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OPENSEQ.org

NR2

ID: 1402711271 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 818 (800)
Sequences: 1008 (714.8)
Seq/Len: 1.260
Nf(neff/√len): 25.3

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: 1.260).

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
675_A679_L4.2561.00
675_A678_S4.0231.00
676_L679_L3.9201.00
671_S679_L3.4361.00
491_V723_A3.3031.00
672_V675_A3.1461.00
672_V679_L3.0901.00
672_V676_L3.0821.00
483_I721_G2.9111.00
467_G471_T2.8771.00
12_V15_T2.8281.00
671_S675_A2.7981.00
435_K438_K2.7801.00
477_A481_L2.7471.00
704_C759_C2.7191.00
671_S678_S2.6891.00
707_V710_G2.5211.00
673_Q679_L2.4921.00
672_V678_S2.4240.99
671_S676_L2.3840.99
434_K438_K2.3260.99
251_S333_V2.2570.99
468_E473_R2.1330.98
435_K746_E2.0750.98
706_L710_G2.0690.98
17_E21_K2.0680.98
466_I491_V2.0410.98
777_A781_Y2.0300.97
494_S734_V2.0200.97
735_D738_I1.9540.97
429_C497_F1.9370.96
23_V26_K1.8950.96
670_R679_L1.8810.95
380_E386_I1.8690.95
746_E749_E1.8200.94
265_D273_A1.7850.94
19_A23_V1.7840.94
214_A226_W1.7480.93
378_T385_V1.7360.92
677_L681_S1.7340.92
469_V723_A1.7240.92
673_Q678_S1.7070.91
669_Q679_L1.6970.91
573_N597_A1.6880.91
670_R674_D1.6870.91
23_V28_D1.6670.90
573_N578_V1.6650.90
437_A444_Y1.6570.90
521_P604_Y1.6450.89
684_L687_F1.6230.88
385_V430_I1.6170.88
670_R675_A1.6010.88
115_Q149_Y1.6000.87
434_K448_L1.6000.87
447_Y468_E1.5940.87
23_V29_F1.5460.85
428_F747_M1.5370.84
333_V345_R1.5350.84
725_Q728_S1.5310.84
748_E752_A1.5270.84
465_M477_A1.5260.84
270_I277_M1.5230.84
690_D693_V1.5180.83
673_Q676_L1.5130.83
226_W246_G1.4980.82
318_D321_F1.4960.82
13_G19_A1.4950.82
674_D678_S1.4840.82
595_F599_I1.4740.81
675_A687_F1.4670.80
16_E19_A1.4610.80
264_R271_T1.4600.80
680_K705_K1.4570.80
51_I55_I1.4540.80
587_K598_V1.4480.79
706_L709_I1.4480.79
347_G571_V1.4420.79
469_V491_V1.4410.79
219_L224_F1.4320.78
114_F309_L1.4040.76
603_S775_N1.3950.76
444_Y448_L1.3940.76
572_F577_P1.3910.75
674_D679_L1.3900.75
671_S674_D1.3880.75
86_S93_I1.3860.75
289_S292_N1.3840.75
27_D30_H1.3780.74
433_L446_L1.3670.74
603_S771_L1.3650.73
451_N454_H1.3630.73
449_V474_A1.3510.72
569_G573_N1.3400.71
269_I314_F1.3400.71
7_I39_E1.3380.71
377_V465_M1.3290.71
680_K703_G1.3260.70
25_E28_D1.3250.70
380_E388_E1.3240.70
397_C447_Y1.3240.70
28_D31_H1.3200.70
739_L771_L1.3180.70
290_S293_N1.3180.70
675_A680_K1.3130.69
384_F723_A1.3130.69
747_M754_W1.3050.69
522_F658_L1.3050.69
23_V27_D1.3050.69
567_L570_L1.3010.68
496_P501_G1.2990.68
569_G578_V1.2930.67
24_H28_D1.2910.67
550_P610_A1.2890.67
570_L575_S1.2870.67
528_V532_V1.2870.67
385_V429_C1.2830.67
