May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org

aRNR_iter

ID: 1470692576 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 735 (713)
Sequences: 1105 (452.8)
Seq/Len: 1.550
Nf(neff/√len): 17.0

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: 1.550).

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
468_D557_Y4.0431.00
479_H573_Y4.0241.00
146_E476_R3.8031.00
523_G576_L2.9791.00
139_D152_T2.7801.00
537_L547_A2.7461.00
564_Q568_Q2.6161.00
391_A394_N2.5501.00
591_D607_Y2.5141.00
559_R563_N2.4621.00
235_S287_R2.3561.00
577_A635_T2.3511.00
337_Y376_K2.3491.00
314_S352_I2.3090.99
561_R564_Q2.2870.99
558_M575_V2.2770.99
448_I598_L2.2650.99
491_K510_N2.2600.99
5_V60_I2.2240.99
523_G637_G2.2020.99
613_V627_V2.1910.99
61_Q65_E2.1340.99
450_C535_A2.0810.99
694_E699_G2.0340.98
460_I553_K2.0240.98
551_G631_Y2.0220.98
548_Q631_Y1.9880.98
726_A730_D1.9530.98
285_V330_R1.9480.98
64_V80_Y1.9440.98
475_A573_Y1.9370.98
586_K590_I1.9210.97
21_A40_I1.9210.97
515_S518_N1.9040.97
149_D153_Q1.8910.97
576_L637_G1.8860.97
450_C462_R1.8840.97
145_E149_D1.8690.97
574_S637_G1.8690.97
486_K514_A1.8590.97
569_Y573_Y1.8390.96
549_E553_K1.8380.96
620_S623_H1.8360.96
475_A568_Q1.8350.96
58_E62_D1.8350.96
317_Y351_Q1.8260.96
233_R237_I1.8230.96
445_R591_D1.8170.96
598_L601_I1.7960.96
61_Q91_R1.7930.96
181_K231_Y1.7770.95
65_E81_I1.7770.95
626_E662_M1.7660.95
550_L554_I1.7480.95
545_G549_E1.7410.95
242_N283_K1.7390.95
464_F553_K1.7390.95
87_R90_A1.7360.95
479_H569_Y1.7320.95
157_H586_K1.7220.94
483_E514_A1.7160.94
694_E701_K1.7030.94
445_R607_Y1.6890.94
721_N724_K1.6810.93
23_A87_R1.6800.93
180_L200_A1.6780.93
475_A569_Y1.6740.93
320_D325_G1.6560.93
139_D161_K1.6540.93
195_K234_N1.6510.93
58_E61_Q1.6500.92
61_Q81_I1.6360.92
466_K470_M1.6350.92
61_Q87_R1.6220.92
23_A61_Q1.6190.92
471_L558_M1.6100.91
144_S480_E1.6090.91
449_E466_K1.5870.90
468_D561_R1.5850.90
556_T560_D1.5850.90
447_G450_C1.5770.90
475_A565_F1.5710.90
467_L471_L1.5620.90
67_E70_K1.5530.89
57_V61_Q1.5520.89
472_E561_R1.5510.89
40_I44_T1.5310.88
28_M76_V1.5260.88
471_L561_R1.5220.88
170_T216_H1.5200.88
712_Y727_E1.5170.88
533_L551_G1.5090.87
584_S724_K1.5050.87
23_A91_R1.5050.87
326_R369_D1.5050.87
200_A231_Y1.5000.87
169_L215_M1.4990.87
357_R362_L1.4970.87
204_G224_F1.4930.86
23_A57_V1.4920.86
77_A81_I1.4910.86
592_R597_T1.4880.86
460_I550_L1.4880.86
536_L550_L1.4730.85
42_Q71_S1.4670.85
65_E84_R1.4630.85
5_V595_F1.4460.84
