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OPENSEQ.org

Nterm

ID: 1410105017 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 716 (715)
Sequences: 1039 (961.3)
Seq/Len: 1.453
Nf(neff/√len): 36.0

Jackhmmer Results: (2014_04_16)
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: 1.453).

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
49_G62_D4.9981.00
596_V612_V3.6291.00
140_L143_V2.4711.00
75_G100_D2.4661.00
101_I143_V2.3781.00
479_G483_M2.1510.99
82_G85_C2.1310.99
428_G453_I2.0600.98
98_L101_I2.0180.98
29_T32_L1.9850.98
522_L525_N1.9120.97
483_M487_E1.8950.97
568_G573_P1.8720.96
76_N99_K1.8420.96
247_G250_D1.8350.96
103_V145_I1.8240.96
28_T31_G1.7250.94
43_V67_Q1.7060.93
317_M325_L1.7000.93
531_G540_L1.6770.92
99_K141_D1.6640.92
233_L240_G1.6520.92
31_G53_G1.6410.91
227_V230_P1.5940.90
235_I238_F1.5700.89
85_C92_C1.5690.89
402_P425_A1.5490.88
28_T32_L1.5440.88
646_G651_G1.5310.87
522_L531_G1.5280.87
120_E124_P1.5090.86
218_R221_L1.5070.86
3_L6_K1.5060.86
309_K312_K1.4920.85
418_L434_A1.4710.84
32_L44_P1.4660.84
79_L85_C1.4580.83
91_V107_S1.4460.83
34_L38_A1.4240.81
425_A428_G1.4160.81
101_I135_L1.4130.81
26_V31_G1.4110.80
464_S468_G1.4040.80
400_I427_E1.4000.80
522_L527_A1.3950.79
313_V329_V1.3890.79
434_A445_R1.3890.79
342_Q345_L1.3880.79
525_N562_G1.3870.79
444_W476_L1.3860.79
468_G474_G1.3830.79
515_I524_P1.3810.78
623_N627_V1.3780.78
46_L65_Y1.3770.78
74_A77_L1.3700.78
308_L311_E1.3690.78
409_A416_V1.3670.77
3_L7_I1.3640.77
637_Q654_N1.3610.77
643_R648_P1.3600.77
79_L82_G1.3530.76
32_L50_K1.3510.76
131_Y432_L1.3500.76
227_V231_L1.3460.76
400_I458_E1.3430.76
618_S627_V1.3410.75
558_G562_G1.3400.75
259_K274_I1.3380.75
10_G14_V1.3300.75
629_L642_L1.3230.74
79_L84_E1.3200.74
5_K9_L1.3180.74
635_E640_L1.3150.73
254_S260_V1.3140.73
520_L523_G1.3100.73
314_K317_M1.3030.72
79_L93_I1.2870.71
226_D230_P1.2860.71
515_I523_G1.2810.71
63_V74_A1.2810.71
524_P527_A1.2780.70
522_L558_G1.2750.70
617_I620_P1.2730.70
636_K646_G1.2730.70
11_V14_V1.2690.70
326_E329_V1.2670.69
297_I301_S1.2580.69
635_E638_H1.2580.69
313_V319_G1.2570.69
473_R483_M1.2560.68
267_T271_A1.2540.68
272_L275_D1.2510.68
428_G460_P1.2480.68
427_E434_A1.2470.68
415_Q437_D1.2460.68
389_L393_T1.2450.68
333_G338_D1.2440.67
49_G63_V1.2420.67
474_G483_M1.2410.67
522_L533_L1.2410.67
464_S474_G1.2350.67
638_H646_G1.2310.66
529_V542_A1.2290.66
645_Q648_P1.2290.66
416_V434_A1.2240.66
434_A444_W1.2240.66
53_G56_R1.2210.65
684_L688_I1.2200.65
142_N149_D1.2180.65
530_K534_G1.2170.65
313_V317_M1.2140.65
120_E125_L1.2110.64
600_I610_L1.2100.64
646_G649_V1.2080.64
670_L673_T1.2070.64
138_V161_L1.2040.64
604_D614_V1.2010.63
582_R592_A1.1980.63
53_G70_V1.1970.63
601_K604_D1.1970.63
635_E648_P1.1960.63
430_T520_L1.1940.63
