.3260.81
274_K293_T1.3230.81
184_G187_A1.3200.81
822_V825_W1.3170.80
831_W840_T1.3130.80
280_L311_I1.3090.80
410_L416_A1.3070.80
353_R361_M1.3040.80
479_R482_Q1.3000.79
176_R181_Q1.3000.79
315_R347_D1.2970.79
375_G404_L1.2960.79
198_L202_V1.2930.79
517_F520_D1.2930.79
657_W661_R1.2890.78
522_S528_P1.2860.78
508_D539_T1.2860.78
517_F522_S1.2770.78
697_Q710_G1.2770.78
506_R541_D1.2730.77
562_P603_V1.2700.77
296_V301_V1.2610.76
513_E522_S1.2600.76
661_R669_G1.2560.76
779_K819_W1.2560.76
522_S527_R1.2510.76
656_L696_G1.2500.75
737_F753_F1.2490.75
250_E253_I1.2480.75
414_W452_Y1.2440.75
353_R432_L1.2440.75
315_R341_N1.2360.74
861_R881_G1.2350.74
591_D640_S1.2350.74
270_A852_C1.2290.74
701_F706_V1.2290.74
527_R530_A1.2290.74
888_L894_I1.2280.74
110_W113_R1.2250.73
599_P634_P1.2250.73
249_S255_M1.2240.73
122_A125_G1.2230.73
645_D677_G1.2220.73
349_T367_R1.2180.73
422_R467_Q1.2160.73
289_A292_A1.2110.72
517_F525_G1.2110.72
361_M382_L1.2090.72
625_E681_R1.2090.72
135_P138_P1.2090.72
513_E519_D1.2080.72
199_V215_H1.2070.72
573_L644_F1.2060.72
403_G421_T1.2040.72
524_R530_A1.2030.71
459_G483_I1.2000.71
110_W116_L1.1990.71
602_K629_M1.1960.71
673_Q698_I1.1950.71
134_E138_P1.1950.71
569_T598_L1.1910.70
360_M383_N1.1910.70
326_S332_F1.1890.70
133_I136_V1.1880.70
320_L347_D1.1850.70
101_R104_D1.1810.69
457_F485_F1.1800.69
513_E517_F1.1770.69
689_E692_S1.1760.69
515_I525_G1.1750.69
339_Y347_D1.1740.69
351_Y363_E1.1730.69
565_K659_E1.1690.68
165_Q192_L1.1670.68
506_R574_D1.1620.68
509_R537_R1.1610.68
113_R120_Q1.1610.68
479_R505_V1.1600.67
414_W450_L1.1590.67
496_M551_L1.1570.67
698_I704_R1.1570.67
457_F487_G1.1530.67
691_A695_A1.1490.66
252_A283_A1.1480.66
631_L671_A1.1480.66
827_V847_F1.1450.66
108_L111_I1.1440.66
365_E376_I1.1440.66
631_L698_I1.1410.66
446_Q465_A1.1350.65
773_P779_K1.1340.65
688_F691_A1.1340.65
862_Y880_R1.1330.65
259_G275_G1.1310.65
120_Q124_I1.1310.65
547_P569_T1.1300.64
691_A739_G1.1290.64
161_E164_K1.1270.64
518_N522_S1.1240.64
522_S525_G1.1230.64
653_Y694_S1.1200.63
250_E254_I1.1180.63
696_G704_R1.1150.63
769_F773_P1.1110.63
123_E126_P1.1110.63
336_T352_P1.1080.62
518_N521_G1.1070.62
693_I737_F1.1040.62
121_L124_I1.1030.62
131_S136_V1.1020.62
99_R102_S1.0990.61
152_Y176_R1.0980.61
519_D525_G1.0970.61
124_I127_Y1.0970.61
649_P654_D1.0970.61
145_P148_E1.0950.61
596_R641_L1.0930.61
783_V815_F1.0910.60
443_Y469_A1.0910.60
423_I444_V1.0910.60
213_G227_V1.0890.60
320_L367_R1.0890.60
700_Y706_V1.0880.60
515_I522_S1.0860.60
116_L120_Q1.0840.60
563_T659_E1.0830.60
214_D444_V1.0820.59
696_G706_V1.0800.59
613_T616_A1.0790.59
130_G133_I1.0780.59
902_F906_G1.0770.59
99_R103_A1.0770.59
582_D585_K1.0760.59
122_A126_P1.0760.59
103_A106_S1.0750.59
315_R367_R1.0740.59
365_E378_N1.0730.59
100_S104_D1.0700.58
858_L886_I1.0690.58
254_I483_I1.0670.58
480_L508_D1.0670.58
565_K600_L1.0660.58
114_E117_T1.0640.58
107_H113_R1.0630.57
700_Y705_R1.0600.57
110_W118_A1.0590.57
319_F334_L1.0580.57
521_G524_R1.0560.57
815_F831_W1.0540.56
517_F521_G1.0480.56
131_S134_E1.0460.56
522_S529_D1.0440.55
486_D501_G1.0430.55
112_P115_K1.0420.55
111_I114_E1.0420.55
848_E857_R1.0400.55
697_Q701_F1.0390.55
116_L124_I1.0370.55
446_Q452_Y1.0320.54
623_T681_R1.0310.54
198_L263_R1.0290.54
523_I527_R1.0290.54
187_A466_Y1.0280.54
180_M206_D1.0280.54
525_G530_A1.0280.54
109_D116_L1.0270.54
295_R298_D1.0250.53
299_F424_S1.0240.53
317_S566_Y1.0240.53
149_S178_G1.0240.53
700_Y704_R1.0230.53
670_D706_V1.0220.53
281_N286_F1.0220.53
629_M675_S1.0200.53
516_Y519_D1.0200.53
559_Y607_L1.0200.53
767_A888_L1.0180.53
370_T373_S1.0180.53
676_L699_Y1.0170.52
329_D783_V1.0170.52
187_A198_L1.0160.52
127_Y131_S1.0130.52
294_L888_L1.0130.52
177_Q558_G1.0120.52
240_R850_D1.0100.52
552_P561_T1.0100.52
320_L336_T1.0070.51
450_L461_L1.0070.51
847_F856_L1.0060.51
798_R801_F1.0060.51
243_A256_L1.0050.51
295_R300_P1.0040.51
611_R680_S1.0040.51
656_L736_A1.0040.51
117_T120_Q1.0030.51
562_P604_D1.0010.51
859_I903_L1.0010.51
353_R363_E1.0010.51
315_R318_G1.0010.51
135_P139_G1.0000.51
801_F804_G1.0000.51
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  
4q35A10.81481000.402Contact Map
2r19A20.135199.20.945Contact Map
3my2A10.130798.10.962Contact Map
4epaA10.616672.30.982Contact Map
4fqeA10.173262.80.983Contact Map
2wjrA10.203760.70.983Contact Map
1ormA10.144936.80.986Contact Map
3qraA10.150335.20.986Contact Map
4e1tA10.169935.10.986Contact Map
1qjpA10.141623.70.987Contact 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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