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OPENSEQ.org

Mad1 -force run

ID: 1415965344 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 718 (710)
Sequences: 681 (571.6)
Seq/Len: 0.959
Nf(neff/√len): 21.5

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: 0.959).

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
64_L67_V2.9941.00
265_E270_R2.8581.00
208_I211_L2.5400.99
201_C204_A2.3830.99
57_Q60_S2.3300.98
505_V508_L2.2530.98
180_V183_L2.2290.98
103_N106_L2.1520.97
512_R515_L2.1220.97
194_L197_Q2.0460.96
380_L383_E2.0110.95
283_L286_L2.0020.95
407_E412_R1.9870.95
224_Q229_E1.9350.94
625_K628_E1.9010.93
152_L155_A1.8850.93
124_M127_Q1.8770.93
266_S269_L1.8750.92
415_L418_Y1.8740.92
187_K190_L1.8620.92
401_V404_L1.8280.91
449_S452_M1.8260.91
373_L376_V1.8210.91
96_Y99_E1.7890.90
575_L578_M1.7840.90
564_L568_C1.7670.89
225_I228_L1.7620.89
498_A501_L1.7590.89
173_V176_Q1.7480.89
300_L303_L1.7390.88
473_L477_L1.7330.88
183_L187_K1.6860.86
442_V445_V1.6770.86
504_K509_E1.6660.85
379_Q384_R1.6570.85
693_H702_A1.6300.83
179_R184_E1.6090.82
352_N355_V1.6060.82
387_R390_H1.5340.78
561_H564_L1.5290.78
616_Q620_E1.5230.77
337_F342_Q1.4840.75
574_L579_E1.4590.73
63_H68_E1.4550.72
414_I418_Y1.4530.72
470_A473_L1.4380.71
10_V17_L1.4210.70
366_R369_L1.4160.69
634_Y654_L1.4120.69
643_I649_Y1.4090.69
609_E612_E1.3990.68
229_E233_S1.3850.67
314_L317_W1.3850.67
691_E696_R1.3810.67
519_K523_E1.3740.66
699_S712_F1.3610.65
622_F629_F1.3590.65
359_A362_L1.3550.65
712_F715_Q1.3500.64
699_S702_A1.3460.64
252_L255_L1.3460.64
702_A712_F1.3440.64
6_E9_M1.3430.64
245_M248_E1.3410.63
345_E348_L1.3360.63
693_H697_Q1.3280.62
700_I708_T1.3180.61
567_E572_R1.3180.61
511_E516_E1.3130.61
697_Q702_A1.2990.60
519_K522_L1.2940.59
665_F675_M1.2930.59
166_I169_L1.2890.59
230_Q234_L1.2810.58
633_C712_F1.2790.58
244_N247_S1.2720.57
643_I693_H1.2650.57
692_V697_Q1.2640.57
522_L526_L1.2620.56
18_N21_I1.2590.56
516_E523_E1.2590.56
197_Q200_K1.2580.56
692_V696_R1.2580.56
646_E649_Y1.2560.56
193_Q198_H1.2490.55
441_M445_V1.2470.55
39_G43_M1.2420.55
649_Y652_T1.2410.54
678_L699_S1.2370.54
110_I113_L1.2320.54
650_R662_C1.2310.54
284_E287_Q1.2310.54
9_M13_T1.2300.53
624_T628_E1.2300.53
652_T675_M1.2280.53
617_R620_E1.2280.53
408_R411_M1.2270.53
652_T662_C1.2260.53
477_L480_L1.2250.53
642_D657_E1.2230.53
240_A245_M1.2190.52
693_H713_S1.2150.52
649_Y695_R1.2090.52
344_R349_K1.2090.52
661_D715_Q1.2070.51
207_K212_Q1.2040.51
634_Y712_F1.2030.51
484_S487_A1.2030.51
28_G31_L1.2020.51
648_Q697_Q1.2000.51
394_A397_L1.1990.51
