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OPENSEQ.org

NR1

ID: 1402710031 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 822 (803)
Sequences: 986 (712)
Seq/Len: 1.228
Nf(neff/√len): 25.1

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: 1.228).

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
712_C766_C3.3201.00
685_A688_A3.0111.00
685_A689_V2.9681.00
503_I729_G2.9111.00
686_I689_V2.7771.00
441_K444_R2.7191.00
24_V28_N2.6111.00
495_I727_G2.6051.00
17_E27_A2.5821.00
479_G483_S2.5341.00
489_I493_L2.4100.99
23_A26_Q2.4000.99
679_Y685_A2.2490.99
405_N413_I2.2420.99
440_I444_R2.1790.98
407_D413_I2.1550.98
674_M685_A2.0950.98
19_I28_N2.0480.97
18_Q27_A2.0280.97
682_A686_I2.0210.97
506_S740_V2.0000.97
681_S689_V1.9930.97
674_M689_V1.9870.97
679_Y688_A1.9720.97
383_Q389_V1.9600.96
682_A689_V1.9460.96
256_S259_I1.9220.96
403_T407_D1.9200.96
674_M688_A1.9090.96
361_G367_P1.9020.96
480_E485_Q1.8970.96
435_C509_F1.8930.95
413_I416_G1.8830.95
27_A30_F1.8790.95
17_E21_R1.8720.95
19_I27_A1.8680.95
311_G314_G1.8540.95
679_Y689_V1.8490.95
407_D416_G1.8420.95
560_S563_G1.8400.94
441_K752_F1.8330.94
478_M503_I1.8260.94
381_I389_V1.8220.94
682_A685_A1.8110.94
24_V27_A1.8000.94
782_A786_M1.8000.94
20_F28_N1.7950.93
257_A260_S1.7740.93
248_Q330_S1.7700.93
171_K177_P1.7650.93
382_H389_V1.7630.93
359_W369_G1.7570.93
405_N416_G1.7530.92
679_Y686_I1.7430.92
681_S685_A1.7400.92
17_E20_F1.7390.92
23_A27_A1.7380.92
389_V392_T1.7360.92
261_D269_A1.7220.92
381_I392_T1.7170.91
17_E28_N1.7110.91
17_E30_F1.7060.91
26_Q30_F1.6970.91
687_Q691_D1.6920.91
17_E26_Q1.6850.90
403_T413_I1.6750.90
681_S686_I1.6490.89
752_F755_E1.6430.89
481_L729_G1.6420.89
22_E27_A1.6400.89
379_V391_P1.6350.88
357_I360_P1.6300.88
116_L303_L1.6190.88
20_F27_A1.6030.87
443_A450_Y1.6000.87
20_F26_Q1.5970.87
411_K414_C1.5940.87
381_I390_R1.5900.87
231_E235_S1.5860.86
151_G154_A1.5720.86
284_R287_V1.5680.85
681_S688_A1.5670.85
674_M686_I1.5670.85
405_N414_C1.5650.85
440_I454_L1.5590.85
330_S341_Q1.5570.85
584_N608_A1.5520.85
407_D414_C1.5470.84
22_E28_N1.5390.84
361_G369_G1.5380.84
404_I407_D1.5310.84
380_T387_V1.5240.83
18_Q26_Q1.5210.83
22_E26_Q1.5010.82
682_A688_A1.4930.81
457_D460_F1.4930.81
23_A28_N1.4920.81
20_F24_V1.4860.81
381_I391_P1.4840.81
694_L697_F1.4770.80
357_I367_P1.4750.80
243_G249_L1.4750.80
464_E471_A1.4670.80
674_M677_H1.4630.80
171_K174_Q1.4600.79
453_H480_E1.4570.79
741_S744_I1.4500.79
403_T414_C1.4470.79
405_N408_P1.4400.78
24_V30_F1.4340.78
151_G155_Q1.4340.78
19_I24_V1.4330.78
243_G247_L1.4320.78
245_I248_Q1.4290.77
680_E684_E1.4220.77
17_E22_E1.4210.77
404_I409_I1.4200.77
173_L178_G1.4170.77
408_P413_I1.4150.76
533_P615_Y1.4150.76
52_M56_V1.4130.76
382_H391_P1.4120.76
405_N415_N1.4060.76
378_I386_F1.4050.76
754_E758_K1.4010.75
256_S260_S1.4000.75
683_A689_V1.3810.74
173_L177_P1.3810.74
411_K416_G1.3800.74
