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PilF

ID: 1513362242 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 675 (566)
Sequences: 2217 (1563.6)
Seq/Len: 3.917
Nf(neff/√len): 65.7

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: 3.917).

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
556_L599_P5.4111.00
623_D646_K5.3361.00
562_E600_V4.4911.00
184_K188_L3.6751.00
382_D447_K3.6361.00
206_V235_A3.5731.00
409_F437_A3.4421.00
335_I383_V3.3331.00
449_W482_F3.3091.00
629_Y642_L3.2931.00
561_K597_F3.2771.00
522_S525_E3.2151.00
556_L665_T3.2031.00
235_A240_L3.1411.00
563_L595_T3.1211.00
629_Y634_K3.1151.00
446_K489_I3.0791.00
119_K122_E3.0651.00
557_C605_C2.8471.00
412_I546_G2.8201.00
441_L489_I2.6801.00
351_L471_I2.6741.00
644_I653_Q2.6331.00
622_P630_I2.5981.00
625_E646_K2.5691.00
654_D658_K2.5331.00
423_V518_L2.5321.00
564_Y596_F2.5321.00
495_T504_L2.5031.00
451_A478_V2.4561.00
410_K440_Y2.4441.00
559_E604_Q2.4051.00
377_V455_V2.3861.00
284_V334_V2.3791.00
365_K389_G2.2671.00
148_K151_E2.2621.00
599_P665_T2.2421.00
628_E632_K2.2251.00
560_C602_C2.2141.00
310_L331_K2.2081.00
555_R614_M2.1801.00
556_L561_K2.1731.00
411_R621_I2.1651.00
522_S640_R2.1631.00
373_T383_V2.1621.00
374_L465_V2.1441.00
382_D463_R2.1391.00
626_L639_I2.1331.00
655_G669_V2.1121.00
548_L619_L2.1101.00
527_I544_L2.1021.00
562_E598_R2.0861.00
406_Y410_K2.0651.00
642_L645_T2.0471.00
319_E671_A2.0181.00
344_L373_T2.0121.00
642_L646_K2.0101.00
120_I124_L2.0081.00
468_N471_I1.9801.00
413_L437_A1.9641.00
560_C601_G1.9611.00
524_P620_L1.9531.00
421_L516_S1.9161.00
625_E645_T1.9101.00
524_P639_I1.9101.00
560_C605_C1.9061.00
219_V230_L1.9011.00
557_C560_C1.8961.00
638_E641_N1.8751.00
195_L233_S1.8631.00
620_L648_F1.8581.00
209_D212_D1.8561.00
557_C602_C1.8501.00
126_L141_L1.8371.00
149_K238_E1.7910.99
502_H506_E1.7880.99
623_D642_L1.7850.99
441_L515_L1.7760.99
407_Q411_R1.7740.99
567_S570_E1.7580.99
135_K143_E1.7570.99
659_V669_V1.7300.99
442_N448_I1.7290.99
295_R611_K1.7120.99
614_M663_E1.7120.99
556_L600_V1.7090.99
501_A535_I1.6910.99
115_K158_T1.6860.99
369_I387_I1.6770.99
401_L433_T1.6770.99
207_C232_L1.6740.99
602_C605_C1.6580.99
204_Y233_S1.6380.99
372_A384_V1.6330.99
596_F659_V1.6320.99
147_V152_I1.6310.99
202_R231_V1.6270.99
556_L597_F1.6180.99
403_E407_Q1.6180.99
372_A485_A1.6150.99
165_I235_A1.6110.99
369_I385_M1.6090.99
564_Y598_R1.5930.98
367_F387_I1.5870.98
643_A647_G1.5780.98
632_K638_E1.5730.98
465_V482_F1.5700.98
166_D239_D1.5670.98
641_N645_T1.5670.98
236_I239_D1.5640.98
404_E649_T1.5640.98
540_F544_L1.5510.98
405_N617_H1.5510.98
635_P638_E1.5450.98
495_T516_S1.5350.98
610_F664_T1.5300.98
206_V240_L1.5190.98
322_H325_T1.5190.98
616_I655_G1.5150.98
643_A648_F1.5090.98
478_V482_F1.5060.98
342_A371_V1.5010.97
118_L123_L1.4890.97
126_L140_L1.4810.97
564_Y570_E1.4800.97
656_I660_L1.4780.97
187_F248_F1.4740.97