299_T304_E1.1980.51
630_R699_S1.1960.50
697_Q715_Q1.1930.50
608_V611_A1.1930.50
635_T643_I1.1920.50
27_G30_G1.1920.50
435_M439_E1.1880.50
648_Q676_Q1.1880.50
634_Y656_A1.1880.50
605_K612_E1.1850.49
123_K128_L1.1850.49
473_L476_E1.1840.49
633_C697_Q1.1830.49
224_Q228_L1.1810.49
287_Q611_A1.1810.49
338_V342_Q1.1790.49
31_L34_S1.1770.49
8_T12_S1.1750.48
635_T649_Y1.1740.48
649_Y685_T1.1720.48
641_I681_E1.1720.48
115_E118_A1.1710.48
661_D678_L1.1690.48
483_Q487_A1.1670.48
224_Q227_D1.1670.48
643_I702_A1.1670.48
39_G46_Q1.1660.48
694_L711_L1.1650.48
649_Y683_S1.1580.47
694_L699_S1.1580.47
431_L435_M1.1480.46
43_M47_Q1.1450.46
643_I676_Q1.1440.46
518_E525_Q1.1440.46
680_T683_S1.1420.45
277_G284_E1.1420.45
676_Q697_Q1.1370.45
649_Y697_Q1.1370.45
306_E311_L1.1330.45
64_L84_E1.1330.45
282_E287_Q1.1320.45
652_T695_R1.1310.44
49_M52_E1.1300.44
640_Q649_Y1.1300.44
400_R405_T1.1290.44
662_C675_M1.1280.44
14_L20_F1.1280.44
29_S33_I1.1270.44
253_P262_L1.1260.44
693_H696_R1.1240.44
199_K203_E1.1230.44
659_P679_E1.1230.44
215_Q219_A1.1160.43
651_L667_A1.1150.43
568_C571_L1.1150.43
666_K676_Q1.1150.43
654_L691_E1.1120.43
22_S25_V1.1120.43
658_H661_D1.1120.43
443_Q446_H1.1120.43
624_T627_Q1.1100.43
154_Q159_I1.1080.42
644_T649_Y1.1080.42
522_L525_Q1.1080.42
625_K643_I1.1060.42
303_L307_N1.1060.42
665_F700_I1.1060.42
652_T697_Q1.1050.42
630_R642_D1.1050.42
590_A594_S1.1050.42
36_S41_L1.1020.42
677_L686_V1.1010.42
436_R439_E1.1010.42
206_Q210_E1.1010.42
656_A712_F1.1010.42
692_V702_A1.1010.42
659_P689_L1.0990.42
434_R439_E1.0980.41
630_R634_Y1.0940.41
418_Y422_L1.0930.41
170_Q174_M1.0930.41
25_V28_G1.0930.41
26_E33_I1.0900.41
26_E31_L1.0890.41
634_Y642_D1.0880.41
626_I630_R1.0870.40
656_A679_E1.0860.40
631_K646_E1.0840.40
459_A462_E1.0840.40
642_D652_T1.0830.40
615_N618_L1.0820.40
681_E684_H1.0820.40
644_T689_L1.0810.40
642_D654_L1.0800.40
635_T674_K1.0790.40
96_Y119_G1.0790.40
645_T667_A1.0780.40
665_F673_S1.0780.40
632_A662_C1.0780.40
286_L289_K1.0780.40
651_L705_S1.0770.40
674_K692_V1.0750.39
236_E246_K1.0750.39
17_L20_F1.0740.39
186_E193_Q1.0740.39
6_E13_T1.0730.39
567_E571_L1.0730.39
347_A350_D1.0680.39
9_M14_L1.0680.39
648_Q666_K1.0680.39
289_K294_E1.0680.39
635_T697_Q1.0680.39
661_D682_F1.0670.39
145_L148_K1.0670.39
479_M483_Q1.0660.39
15_R23_Q1.0660.39
632_A688_E1.0650.39
310_L398_Q1.0640.38
176_Q180_V1.0630.38
656_A699_S1.0630.38
307_N310_L1.0630.38
253_P256_E1.0620.38
15_R19_N1.0620.38
21_I25_V1.0610.38
658_H699_S1.0590.38
648_Q695_R1.0560.38
251_R256_E1.0560.38
678_L683_S1.0540.38
412_R442_V1.0540.38