665_R691_D1.1940.63
229_L241_E1.1930.63
397_G400_I1.1920.63
226_D229_L1.1910.62
154_V159_S1.1900.62
318_G321_L1.1890.62
199_E202_Q1.1890.62
635_E639_E1.1850.62
235_I240_G1.1830.62
9_L13_I1.1820.62
454_N457_K1.1810.62
229_L240_G1.1810.62
577_A581_A1.1800.61
400_I425_A1.1790.61
7_I11_V1.1750.61
588_E592_A1.1750.61
288_Q292_N1.1740.61
607_A610_L1.1730.61
69_G73_K1.1730.61
559_T582_R1.1720.61
648_P651_G1.1720.61
222_P226_D1.1710.61
402_P427_E1.1700.60
645_Q650_S1.1680.60
320_A323_E1.1680.60
356_V363_W1.1680.60
232_N235_I1.1670.60
705_C714_C1.1670.60
361_L365_F1.1670.60
272_L283_A1.1660.60
677_T680_G1.1630.60
340_R344_R1.1610.60
218_R222_P1.1610.60
40_D44_P1.1600.59
533_L540_L1.1600.59
351_P354_V1.1600.59
32_L48_I1.1580.59
522_L535_V1.1580.59
588_E600_I1.1540.59
703_P706_W1.1540.59
53_G81_V1.1520.59
122_S125_L1.1510.59
666_W706_W1.1490.58
70_V73_K1.1480.58
607_A611_D1.1460.58
483_M486_P1.1450.58
520_L531_G1.1450.58
542_A564_V1.1440.58
417_N435_L1.1440.58
272_L290_S1.1430.58
559_T564_V1.1410.58
48_I276_S1.1400.57
684_L687_D1.1390.57
562_G579_I1.1390.57
576_L599_D1.1390.57
329_V332_S1.1370.57
570_V573_P1.1360.57
633_G646_G1.1360.57
309_K315_L1.1360.57
329_V341_A1.1350.57
515_I518_L1.1340.57
79_L86_L1.1330.57
6_K10_G1.1320.57
603_T614_V1.1310.57
633_G638_H1.1300.56
348_A351_P1.1300.56
216_F219_P1.1240.56
685_T688_I1.1230.56
423_V428_G1.1220.56
453_I460_P1.1220.56
13_I27_G1.1210.56
595_R599_D1.1200.55
55_W131_Y1.1190.55
621_D625_N1.1180.55
651_G654_N1.1180.55
618_S622_V1.1170.55
686_R689_A1.1160.55
315_L333_G1.1140.55
624_I642_L1.1130.55
514_M534_G1.1120.55
672_N678_P1.1120.55
518_L534_G1.1120.55
324_Q329_V1.1110.55
46_L67_Q1.1110.55
382_G558_G1.1100.54
514_M539_N1.1090.54
420_K432_L1.1090.54
513_W522_L1.1080.54
24_F29_T1.1040.54
643_R646_G1.1040.54
589_L592_A1.1030.54
515_I525_N1.1030.54
613_R630_N1.1020.54
553_L556_L1.1020.54
618_S621_D1.1010.54
539_N542_A1.1000.53
210_E214_D1.0990.53
421_L434_A1.0990.53
455_T459_F1.0970.53
428_G446_G1.0960.53
53_G71_A1.0960.53
586_W610_L1.0930.53
534_G537_D1.0920.53
271_A274_I1.0920.53
596_V614_V1.0910.52
409_A418_L1.0910.52
75_G99_K1.0890.52
635_E646_G1.0870.52
622_V629_L1.0840.52
559_T562_G1.0840.52
617_I624_I1.0830.52
420_K431_E1.0830.52
225_T230_P1.0820.52
93_I135_L1.0820.52
26_V32_L1.0810.51
274_I568_G1.0800.51
423_V430_T1.0800.51
216_F221_L1.0790.51
339_L342_Q1.0780.51
636_K643_R1.0780.51
281_V301_S1.0780.51
60_L63_V1.0780.51
492_G497_N1.0760.51
632_K643_R1.0760.51
674_R698_K1.0760.51
555_G561_K1.0760.51
28_T53_G1.0750.51
636_K650_S1.0750.51
185_V189_A1.0740.51
666_W704_H1.0730.51
267_T274_I1.0720.51
143_V262_S1.0720.51
85_C511_M1.0720.51
240_G247_G1.0700.50
514_M532_E1.0700.50
676_Q683_S1.0700.50
618_S623_N1.0670.50
39_A46_L1.0670.50
345_L354_V1.0670.50
