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Run for P5

ID: 1504735639 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 999 (985)
Sequences: 1039 (882.4)
Seq/Len: 1.055
Nf(neff/√len): 28.1

Jackhmmer Results: (2016_04)
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: 1.055).

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
162_L179_E4.1821.00
58_V85_V3.1051.00
72_P98_V2.9571.00
67_I95_A2.7571.00
100_V109_R2.7441.00
58_V89_G2.7381.00
402_R410_E2.7231.00
789_M792_L2.6831.00
70_G373_L2.6521.00
115_K167_F2.4480.99
438_H878_F2.4190.99
962_D967_T2.3650.99
955_N958_E2.3460.99
964_L973_V2.3120.99
202_D280_R2.2740.99
940_I969_L2.2710.98
214_L256_N2.2520.98
937_M973_V2.2130.98
27_N31_S2.1860.98
25_F52_A2.1840.98
27_N30_E2.1840.98
256_N285_S2.1840.98
256_N318_W2.1740.98
736_C742_E2.1630.98
70_G161_S2.1180.97
964_L967_T2.1140.97
208_S214_L2.1070.97
962_D973_V2.0930.97
739_L744_D2.0910.97
203_R228_S2.0620.97
67_I93_A2.0410.96
462_L875_L2.0410.96
834_L840_Q2.0370.96
560_Y564_V2.0290.96
348_V409_I1.9850.96
860_V864_P1.9700.95
560_Y563_L1.9470.95
964_L990_P1.9450.95
184_G316_S1.9420.95
367_G394_W1.9290.95
214_L318_W1.9190.95
736_C741_M1.9110.94
349_V365_W1.8880.94
345_S367_G1.8870.94
160_D183_A1.8870.94
84_I219_V1.8740.94
256_N309_M1.8680.93
214_L257_S1.8590.93
674_A700_F1.8560.93
361_A412_L1.8530.93
221_G256_N1.8440.93
364_L401_G1.8430.93
852_H855_G1.8430.93
736_C739_L1.8390.93
710_A735_Q1.8370.93
859_I862_Q1.8350.93
760_A764_L1.8340.93
245_Q249_E1.8320.93
285_S318_W1.8200.92
31_S34_R1.8030.92
46_L85_V1.8020.92
187_N343_R1.7920.91
104_Q112_I1.7830.91
774_L789_M1.7810.91
315_A366_I1.7810.91
260_V287_D1.7690.91
54_R82_E1.7660.91
284_L289_I1.7640.91
962_D983_L1.7620.91
689_I777_A1.7620.91
560_Y565_Q1.7610.91
89_G93_A1.7610.91
305_E323_D1.7530.90
734_V741_M1.7400.90
69_N161_S1.7360.90
320_N346_Y1.7220.89
207_V318_W1.7180.89
734_V739_L1.7130.89
840_Q844_F1.7050.89
206_A229_I1.6900.88
674_A681_G1.6850.88
217_Y256_N1.6750.87
309_M318_W1.6750.87
419_V428_L1.6640.87
181_T373_L1.6630.87
77_L122_L1.6620.87
861_A864_P1.6580.87
56_L92_A1.6570.87
165_I376_R1.6520.86
437_Q882_K1.6470.86
561_R564_V1.6440.86
75_V87_V1.6430.86
350_D354_R1.6370.86
941_W992_I1.6310.85
184_G371_V1.6310.85
674_A703_V1.6230.85
739_L742_E1.6190.85
750_Y780_L1.6130.85
202_D253_T1.6120.84
258_V285_S1.6120.84
762_D765_H1.6100.84
162_L373_L1.6060.84
188_T217_Y1.5990.84
696_L700_F1.5970.84
83_Q210_L1.5950.84
734_V742_E1.5780.83
991_T994_E1.5730.82
72_P165_I1.5730.82
214_L220_F1.5680.82
349_V394_W1.5650.82
564_V567_W1.5620.82
208_S257_S1.5620.82
736_C740_D1.5600.82
927_A953_T1.5590.82
357_P360_V1.5570.82
432_E446_V1.5550.81
967_T973_V1.5540.81
557_L560_Y1.5470.81
964_L983_L1.5440.81
943_Q972_L1.5320.80
214_L284_L1.5320.80
86_A90_I1.5310.80
188_T256_N1.5260.80
353_G365_W1.5230.80
52_A92_A1.5210.79
257_S318_W1.5200.79
964_L968_R1.5160.79
256_N261_L1.5140.79
428_L446_V1.5110.79
221_G318_W1.5100.79
191_E195_R1.5050.78
217_Y318_W1.4990.78
188_T318_W1.4960.78
204_V214_L1.4950.78
208_S261_L1.4950.78
193_N217_Y1.4940.78
67_I71_E1.4940.78
837_S844_F1.4920.78
450_G453_R1.4900.77
962_D965_L1.4880.77
208_S256_N1.4810.77
952_M992_I1.4740.76
71_E95_A1.4590.75
9_D343_R1.4570.75
19_C22_E1.4540.75
734_V744_D1.4520.75
697_T701_L1.4460.74
258_V309_M1.4430.74
25_F92_A1.4420.74
855_G858_V1.4390.74
688_E711_Y1.4370.74
962_D966_A1.4340.74
840_Q843_A1.4300.73
207_V256_N1.4280.73