648_S722_I1.2820.67
57_D61_D1.2810.66
385_V433_L1.2790.66
319_L322_S1.2720.66
35_T39_E1.2690.65
674_D681_S1.2680.65
689_Y694_L1.2630.65
357_W360_F1.2610.65
20_I23_V1.2590.64
64_V130_I1.2550.64
595_F598_V1.2540.64
721_G739_L1.2480.63
613_I617_Y1.2460.63
590_V597_A1.2420.63
569_G610_A1.2390.63
214_A220_T1.2360.62
350_K353_S1.2350.62
781_Y784_A1.2330.62
695_N751_E1.2290.62
433_L478_V1.2280.62
13_G18_V1.2200.61
555_G559_T1.2190.61
606_A609_A1.2190.61
7_I10_I1.2180.61
267_I271_T1.2160.60
214_A729_G1.2140.60
149_Y153_E1.2120.60
487_R493_F1.2110.60
768_S780_F1.2080.60
433_L480_S1.2080.60
589_M790_S1.2060.60
358_P365_N1.2040.59
226_W647_G1.2020.59
98_G120_I1.2010.59
5_M8_A1.2010.59
280_E308_Y1.2000.59
59_M91_T1.1970.59
613_I627_K1.1950.58
689_Y693_V1.1940.58
670_R676_L1.1940.58
378_T386_I1.1930.58
431_D754_W1.1930.58
605_T612_M1.1900.58
708_T721_G1.1890.58
264_R273_A1.1880.58
378_T389_D1.1880.58
13_G17_E1.1860.58
669_Q678_S1.1850.58
58_L64_V1.1810.57
19_A28_D1.1810.57
599_I603_S1.1780.57
515_P777_A1.1750.57
371_D374_L1.1750.57
388_E426_K1.1720.56
115_Q120_I1.1710.56
481_L723_A1.1690.56
183_D213_V1.1670.56
669_Q675_A1.1650.56
641_F653_I1.1650.56
386_I389_D1.1630.55
536_I788_A1.1630.55
709_I772_D1.1610.55
115_Q230_S1.1610.55
28_D36_P1.1600.55
359_V363_Y1.1590.55
12_V19_A1.1550.55
11_L20_I1.1540.55
28_D34_V1.1530.54
566_L573_N1.1510.54
319_L323_E1.1510.54
46_S51_I1.1470.54
630_Q638_A1.1450.54
676_L680_K1.1430.53
687_F704_C1.1430.53
550_P559_T1.1420.53
378_T388_E1.1380.53
540_V790_S1.1370.53
546_E576_L1.1370.53
290_S294_I1.1360.53
605_T609_A1.1350.53
68_V428_F1.1330.52
719_G728_S1.1320.52
501_G606_A1.1320.52
549_S558_F1.1320.52
746_E753_L1.1320.52
598_V602_A1.1310.52
136_W642_G1.1300.52
455_G464_G1.1300.52
64_V91_T1.1290.52
502_I652_N1.1280.52
502_I649_T1.1270.52
741_L754_W1.1250.52
377_V449_V1.1250.52
6_D10_I1.1240.52
54_R67_V1.1200.51
725_Q798_H1.1180.51
200_L552_G1.1180.51
98_G115_Q1.1180.51
25_E31_H1.1180.51
665_V668_N1.1180.51
21_K25_E1.1170.51
33_P36_P1.1160.51
197_V246_G1.1150.51
227_I342_K1.1130.50
219_L226_W1.1130.50
566_L739_L1.1130.50
550_P558_F1.1120.50
200_L600_F1.1120.50
738_I741_L1.1120.50
570_L573_N1.1100.50
200_L210_I1.1060.50
288_K792_I1.1050.50
21_K27_D1.1040.50
483_I496_P1.1030.49
559_T562_K1.1030.49
379_L479_G1.1020.49
265_D316_G1.1020.49
521_P719_G1.1010.49
721_G771_L1.1000.49
464_G474_A1.1000.49
674_D677_L1.0970.49
26_K38_V1.0970.49
466_I645_P1.0960.49
480_S693_V1.0960.49
313_T318_D1.0960.49
6_D39_E1.0960.49
346_V376_I1.0940.49
288_K293_N1.0940.49
71_D99_G1.0900.48
562_K777_A1.0860.48
378_T387_V1.0860.48
229_P519_L1.0860.48
440_V737_A1.0830.48
444_Y451_N1.0820.47
7_I24_H1.0780.47