621_D624_I1.0660.50
219_P227_V1.0660.50
121_D124_P1.0650.50
324_Q328_G1.0640.50
356_V359_K1.0640.50
156_D159_S1.0630.50
586_W591_V1.0630.50
425_A459_F1.0630.50
645_Q652_Q1.0620.50
503_G513_W1.0610.49
283_A286_T1.0610.49
402_P405_I1.0610.49
525_N556_L1.0600.49
679_V698_K1.0600.49
444_W474_G1.0590.49
121_D125_L1.0580.49
154_V157_F1.0540.49
430_T566_V1.0540.49
577_A580_T1.0500.48
523_G531_G1.0490.48
476_L483_M1.0490.48
518_L525_N1.0470.48
107_S149_D1.0460.48
481_W488_L1.0450.48
562_G578_D1.0450.48
258_L264_D1.0410.47
233_L237_E1.0410.47
639_E645_Q1.0410.47
642_L650_S1.0400.47
76_N100_D1.0400.47
225_T231_L1.0400.47
579_I596_V1.0390.47
414_Q435_L1.0380.47
67_Q409_A1.0380.47
194_V201_P1.0370.47
358_S376_L1.0370.47
325_L378_L1.0360.47
15_I140_L1.0360.47
69_G132_P1.0350.47
267_T286_T1.0350.47
271_A282_N1.0350.47
14_V18_L1.0350.47
639_E650_S1.0340.47
590_S600_I1.0330.47
187_E192_E1.0330.47
639_E644_I1.0330.47
586_W593_Q1.0330.47
517_G530_K1.0310.46
627_V642_L1.0310.46
669_T674_R1.0300.46
48_I54_G1.0300.46
382_G392_R1.0300.46
673_T706_W1.0290.46
404_T409_A1.0280.46
673_T704_H1.0280.46
218_R245_V1.0270.46
643_R653_L1.0270.46
479_G485_V1.0270.46
522_L562_G1.0270.46
644_I652_Q1.0260.46
548_G551_N1.0260.46
655_L690_L1.0250.46
278_Q283_A1.0240.46
260_V285_G1.0230.46
673_T677_T1.0230.46
267_T272_L1.0200.45
295_V301_S1.0200.45
380_L572_A1.0200.45
544_I550_D1.0190.45
272_L356_V1.0180.45
617_I627_V1.0170.45
254_S258_L1.0170.45
666_W673_T1.0150.45
591_V614_V1.0140.45
605_Q610_L1.0140.45
402_P428_G1.0140.45
533_L542_A1.0140.45
49_G98_L1.0130.45
649_V652_Q1.0120.44
635_E651_G1.0110.44
303_L563_L1.0110.44
297_I300_N1.0100.44
35_V560_A1.0100.44
522_L538_L1.0090.44
27_G32_L1.0090.44
6_K9_L1.0090.44
201_P204_D1.0090.44
601_K605_Q1.0080.44
610_L627_V1.0080.44
524_P533_L1.0080.44
29_T50_K1.0060.44
601_K613_R1.0060.44
612_V620_P1.0060.44
637_Q645_Q1.0050.44
691_D697_Q1.0050.44
163_W182_L1.0050.44
518_L556_L1.0050.44
669_T672_N1.0040.44
567_R571_E1.0040.44
626_L643_R1.0030.44
591_V601_K1.0030.44
87_W174_S1.0030.44
71_A105_I1.0020.43
300_N309_K1.0020.43
659_F664_E1.0020.43
614_V621_D1.0010.43
108_K111_P1.0010.43
223_E227_V1.0000.43
520_L527_A1.0000.43
524_P531_G1.0000.43
402_P458_E1.0000.43
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: (17Jul14)
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  
3lycA160.31760.50.963Contact Map
3jx8A60.32450.90.965Contact Map
4opwA20.321250.50.965Contact Map
3petA20.286347.20.966Contact Map
1m56D20.032111.20.975Contact Map
1qleD10.0321110.975Contact Map
3j2wE40.04619.20.976Contact Map
4bbjA10.08387.90.977Contact Map
3rwxA10.28776.60.977Contact Map
3lw5I10.04194.90.979Contact 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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