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OPENSEQ.org

Nicole Wheatley -force run

ID: 1424315958 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 812 (795)
Sequences: 518 (429.8)
Seq/Len: 0.652
Nf(neff/√len): 15.2

Jackhmmer Results: (2015_01_07)
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: 0.652).

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
483_R572_D4.8821.00
299_R543_D4.8761.00
470_A536_R3.6011.00
467_E536_R3.3661.00
466_V532_E3.3111.00
665_L740_I2.8810.99
483_R569_H2.7400.99
488_T549_G2.6760.99
469_A524_C2.5620.98
669_M738_T2.4470.98
662_E753_D2.3990.97
351_A516_N2.3700.97
534_R539_D2.3630.97
465_K526_D2.3040.96
493_E552_N2.2820.96
747_V770_V2.1880.95
39_M47_Q2.0930.93
276_Y626_A2.0760.92
177_P231_G2.0730.92
304_L486_V2.0540.92
627_G645_A1.9950.90
58_P63_F1.9700.90
569_H572_D1.9690.90
326_E649_S1.9510.89
680_Y684_V1.9440.89
719_L722_L1.9180.88
485_V546_F1.9040.87
470_A474_E1.8720.86
635_L741_H1.8710.86
135_D138_Q1.8500.85
706_Y711_G1.8460.85
83_D270_S1.7950.83
76_V278_D1.7740.82
67_L268_F1.7710.82
696_T707_Q1.7510.81
67_L74_P1.7480.80
499_Y718_P1.7400.80
516_N529_V1.7350.80
303_Q482_G1.7200.79
352_C649_S1.7020.78
58_P62_T1.6940.77
737_S769_T1.6790.77
556_D591_R1.6770.76
127_T711_G1.6640.76
136_E214_R1.6470.75
227_I231_G1.6470.75
485_V544_T1.6420.74
305_V328_H1.6370.74
173_L238_A1.6350.74
122_V700_V1.6340.74
461_T464_E1.6340.74
495_A621_G1.6090.72
176_S179_E1.5990.71
481_F540_I1.5890.71
33_L681_F1.5820.70
30_A678_Q1.5730.70
483_R543_D1.5500.68
150_F235_A1.5370.67
314_V587_A1.4990.64
469_A523_I1.4950.64
181_I234_A1.4890.64
673_Q677_A1.4600.61
141_W684_V1.4590.61
328_H476_M1.4550.61
60_P264_L1.4520.61
498_P699_P1.4440.60
486_V580_L1.4430.60
90_P94_L1.4410.60
304_L488_T1.4380.60
277_R767_S1.4380.60
545_V569_H1.4330.59
632_P741_H1.4270.59
310_T503_L1.4230.58
60_P265_A1.4230.58
486_V549_G1.4140.58
630_I672_T1.4040.57
608_R615_E1.3990.56
20_S29_T1.3960.56
27_F41_F1.3760.54
28_V139_A1.3750.54
518_R562_D1.3670.54
503_L721_S1.3600.53
481_F541_P1.3570.53
201_L208_T1.3460.52
180_T238_A1.3310.51
19_G22_W1.3310.51
576_L580_L1.3270.50
666_T754_H1.3180.50
34_S673_Q1.3130.49
30_A34_S1.3120.49
181_I188_Y1.3100.49
484_L576_L1.3100.49
524_C678_Q1.3090.49
332_G513_G1.3080.49
668_P674_W1.3060.49
29_T678_Q1.3050.49
612_D615_E1.3040.49
314_V590_E1.3040.49
24_V57_Y1.3040.49
514_G550_E1.2970.48
272_W734_L1.2960.48
75_A267_A1.2950.48
749_D753_D1.2910.47
592_A602_A1.2910.47
622_L674_W1.2910.47
269_L695_V1.2820.47
197_F276_Y1.2820.47
620_W643_G1.2770.46
312_S622_L1.2760.46
504_D610_A1.2750.46
477_G773_P1.2750.46
520_L524_C1.2740.46
469_A520_L1.2720.46
362_V504_D1.2720.46
475_L663_A1.2700.46
312_S620_W1.2680.46
158_A689_Y1.2680.46
421_P631_G1.2680.46
219_G226_P1.2660.45
305_V487_F1.2660.45
185_V197_F1.2620.45
662_E754_H1.2610.45
622_L668_P1.2520.44