686_A737_A1.0770.47
179_L209_Y1.0760.47
299_V302_A1.0740.47
465_M468_E1.0740.47
34_V41_V1.0700.46
288_K291_C1.0700.46
472_K725_Q1.0700.46
675_A696_Y1.0700.46
28_D32_L1.0700.46
628_K653_I1.0700.46
27_D31_H1.0690.46
85_I97_H1.0690.46
277_M304_M1.0680.46
200_L211_F1.0670.46
725_Q794_F1.0660.46
31_H34_V1.0660.46
463_N646_N1.0650.46
644_V689_Y1.0630.46
563_A611_F1.0610.45
650_E661_H1.0600.45
521_P690_D1.0600.45
94_L249_S1.0590.45
258_D333_V1.0590.45
546_E591_S1.0590.45
442_F530_M1.0590.45
609_A750_L1.0570.45
35_T40_L1.0560.45
624_L641_F1.0560.45
21_K28_D1.0540.45
806_E810_M1.0520.44
719_G724_I1.0520.44
191_C749_E1.0520.44
495_V736_L1.0520.44
425_C448_L1.0520.44
570_L580_N1.0520.44
379_L480_S1.0510.44
770_Q773_I1.0510.44
514_S725_Q1.0500.44
566_L614_Q1.0500.44
461_V609_A1.0490.44
247_L305_L1.0480.44
429_C522_F1.0480.44
463_N560_I1.0460.44
305_L781_Y1.0460.44
645_P670_R1.0460.44
448_L474_A1.0460.44
74_D100_S1.0440.44
8_A11_L1.0430.44
17_E20_I1.0430.44
46_S76_E1.0420.44
428_F646_N1.0420.44
27_D34_V1.0400.43
605_T771_L1.0390.43
288_K292_N1.0380.43
771_L775_N1.0380.43
647_G690_D1.0380.43
519_L710_G1.0380.43
64_V67_V1.0370.43
553_Y574_N1.0360.43
499_E656_N1.0360.43
500_T692_A1.0350.43
585_T641_F1.0340.43
66_G71_D1.0340.43
783_L786_A1.0300.42
20_I28_D1.0290.42
521_P598_V1.0290.42
246_G252_Y1.0270.42
141_I795_I1.0260.42
230_S332_L1.0260.42
436_I442_F1.0250.42
486_E655_N1.0240.42
55_I58_L1.0240.42
59_M94_L1.0240.42
428_F742_F1.0240.42
94_L681_S1.0230.42
144_T203_T1.0220.42
47_D688_I1.0220.42
624_L688_I1.0200.41
534_L597_A1.0200.41
686_A721_G1.0190.41
74_D98_G1.0180.41
67_V86_S1.0150.41
691_A715_F1.0130.41
55_I67_V1.0120.41
14_T21_K1.0120.41
246_G336_L1.0110.41
496_P518_F1.0090.40
727_D781_Y1.0080.40
205_E309_L1.0080.40
380_E389_D1.0080.40
429_C444_Y1.0060.40
114_F127_M1.0060.40
197_V225_T1.0040.40
249_S334_I1.0040.40
14_T19_A1.0040.40
575_S597_A1.0040.40
433_L442_F1.0020.40
319_L522_F1.0020.40
687_F720_Y1.0020.40
182_I186_I1.0020.40
573_N602_A1.0020.40
671_S681_S1.0020.40
616_R791_L1.0010.40
401_T448_L1.0000.39
261_A266_G1.0000.39
132_E528_V1.0000.39
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: (07Jun14)
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  
4pe5B20.89731000.376Contact Map
4pe5A20.90951000.397Contact Map
3kg2A40.88511000.432Contact Map
4jwxA10.34231000.785Contact Map
3qelB20.4341000.794Contact Map
2rc8A20.33131000.795Contact Map
1yaeA60.30811000.808Contact Map
3qekA20.42541000.813Contact Map
4gpaA10.41811000.822Contact Map
3o21A40.41321000.823Contact 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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