69_M74_K1.4440.84
372_Q657_M1.4430.84
17_E40_I1.4420.84
236_F277_V1.4380.84
87_R91_R1.4330.83
643_V659_V1.4310.83
708_R711_G1.4270.83
330_R334_K1.4240.83
711_G724_K1.4210.83
222_P431_I1.4190.82
474_T524_I1.4180.82
5_V13_V1.4180.82
711_G727_E1.4110.82
57_V65_E1.4100.82
69_M81_I1.4070.82
244_E276_I1.3990.81
202_I298_N1.3960.81
23_A84_R1.3930.81
280_A284_T1.3890.81
330_R373_L1.3860.80
711_G731_R1.3800.80
289_H338_Q1.3800.80
537_L550_L1.3790.80
12_V54_Q1.3780.80
712_Y731_R1.3680.79
285_V331_E1.3670.79
84_R91_R1.3620.79
56_T59_A1.3620.79
720_W728_L1.3600.79
475_A479_H1.3530.78
712_Y724_K1.3530.78
233_R324_E1.3430.77
682_E702_H1.3400.77
557_Y561_R1.3360.77
83_Y91_R1.3320.77
154_N590_I1.3310.76
537_L595_F1.3310.76
28_M33_K1.3270.76
147_V476_R1.3250.76
61_Q84_R1.3240.76
65_E91_R1.3240.76
372_Q654_E1.3230.76
727_E731_R1.3230.76
706_L713_L1.3150.75
336_T351_Q1.3090.75
539_K544_S1.3090.75
449_E595_F1.3080.75
446_L470_M1.3050.74
57_V84_R1.3030.74
65_E87_R1.2990.74
482_M486_K1.2990.74
23_A83_Y1.2990.74
483_E486_K1.2930.74
236_F240_V1.2920.73
73_R76_V1.2900.73
28_M73_R1.2860.73
724_K727_E1.2850.73
387_L413_T1.2840.73
356_K389_L1.2830.73
286_S290_Q1.2770.72
33_K76_V1.2740.72
28_M31_T1.2730.72
331_E334_K1.2710.72
726_A729_N1.2690.72
724_K731_R1.2670.71
156_L474_T1.2610.71
154_N445_R1.2590.71
25_R28_M1.2560.70
606_Y730_D1.2470.70
552_L631_Y1.2450.69
532_C554_I1.2420.69
36_D40_I1.2410.69
245_E282_N1.2390.69
30_H79_K1.2340.68
440_T583_L1.2320.68
69_M76_V1.2260.68
276_I280_A1.2260.68
243_L246_L1.2230.67
382_F677_R1.2230.67
334_K373_L1.2220.67
239_E284_T1.2220.67
65_E83_Y1.2210.67
23_A80_Y1.2200.67
57_V81_I1.2130.67
171_C416_C1.2100.66
548_Q630_P1.2090.66
78_Q82_A1.2080.66
357_R361_Y1.2030.66
462_R466_K1.2000.65
708_R712_Y1.1990.65
246_L279_H1.1970.65
695_C698_C1.1950.65
176_L204_G1.1930.65
559_R636_R1.1930.65
443_I532_C1.1920.65
150_A473_V1.1900.64
294_A298_N1.1890.64
534_V604_R1.1870.64
725_L728_L1.1860.64
533_L554_I1.1820.64
711_G721_N1.1780.63
239_E280_A1.1760.63
101_E133_T1.1760.63
23_A65_E1.1750.63
42_Q67_E1.1740.63
471_L557_Y1.1610.62
224_F315_I1.1580.61
709_I724_K1.1550.61
99_F102_I1.1540.61
239_E279_H1.1520.61
61_Q83_Y1.1520.61
8_R91_R1.1470.60
6_L54_Q1.1470.60
715_G718_D1.1430.60
295_F315_I1.1410.60
177_D181_K1.1360.59
224_F295_F1.1320.59
464_F550_L1.1320.59
716_T719_R1.1300.58
5_V55_M1.1250.58
613_V619_C1.1220.58
5_V57_V1.1220.58
553_K560_D1.1220.58
155_Y470_M1.1210.58
26_K78_Q1.1210.58
