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OPENSEQ.org

TTLL10-coEv2

ID: 1485515131 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 50% gaps before running GREMLIN.
Length: 673 (481)
Sequences: 1505 (995.9)
Seq/Len: 3.129
Nf(neff/√len): 45.4

Jackhmmer Results: (2016_04)
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: 3.129).

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 > 50% 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
500_L510_L2.2711.00
300_F304_F2.1481.00
367_N503_D2.1111.00
392_I478_F2.0731.00
373_G405_L2.0691.00
532_V536_T1.9701.00
262_L265_L1.9611.00
221_L231_T1.9241.00
396_H441_E1.8870.99
190_Y193_K1.7900.99
466_L501_I1.7710.99
465_T469_R1.7310.99
309_I325_L1.7050.99
502_D508_W1.6910.98
262_L266_P1.6880.98
473_I499_F1.6330.98
401_L438_W1.5970.98
377_D400_R1.5720.97
399_A443_L1.5660.97
232_L285_F1.5560.97
211_Q215_Q1.5460.97
224_T227_G1.5450.97
579_S584_R1.5450.97
437_V525_L1.5190.96
525_L529_I1.5090.96
394_F532_V1.5030.96
381_Y528_V1.4640.95
300_F303_L1.4630.95
214_Y225_K1.4500.95
502_D506_K1.4410.95
572_P584_R1.4180.94
472_Q476_H1.3990.94
591_R594_K1.3940.93
451_F456_G1.3830.93
312_C324_F1.3750.93
477_C497_C1.3680.92
517_A529_I1.3610.92
379_R511_E1.3550.92
378_V399_A1.3270.91
398_Y420_Q1.3230.91
496_G511_E1.3170.91
371_V401_L1.3070.90
476_H479_L1.3070.90
577_G584_R1.3030.90
299_A303_L1.3020.90
265_L268_T1.2900.89
517_A525_L1.2870.89
298_E304_F1.2820.89
420_Q437_V1.2650.88
599_P609_A1.2610.88
383_L539_L1.2610.88
223_T514_S1.2560.88
266_P269_S1.2540.87
383_L536_T1.2540.87
281_M288_T1.2530.87
533_V537_L1.2460.87
402_T418_T1.2340.86
413_L422_M1.2310.86
474_M497_C1.2270.86
603_A608_G1.2130.85
588_L594_K1.2090.85
600_M605_D1.2070.85
608_G611_R1.2070.85
607_P611_R1.2060.85
603_A613_A1.1970.84
312_C361_V1.1970.84
384_I478_F1.1950.84
308_Q363_R1.1900.83
551_Q554_L1.1890.83
615_P620_Q1.1890.83
620_Q623_R1.1860.83
575_H583_R1.1770.82
609_A613_A1.1760.82
595_S598_P1.1750.82
601_P610_R1.1730.82
215_Q493_D1.1710.82
485_L495_I1.1690.82
613_A616_P1.1670.82
604_P607_P1.1660.82
613_A618_V1.1660.82
439_S528_V1.1660.82
565_L568_G1.1640.82
618_V621_R1.1630.81
572_P575_H1.1600.81
584_R587_P1.1600.81
581_S587_P1.1600.81
581_S584_R1.1570.81
587_P593_A1.1560.81
605_D610_R1.1550.81
158_F161_I1.1530.81
601_P608_G1.1500.80
420_Q436_T1.1490.80
215_Q225_K1.1490.80
326_L332_V1.1460.80
601_P606_Q1.1460.80
170_I192_L1.1440.80
494_L536_T1.1440.80
577_G581_S1.1430.80
600_M604_P1.1430.80
146_G152_S1.1410.80
201_D213_L1.1370.79
610_R616_P1.1370.79
590_T593_A1.1290.79
606_Q615_P1.1260.78
513_N516_P1.1250.78
281_M285_F1.1250.78
363_R366_Q1.1240.78
613_A617_L1.1230.78
604_P610_R1.1220.78
406_Y442_H1.1210.78
608_G612_P1.1210.78
118_N127_D1.1210.78
365_I500_L1.1200.78
587_P592_Q1.1200.78
469_R506_K1.1200.78
610_R613_A1.1190.78
596_S612_P1.1190.78
396_H440_M1.1180.78
606_Q612_P1.1180.78
128_T135_A1.1180.78
601_P605_D1.1150.78
603_A609_A1.1130.77
318_N321_K1.1120.77
602_H612_P1.1090.77
374_R405_L1.1090.77