614_S780_N1.3760.74
383_Q392_T1.3720.73
434_F753_M1.3710.73
674_M681_S1.3690.73
403_T416_G1.3640.73
407_D419_E1.3640.73
382_H392_T1.3570.72
731_R734_S1.3510.72
382_H388_Y1.3490.71
19_I26_Q1.3490.71
359_W367_P1.3480.71
413_I417_P1.3460.71
700_D703_V1.3430.71
89_A96_V1.3420.71
23_A29_F1.3420.71
413_I418_D1.3420.71
677_H688_A1.3390.71
383_Q391_P1.3350.70
17_E23_A1.3300.70
245_I251_N1.3290.70
413_I419_E1.3280.70
17_E24_V1.3270.70
680_E689_V1.3240.69
307_K310_D1.3200.69
383_Q390_R1.3160.69
277_E281_D1.3160.69
245_I249_L1.3160.69
199_L210_Y1.3090.68
606_G610_I1.3090.68
404_I416_G1.3080.68
403_T409_I1.3080.68
405_N411_K1.3070.68
680_E685_A1.3050.68
58_E62_S1.3030.68
359_W392_T1.3030.68
358_I361_G1.3030.68
18_Q28_N1.2990.67
293_W296_G1.2980.67
379_V383_Q1.2960.67
243_G248_Q1.2910.67
455_V486_A1.2900.66
117_R151_G1.2830.66
276_M279_I1.2830.66
414_C418_D1.2820.66
19_I30_F1.2780.65
255_E259_I1.2770.65
255_E260_S1.2730.65
18_Q23_A1.2700.65
18_Q24_V1.2690.65
285_G291_N1.2640.64
477_M489_I1.2520.63
583_L589_E1.2470.63
598_R609_M1.2470.63
404_I414_C1.2390.62
405_N409_I1.2380.62
674_M682_A1.2380.62
385_P388_Y1.2350.61
409_I414_C1.2350.61
343_G582_L1.2350.61
508_P513_G1.2340.61
708_A714_L1.2340.61
656_S728_I1.2330.61
243_G246_G1.2310.61
265_V308_Y1.2300.61
407_D417_P1.2300.61
18_Q30_F1.2290.61
685_A697_F1.2280.61
416_G421_I1.2200.60
183_T212_S1.2200.60
11_L20_F1.2180.60
677_H689_V1.2160.60
19_I23_A1.2110.59
614_S776_L1.2080.59
439_L452_V1.2070.59
199_L611_I1.1990.58
404_I413_I1.1990.58
387_V436_V1.1980.58
367_P370_Y1.1980.58
359_W381_I1.1920.57
403_T415_N1.1890.57
405_N417_P1.1870.57
610_I614_S1.1870.57
285_G288_G1.1800.56
18_Q25_N1.1800.56
171_K175_F1.1790.56
26_Q29_F1.1780.56
378_I385_P1.1780.56
360_P369_G1.1770.56
360_P370_Y1.1750.56
409_I413_I1.1700.55
404_I408_P1.1700.55
69_L434_F1.1680.55
668_S675_E1.1670.55
677_H681_S1.1660.55
7_I40_A1.1580.54
378_I381_I1.1580.54
705_E757_D1.1570.54
218_M223_Y1.1570.54
213_A225_W1.1560.54
18_Q22_E1.1540.54
407_D415_N1.1510.53
649_Y661_F1.1510.53
408_P419_E1.1440.53
434_F654_Q1.1440.53
310_D315_R1.1420.53
617_A620_A1.1420.53
601_G608_A1.1420.53
699_W703_V1.1410.52
401_E405_N1.1410.52
460_F464_E1.1400.52
577_F584_N1.1400.52
403_T408_P1.1350.52
551_V795_G1.1350.52
514_L660_Y1.1340.52
684_E687_Q1.1330.52
680_E686_I1.1320.52
359_W382_H1.1310.51
266_V273_L1.1300.51
65_V132_M1.1300.51
379_V389_V1.1290.51
690_R713_D1.1290.51
409_I416_G1.1270.51
580_R584_N1.1260.51
439_L492_P1.1260.51
727_G745_L1.1260.51
493_L729_G1.1260.51
380_T383_Q1.1250.51
378_I392_T1.1220.51
71_S102_R1.1210.51
20_F23_A1.1180.50
563_G573_S1.1180.50
439_L490_V1.1180.50
624_V628_P1.1170.50
405_N412_V1.1170.50
649_Y670_M1.1170.50
170_D173_L1.1150.50
681_S684_E1.1140.50
359_W390_R1.1140.50
416_G419_E1.1110.50
437_D760_W1.1110.50
283_P288_G1.1100.49
336_N340_V1.1080.49
6_N39_N1.1070.49
346_D349_Y1.1070.49
677_H686_I1.1060.49