630_I668_P1.2510.44
483_R568_S1.2500.44
545_V566_P1.2490.44
310_T622_L1.2470.44
557_E607_E1.2460.44
524_C632_P1.2440.44
393_K503_L1.2380.43
757_L761_L1.2370.43
613_W668_P1.2350.43
469_A632_P1.2340.43
565_V573_L1.2300.42
560_L573_L1.2290.42
354_P509_A1.2280.42
622_L721_S1.2280.42
89_D92_T1.2260.42
65_A547_V1.2250.42
629_V636_T1.2230.42
59_S577_R1.2220.42
758_T762_D1.2140.41
143_M146_R1.2110.41
33_L48_A1.2090.41
414_L549_G1.2090.41
280_V627_G1.2030.40
472_A631_G1.2000.40
596_G686_N1.1950.40
308_I513_G1.1950.40
481_F538_F1.1950.40
355_I513_G1.1950.40
503_L622_L1.1950.40
408_S596_G1.1930.40
312_S674_W1.1910.39
310_T643_G1.1850.39
11_I49_A1.1830.39
628_F672_T1.1800.38
645_A740_I1.1790.38
127_T706_Y1.1770.38
267_A501_S1.1770.38
135_D141_W1.1750.38
652_H658_G1.1750.38
68_E289_E1.1740.38
698_N711_G1.1730.38
150_F227_I1.1710.38
628_F670_V1.1710.38
624_G730_Y1.1700.38
312_S668_P1.1690.38
32_P668_P1.1680.38
167_D208_T1.1680.38
275_S732_Q1.1660.37
613_W622_L1.1650.37
272_W275_S1.1640.37
403_V613_W1.1630.37
421_P477_G1.1630.37
185_V193_W1.1580.37
308_I648_H1.1560.37
95_E98_D1.1560.37
518_R564_D1.1530.36
503_L743_P1.1490.36
472_A480_E1.1430.36
337_P468_Y1.1430.36
338_M516_N1.1420.36
697_Q707_Q1.1410.35
503_L620_W1.1390.35
19_G29_T1.1390.35
153_A194_V1.1380.35
613_W620_W1.1370.35
355_I667_G1.1350.35
305_V638_G1.1350.35
643_G693_S1.1340.35
404_E503_L1.1340.35
501_S585_E1.1330.35
135_D139_A1.1320.35
29_T679_Y1.1320.35
622_L648_H1.1310.35
528_T599_G1.1310.35
148_D574_D1.1310.35
67_L354_P1.1300.35
500_D503_L1.1300.35
310_T620_W1.1280.35
305_V476_M1.1270.34
646_F676_N1.1270.34
404_E622_L1.1270.34
65_A738_T1.1270.34
131_S700_V1.1260.34
189_P193_W1.1250.34
130_L625_N1.1240.34
532_E638_G1.1230.34
408_S685_D1.1230.34
71_Q732_Q1.1220.34
7_I463_D1.1210.34
11_I180_T1.1190.34
304_L697_Q1.1170.34
338_M362_V1.1170.34
620_W668_P1.1130.33
330_Y667_G1.1120.33
597_A602_A1.1100.33
181_I415_A1.1100.33
21_V27_F1.1100.33
658_G746_R1.1070.33
744_V780_F1.1070.33
494_T678_Q1.1060.33
462_D528_T1.1050.33
540_I546_F1.1050.33
175_E415_A1.1040.33
108_D549_G1.1030.33
503_L674_W1.1030.33
649_S696_T1.1020.33
41_F680_Y1.1010.33
34_S678_Q1.1000.32
582_V585_E1.1000.32
662_E750_V1.1000.32
61_E727_D1.1000.32
492_S554_T1.1000.32
707_Q714_M1.0990.32
29_T34_S1.0980.32
26_S501_S1.0980.32
686_N719_L1.0980.32
620_W674_W1.0960.32
41_F185_V1.0960.32
32_P622_L1.0950.32
310_T642_D1.0950.32
352_C520_L1.0940.32
393_K613_W1.0920.32
306_F335_G1.0920.32
48_A235_A1.0900.32
648_H668_P1.0900.32
32_P721_S1.0880.32
412_L484_L1.0880.32
11_I197_F1.0870.32
338_M519_V1.0860.31
605_E615_E1.0850.31
404_E668_P1.0830.31
683_T729_P1.0820.31
24_V30_A1.0790.31
73_D549_G1.0780.31
37_E673_Q1.0770.31
461_T773_P1.0770.31
312_S503_L1.0770.31
332_G335_G1.0760.31
462_D466_V1.0750.31
22_W554_T1.0730.31
520_L616_T1.0730.31
310_T502_S1.0730.31