341_M357_I1.4710.97
107_E110_K1.4680.97
474_T477_K1.4440.97
401_L617_H1.4380.96
319_E554_K1.4380.96
164_V236_I1.4300.96
109_L138_E1.4270.96
319_E445_N1.4180.96
601_G605_C1.4160.96
179_V247_Y1.4120.96
413_L416_P1.4120.96
376_T463_R1.4110.96
420_I513_L1.4080.96
451_A467_V1.4010.96
559_E611_K1.3950.96
476_A499_E1.3860.95
122_E125_K1.3830.95
208_Y235_A1.3800.95
187_F244_V1.3720.95
205_L219_V1.3580.95
402_L405_N1.3570.95
652_K673_T1.3540.95
127_Y130_S1.3520.95
127_Y138_E1.3380.94
404_E408_N1.3380.94
153_L234_F1.3360.94
109_L123_L1.3230.94
188_L245_D1.3190.94
109_L127_Y1.3080.93
649_T657_L1.3070.93
157_K164_V1.2980.93
382_D449_W1.2940.93
563_L597_F1.2940.93
558_K561_K1.2850.92
111_Y155_S1.2800.92
414_D440_Y1.2750.92
498_E534_G1.2640.92
421_L495_T1.2600.91
357_I369_I1.2600.91
151_E154_E1.2600.91
405_N619_L1.2580.91
566_P596_F1.2510.91
557_C601_G1.2450.91
359_F369_I1.2440.91
388_L457_I1.2220.90
216_I232_L1.2100.89
182_I187_F1.2080.89
413_L420_I1.2020.89
474_T499_E1.2010.89
135_K140_L1.2000.88
157_K162_I1.1930.88
123_L137_L1.1890.88
419_L545_L1.1880.88
195_L206_V1.1870.88
524_P640_R1.1860.88
382_D485_A1.1840.88
624_E627_K1.1810.87
419_L546_G1.1740.87
644_I650_T1.1740.87
309_G325_T1.1710.87
655_G658_K1.1640.86
367_F389_G1.1620.86
554_K668_Q1.1550.86
657_L661_K1.1520.86
451_A482_F1.1510.86
420_I546_G1.1500.85
157_K163_P1.1460.85
415_Y545_L1.1440.85
408_N621_I1.1410.85
405_N408_N1.1410.85
213_Q217_E1.1390.85
434_L491_M1.1360.85
296_A316_V1.1350.84
616_I672_V1.1340.84
106_I114_K1.1320.84
447_K463_R1.1310.84
378_D458_L1.1150.83
417_Y522_S1.1110.83
502_H536_D1.1100.83
295_R316_V1.1000.82
342_A357_I1.0990.82
541_A630_I1.0970.82
140_L144_R1.0950.81
368_E390_G1.0940.81
302_E313_R1.0920.81
149_K153_L1.0910.81
495_T501_A1.0890.81
191_L241_I1.0870.81
509_L539_N1.0840.81
531_L540_F1.0790.80
237_K241_I1.0730.80
650_T653_Q1.0710.79
668_Q671_A1.0680.79
491_M533_M1.0680.79
108_R159_V1.0670.79
345_N470_K1.0510.78
301_W310_L1.0480.77
162_I234_F1.0440.77
182_I194_P1.0410.77
166_D169_D1.0390.76
322_H444_P1.0380.76
658_K663_E1.0350.76
634_K638_E1.0330.76
195_L204_Y1.0330.76
275_L281_V1.0320.76
549_A651_L1.0300.76
126_L137_L1.0290.76
622_P626_L1.0280.75
279_A282_Q1.0280.75
527_I630_I1.0260.75
311_Q322_H1.0240.75
191_L237_K1.0200.75
438_L491_M1.0170.74
109_L159_V1.0170.74
568_E572_E1.0150.74
106_I110_K1.0120.74
111_Y159_V1.0110.74
193_V240_L1.0100.74
167_T206_V1.0020.73
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  
4phtA30.6431000.469Contact Map
4ksrA301000.54Contact Map
1p9rA10.55851000.556Contact Map
2ewvA10.47561000.701Contact Map
3jvvA30.47261000.709Contact Map
2oap120.66671000.75Contact Map
4bloA120.37041000.779Contact Map
2eyuA20.33041000.785Contact Map
4ihqA30.68741000.789Contact Map
2b8tA40.28441000.845Contact 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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