713_L724_K1.1180.57
209_E302_I1.1160.57
33_K75_D1.1110.56
57_V91_R1.1090.56
498_S509_P1.1080.56
447_G532_C1.1050.56
487_T512_T1.1050.56
236_F280_A1.1050.56
449_E470_M1.1020.56
23_A27_A1.1010.55
17_E44_T1.1010.55
7_K83_Y1.0990.55
355_K388_N1.0990.55
450_C465_A1.0990.55
464_F467_L1.0990.55
557_Y560_D1.0970.55
717_T720_W1.0970.55
55_M63_L1.0920.55
181_K230_P1.0910.54
275_R278_Q1.0900.54
58_E65_E1.0860.54
604_R616_Y1.0860.54
568_Q573_Y1.0850.54
496_L529_L1.0830.54
176_L227_Y1.0810.53
176_L229_A1.0790.53
708_R724_K1.0790.53
720_W724_K1.0790.53
243_L283_K1.0760.53
80_Y84_R1.0700.52
232_V288_V1.0690.52
80_Y83_Y1.0680.52
534_V547_A1.0670.52
258_E265_Q1.0670.52
84_R87_R1.0650.52
202_I205_C1.0640.52
240_V276_I1.0640.52
170_T576_L1.0640.52
397_E408_Q1.0620.51
707_Q720_W1.0620.51
57_V62_D1.0610.51
286_S289_H1.0600.51
623_H626_E1.0600.51
319_T354_K1.0580.51
228_L328_I1.0570.51
357_R664_D1.0560.51
78_Q81_I1.0550.51
530_A616_Y1.0520.50
65_E76_V1.0510.50
354_K389_L1.0490.50
65_E78_Q1.0490.50
605_D729_N1.0480.50
238_E286_S1.0480.50
709_I721_N1.0470.50
55_M64_V1.0460.50
679_R686_E1.0450.50
389_L393_F1.0450.50
710_T713_L1.0430.49
113_E558_M1.0430.49
39_L76_V1.0430.49
153_Q545_G1.0420.49
707_Q721_N1.0420.49
714_V717_T1.0410.49
436_I485_Q1.0400.49
708_R731_R1.0360.49
196_R287_R1.0360.49
616_Y730_D1.0340.48
132_E136_P1.0340.48
265_Q270_L1.0330.48
171_C417_R1.0280.48
539_K546_E1.0270.48
180_L231_Y1.0270.48
57_V83_Y1.0250.48
258_E262_Y1.0240.47
548_Q627_V1.0230.47
663_M671_G1.0230.47
486_K518_N1.0220.47
421_F572_N1.0210.47
714_V718_D1.0210.47
8_R61_Q1.0210.47
556_T634_L1.0190.47
61_Q76_V1.0190.47
450_C466_K1.0150.47
128_K132_E1.0150.47
83_Y87_R1.0120.46
144_S147_V1.0120.46
176_L230_P1.0110.46
177_D230_P1.0110.46
39_L71_S1.0090.46
551_G554_I1.0050.45
449_E594_K1.0050.45
533_L550_L1.0050.45
27_A77_A1.0040.45
151_V586_K1.0040.45
65_E69_M1.0040.45
329_I351_Q1.0030.45
527_I584_S1.0020.45
139_D148_L1.0010.45
15_F76_V1.0000.45
239_E242_N1.0000.45
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  
1h7bA10.71161000.289Contact Map
4u3eA20.79051000.41Contact Map
1r9dA20.790599.70.928Contact Map
2y8nA20.806899.50.937Contact Map
3hncA20.771499.40.94Contact Map
3k8tA10.666799.40.941Contact Map
5a0uA8099.30.943Contact Map
2f3oA20.760599.30.944Contact Map
1h16A10.81999.10.949Contact Map
2xapA30.76698.90.952Contact 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.

Page generated in 0.7507 seconds.