576_L579_S1.1070.77
288_T292_D1.1070.77
127_D131_A1.1070.77
392_I475_A1.1060.77
149_S152_S1.1060.77
581_S585_W1.1000.76
579_S583_R1.0980.76
383_L492_F1.0950.76
606_Q620_Q1.0940.76
126_D129_N1.0930.76
444_N467_K1.0920.75
592_Q597_G1.0910.75
264_D269_S1.0890.75
382_L497_C1.0870.75
617_L621_R1.0870.75
268_T272_Y1.0870.75
262_L272_Y1.0870.75
127_D132_G1.0850.75
608_G614_P1.0850.75
577_G583_R1.0840.75
320_G417_L1.0810.74
618_V622_P1.0810.74
599_P608_G1.0780.74
365_I510_L1.0780.74
605_D608_G1.0760.74
610_R615_P1.0760.74
596_S605_D1.0750.74
613_A620_Q1.0750.74
286_P292_D1.0740.74
281_M289_Y1.0700.73
416_H419_N1.0690.73
594_K601_P1.0690.73
420_Q517_A1.0690.73
404_S412_D1.0680.73
609_A617_L1.0680.73
369_L480_A1.0680.73
608_G613_A1.0670.73
586_P595_S1.0650.73
129_N135_A1.0650.73
619_P623_R1.0640.73
589_P595_S1.0630.73
584_R589_P1.0630.73
126_D133_P1.0610.72
602_H605_D1.0600.72
597_G601_P1.0580.72
166_G169_I1.0570.72
599_P607_P1.0570.72
615_P621_R1.0560.72
575_H578_G1.0560.72
169_I173_Y1.0540.72
615_P618_V1.0540.72
552_K558_S1.0500.71
615_P622_P1.0480.71
130_A134_S1.0480.71
595_S613_A1.0480.71
131_A134_S1.0480.71
298_E302_T1.0460.71
596_S609_A1.0450.71
379_R498_D1.0440.71
611_R616_P1.0440.71
598_P607_P1.0430.71
146_G149_S1.0430.71
592_Q595_S1.0420.70
596_S604_P1.0420.70
201_D204_G1.0410.70
602_H607_P1.0410.70
586_P591_R1.0400.70
437_V529_I1.0380.70
118_N126_D1.0370.70
265_L286_P1.0370.70
265_L272_Y1.0370.70
586_P594_K1.0370.70
400_R496_G1.0360.70
598_P610_R1.0350.70
616_P619_P1.0350.70
597_G606_Q1.0350.70
616_P622_P1.0340.70
319_Q493_D1.0340.70
397_G440_M1.0330.70
577_G582_L1.0330.70
130_A136_A1.0330.70
605_D612_P1.0320.69
498_D511_E1.0310.69
602_H606_Q1.0310.69
604_P614_P1.0310.69
125_S134_S1.0290.69
128_T133_P1.0290.69
124_D127_D1.0270.69
581_S588_L1.0270.69
117_L126_D1.0260.69
608_G620_Q1.0260.69
598_P602_H1.0250.69
606_Q609_A1.0250.69
123_A133_P1.0220.68
403_L436_T1.0220.68
127_D143_L1.0220.68
429_Y435_H1.0210.68
219_N495_I1.0200.68
318_N421_F1.0190.68
299_A304_F1.0180.68
554_L557_L1.0180.68
614_P619_P1.0170.68
604_P608_G1.0160.68
266_P270_P1.0150.68
592_Q596_S1.0130.67
597_G609_A1.0130.67
261_A264_D1.0120.67
619_P622_P1.0120.67
605_D611_R1.0110.67
589_P592_Q1.0110.67
601_P611_R1.0110.67
120_H127_D1.0090.67
321_K535_E1.0090.67
605_D609_A1.0090.67
501_I507_V1.0080.67
315_T358_A1.0060.67
595_S608_G1.0060.67
611_R614_P1.0050.66
582_L585_W1.0050.66
138_L141_L1.0050.66
604_P609_A1.0040.66
263_E266_P1.0030.66
614_P621_R1.0010.66
605_D621_R1.0000.66
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  
4ylrA101000.443Contact Map
4i4tF10.49481000.515Contact Map
4iwxA10.426499.40.9Contact Map
3vpbA40.41699.30.902Contact Map
3se7A60.430999.20.906Contact Map
1i7nA20.42299.20.908Contact Map
4fu0A20.435499.10.909Contact Map
3r5xA40.430999.10.91Contact Map
2q7dA20.47499.10.91Contact Map
3i12A40.457799.10.91Contact 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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