689_L706_S1.0530.38
338_V341_L1.0530.38
44_Q47_Q1.0530.38
643_I697_Q1.0530.38
19_N24_R1.0530.38
692_V713_S1.0510.37
60_S78_H1.0500.37
688_E695_R1.0490.37
689_L711_L1.0490.37
590_A593_A1.0480.37
630_R665_F1.0460.37
36_S40_S1.0460.37
15_R20_F1.0450.37
522_L567_E1.0440.37
661_D680_T1.0430.37
536_D539_R1.0420.37
661_D697_Q1.0410.36
634_Y711_L1.0390.36
294_E297_Q1.0390.36
56_E61_K1.0380.36
452_M455_Q1.0380.36
155_A159_I1.0380.36
676_Q702_A1.0370.36
630_R636_L1.0370.36
667_A675_M1.0370.36
636_L707_L1.0370.36
251_R254_R1.0370.36
630_R652_T1.0360.36
705_S708_T1.0360.36
620_E624_T1.0340.36
697_Q713_S1.0330.36
645_T651_L1.0330.36
159_I163_K1.0330.36
256_E260_K1.0330.36
699_S711_L1.0310.36
665_F710_E1.0290.35
228_L231_K1.0280.35
35_T38_P1.0270.35
12_S16_S1.0270.35
249_L262_L1.0260.35
644_T697_Q1.0260.35
151_S156_G1.0260.35
14_L17_L1.0260.35
98_R102_R1.0250.35
252_L435_M1.0250.35
641_I661_D1.0250.35
712_F716_T1.0250.35
370_Q378_G1.0240.35
321_D324_M1.0230.35
691_E698_D1.0220.35
11_L15_R1.0220.35
686_V689_L1.0220.35
599_K602_A1.0210.35
39_G45_Y1.0210.35
695_R698_D1.0200.35
16_S20_F1.0200.35
265_E268_H1.0200.35
649_Y667_A1.0190.35
679_E684_H1.0190.35
25_V32_D1.0180.35
649_Y713_S1.0180.35
10_V16_S1.0180.35
642_D716_T1.0170.34
685_T699_S1.0150.34
680_T693_H1.0150.34
89_A92_S1.0150.34
158_T161_A1.0150.34
82_R86_E1.0150.34
692_V717_V1.0150.34
647_N665_F1.0140.34
23_Q26_E1.0140.34
646_E675_M1.0140.34
663_L678_L1.0140.34
165_R455_Q1.0130.34
197_Q201_C1.0130.34
662_C673_S1.0130.34
366_R373_L1.0110.34
27_G34_S1.0110.34
643_I696_R1.0110.34
686_V707_L1.0110.34
36_S43_M1.0110.34
643_I647_N1.0110.34
16_S31_L1.0100.34
647_N677_L1.0090.34
702_A708_T1.0080.34
617_R625_K1.0080.34
165_R179_R1.0080.34
689_L695_R1.0080.34
642_D699_S1.0070.34
678_L685_T1.0050.33
10_V15_R1.0050.33
667_A673_S1.0040.33
441_M446_H1.0040.33
28_G33_I1.0040.33
64_L601_V1.0040.33
667_A686_V1.0020.33
103_N107_L1.0010.33
31_L35_T1.0010.33
148_K152_L1.0000.33
611_A619_K1.0000.33
24_R29_S1.0000.33
150_D154_Q1.0000.33
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: (06Sep14)
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  
4dzoA20.16851000.607Contact Map
1i84S20.175599.40.86Contact Map
1c1gA40.395599.20.876Contact Map
1go4E40.139398.90.886Contact Map
4linA120.3621970.93Contact Map
2v71A20.2228970.93Contact Map
4iloA20.303696.50.934Contact Map
3kbtA20.394296.40.935Contact Map
1u4qA20.42996.10.936Contact Map
3edvA20.4318960.937Contact 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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