699_W704_L1.1050.49
407_D421_I1.1040.49
697_F712_C1.1040.49
416_G422_P1.1030.49
345_F350_I1.1030.49
690_R711_K1.1030.49
636_N644_S1.1030.49
581_V586_G1.1020.49
481_L503_I1.1010.49
248_Q252_G1.1010.49
232_I236_A1.0980.48
563_G608_A1.0960.48
413_I421_I1.0960.48
48_N698_I1.0950.48
527_L782_A1.0950.48
360_P794_A1.0940.48
232_I235_S1.0930.48
406_G417_P1.0920.48
226_L338_K1.0900.47
679_Y682_A1.0900.47
417_P422_P1.0890.47
606_G609_M1.0880.47
47_P81_T1.0870.47
242_D245_I1.0860.47
696_A727_G1.0860.47
564_R567_D1.0850.47
415_N419_E1.0850.47
381_I388_Y1.0850.47
731_R803_I1.0830.47
379_V392_T1.0820.47
101_T122_Y1.0800.46
225_W655_S1.0780.46
578_S581_V1.0750.46
59_D65_V1.0750.46
35_K54_L1.0740.46
540_L544_L1.0730.46
359_W370_Y1.0730.46
408_P416_G1.0700.46
718_G745_L1.0690.45
627_R796_I1.0690.45
573_S782_A1.0690.45
228_G531_M1.0690.45
415_N418_D1.0690.45
383_Q492_P1.0660.45
635_I649_Y1.0650.45
59_D68_I1.0630.45
65_V94_I1.0630.45
652_V699_W1.0600.45
747_S760_W1.0580.44
392_T395_D1.0570.44
653_K680_E1.0560.44
419_E422_P1.0560.44
404_I417_P1.0560.44
403_T418_D1.0550.44
243_G250_I1.0550.44
409_I421_I1.0550.44
231_E236_A1.0540.44
379_V382_H1.0530.44
231_E234_G1.0520.44
21_R27_A1.0500.44
418_D422_P1.0490.43
117_R229_E1.0480.43
199_L209_V1.0460.43
171_K178_G1.0440.43
727_G776_L1.0440.43
154_A159_E1.0430.43
243_G251_N1.0410.43
752_F759_T1.0410.43
213_A219_T1.0400.43
55_S68_I1.0390.43
403_T411_K1.0390.43
484_G731_R1.0370.42
745_L776_L1.0360.42
648_I677_H1.0360.42
674_M679_Y1.0350.42
403_T417_P1.0340.42
616_T620_A1.0340.42
380_T385_P1.0330.42
172_V176_E1.0330.42
65_V509_F1.0310.42
411_K415_N1.0300.42
7_I24_V1.0290.42
655_S700_D1.0280.41
225_W243_G1.0280.41
775_T778_F1.0270.41
244_I248_Q1.0270.41
411_K421_I1.0270.41
550_A620_A1.0270.41
616_T623_L1.0260.41
673_H677_H1.0260.41
382_H395_D1.0260.41
758_K762_R1.0220.41
68_I773_P1.0220.41
685_A706_F1.0220.41
507_K742_L1.0210.41
213_A735_P1.0210.41
414_C422_P1.0210.41
387_V439_L1.0210.41
407_D410_K1.0200.41
511_Y664_Q1.0170.40
101_T117_R1.0170.40
448_F542_V1.0160.40
725_G734_S1.0160.40
281_D284_R1.0140.40
409_I417_P1.0140.40
413_I420_T1.0100.40
210_Y582_L1.0100.40
670_M673_H1.0070.39
382_H385_P1.0070.39
155_Q438_L1.0060.39
7_I10_V1.0060.39
318_F540_L1.0050.39
359_W389_V1.0040.39
405_N418_D1.0030.39
117_R122_Y1.0030.39
368_Q390_R1.0020.39
584_N587_L1.0010.39
363_E366_R1.0010.39
624_V638_P1.0000.39
22_E25_N1.0000.39
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  
4pe5A20.93431000.353Contact Map
4pe5B20.86371000.423Contact Map
3kg2A40.87831000.433Contact Map
2rc8A20.32731000.79Contact Map
3qekA20.42941000.791Contact Map
4jwxA10.32851000.807Contact Map
3qelB20.41851000.809Contact Map
1yaeA60.31271000.81Contact Map
4gpaA10.41241000.812Contact Map
3o21A40.40751000.812Contact 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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