200_Q240_L1.0720.30
35_G215_A1.0720.30
69_G657_D1.0710.30
11_I41_F1.0700.30
31_N278_D1.0700.30
613_W674_W1.0700.30
310_T674_W1.0690.30
139_A517_A1.0690.30
57_Y266_E1.0680.30
414_L542_E1.0680.30
748_T788_W1.0650.30
444_Q447_H1.0650.30
518_R590_E1.0650.30
128_K673_Q1.0650.30
58_P66_A1.0640.30
509_A734_L1.0640.30
484_L645_A1.0630.30
503_L668_P1.0630.30
33_L685_D1.0630.30
494_T625_N1.0600.30
678_Q721_S1.0590.30
128_K706_Y1.0590.30
180_T245_V1.0590.30
645_A761_L1.0580.29
355_I666_T1.0570.29
312_S643_G1.0570.29
404_E709_N1.0560.29
16_T321_A1.0550.29
697_Q714_M1.0550.29
472_A476_M1.0550.29
94_L97_M1.0530.29
625_N676_N1.0530.29
259_E264_L1.0520.29
24_V202_A1.0510.29
700_V706_Y1.0510.29
395_N398_T1.0500.29
13_K621_G1.0490.29
364_E712_D1.0490.29
513_G518_R1.0460.29
302_A305_V1.0460.29
205_P209_G1.0430.28
69_G466_V1.0430.28
674_W721_S1.0410.28
151_Y186_A1.0410.28
470_A609_R1.0390.28
467_E540_I1.0390.28
665_L750_V1.0380.28
397_A782_Y1.0370.28
239_L693_S1.0370.28
489_G623_A1.0360.28
90_P93_L1.0350.28
83_D764_D1.0350.28
194_V358_P1.0350.28
552_N689_Y1.0350.28
77_L268_F1.0340.28
305_V475_L1.0320.28
297_T634_E1.0310.28
11_I718_P1.0300.28
605_E608_R1.0300.28
696_T726_D1.0300.28
76_V275_S1.0300.28
202_A614_A1.0300.28
24_V711_G1.0300.28
7_I484_L1.0290.28
269_L734_L1.0270.27
723_M726_D1.0270.27
86_Y89_D1.0260.27
403_V414_L1.0260.27
161_D356_V1.0250.27
47_Q52_V1.0250.27
312_S404_E1.0250.27
48_A681_F1.0240.27
615_E636_T1.0220.27
404_E743_P1.0220.27
336_I520_L1.0220.27
57_Y269_L1.0200.27
340_Y351_A1.0200.27
404_E674_W1.0200.27
622_L640_D1.0190.27
782_Y788_W1.0180.27
494_T504_D1.0170.27
141_W229_L1.0150.27
341_R361_R1.0150.27
154_F398_T1.0140.27
402_F711_G1.0140.27
35_G580_L1.0140.27
47_Q549_G1.0130.26
269_L667_G1.0130.26
503_L613_W1.0130.26
596_G685_D1.0130.26
201_L407_G1.0130.26
312_S613_W1.0120.26
499_Y691_S1.0120.26
22_W513_G1.0120.26
33_L37_E1.0120.26
48_A54_G1.0110.26
279_E610_A1.0100.26
88_G99_A1.0100.26
711_G762_D1.0100.26
686_N695_V1.0100.26
626_A644_R1.0100.26
261_A547_V1.0080.26
32_P674_W1.0080.26
42_G46_T1.0080.26
741_H773_P1.0070.26
153_A664_I1.0060.26
287_E470_A1.0050.26
209_G670_V1.0040.26
345_A520_L1.0030.26
216_V631_G1.0030.26
400_F403_V1.0030.26
318_H500_D1.0030.26
237_L281_V1.0030.26
169_I335_G1.0020.26
382_R423_R1.0010.26
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: (31Jan15)
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  
2xwsA10.146666.70.987Contact Map
3lyhA20.139243.60.989Contact Map
1ekjA80.208140.60.989Contact Map
2xwpA10.270932.60.989Contact Map
3vqjA10.188432.10.989Contact Map
1ym3A10.187224.10.99Contact Map
3qy1A20.2143210.99Contact Map
3teoA160.200719.60.99Contact Map
4agiA40.082517.70.991Contact Map
4wwrA40.065317.70.991Contact 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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