982_S985_K1.4280.73
705_P710_A1.4280.73
363_E396_R1.4220.73
256_N284_L1.4170.72
319_S370_G1.4080.72
258_V318_W1.4040.71
348_V401_G1.4040.71
895_L898_L1.4020.71
764_L792_L1.4010.71
740_D743_Q1.3990.71
207_V285_S1.3960.71
222_L229_I1.3960.71
285_S309_M1.3930.70
214_L309_M1.3880.70
838_F844_F1.3870.70
967_T990_P1.3850.70
189_I214_L1.3820.70
962_D990_P1.3810.70
841_V844_F1.3780.69
206_A318_W1.3760.69
202_D227_G1.3690.69
192_I208_S1.3680.68
937_M969_L1.3670.68
214_L221_G1.3630.68
734_V740_D1.3630.68
927_A952_M1.3540.67
434_A879_L1.3540.67
214_L258_V1.3510.67
214_L312_A1.3490.67
98_V116_A1.3480.67
710_A754_Q1.3460.67
956_Y961_G1.3350.66
188_T214_L1.3330.66
257_S309_M1.3310.65
312_A318_W1.3260.65
938_A992_I1.3210.65
207_V257_S1.3200.64
781_L787_L1.3200.64
166_I317_I1.3190.64
188_T261_L1.3160.64
964_L979_V1.3160.64
54_R85_V1.3140.64
287_D411_F1.3130.64
837_S845_P1.3120.64
983_L990_P1.3090.63
281_L307_V1.3090.63
206_A256_N1.3070.63
365_W394_W1.3060.63
214_L319_S1.3040.63
216_V317_I1.3020.63
283_M309_M1.2960.62
262_L318_W1.2960.62
198_V227_G1.2940.62
178_V372_A1.2930.62
289_I294_P1.2910.62
216_V220_F1.2900.62
463_V898_L1.2900.62
202_D254_L1.2890.62
261_L318_W1.2880.62
257_S262_L1.2870.62
966_A983_L1.2870.62
188_T319_S1.2870.62
188_T208_S1.2850.61
74_A118_I1.2810.61
206_A297_L1.2810.61
35_T45_H1.2770.61
262_L284_L1.2770.61
431_I434_A1.2770.61
71_E119_R1.2750.60
56_L60_A1.2740.60
967_T983_L1.2740.60
445_V906_V1.2740.60
737_Q742_E1.2700.60
734_V737_Q1.2690.60
204_V318_W1.2690.60
256_N294_P1.2690.60
39_D81_Y1.2680.60
214_L217_Y1.2670.60
256_N289_I1.2650.60
259_P293_L1.2650.60
256_N259_P1.2650.60
49_G53_K1.2610.59
255_W318_W1.2610.59
256_N317_I1.2600.59
739_L743_Q1.2580.59
459_V893_L1.2580.59
207_V261_L1.2570.59
285_S316_S1.2530.58
623_D626_H1.2530.58
940_I973_V1.2520.58
626_H634_V1.2520.58
207_V217_Y1.2510.58
256_N262_L1.2510.58
736_C744_D1.2510.58
838_F845_P1.2510.58
208_S222_L1.2500.58
192_I217_Y1.2490.58
202_D240_A1.2480.58
461_Y912_P1.2450.58
389_W392_G1.2430.58
970_A986_I1.2420.57
208_S318_W1.2410.57
189_I309_M1.2400.57
563_L567_W1.2390.57
967_T979_V1.2390.57
962_D979_V1.2350.57
217_Y258_V1.2350.57
111_R167_F1.2320.57
309_M315_A1.2320.57
930_Q993_A1.2310.56
256_N319_S1.2290.56
216_V256_N1.2290.56
966_A973_V1.2280.56
758_I781_L1.2210.56
691_A713_C1.2200.55
207_V258_V1.2190.55
208_S309_M1.2160.55
206_A257_S1.2150.55
192_I256_N1.2140.55
294_P335_I1.2130.55
157_A161_S1.2130.55
191_E341_L1.2100.55
285_S312_A1.2100.55
951_G954_D1.2050.54
217_Y261_L1.2050.54
25_F55_A1.2050.54
97_Y215_S1.2030.54
685_R710_A1.2030.54
209_S256_N1.2000.54
824_L830_W1.2000.54
214_L285_S1.2000.54
227_G318_W1.1990.53
209_S318_W1.1980.53
353_G371_V1.1970.53
769_D772_V1.1970.53
17_P183_A1.1960.53
973_V983_L1.1960.53
215_S256_N1.1930.53
930_Q952_M1.1920.53
289_I308_A1.1900.53
222_L228_S1.1890.53
879_L888_V1.1840.52
932_P935_T1.1840.52
284_L318_W1.1830.52
77_L124_D1.1820.52
404_W408_T1.1820.52
206_A217_Y1.1810.52
189_I256_N1.1800.52
837_S843_A1.1790.52
149_A153_E1.1780.52
104_Q211_D1.1780.52
736_C743_Q1.1760.51
989_K994_E1.1740.51
221_G312_A1.1740.51
196_Y307_V1.1730.51
188_T221_G1.1730.51
973_V979_V1.1720.51
55_A92_A1.1690.51
852_H856_Q1.1690.51
262_L297_L1.1680.51
733_H736_C1.1680.51
962_D980_E1.1680.51
260_V288_W1.1650.50
979_V982_S1.1650.50
21_H157_A1.1640.50
257_S294_P1.1630.50
319_S366_I1.1620.50
957_F987_F1.1620.50
962_D982_S1.1610.50
293_L318_W1.1610.50
230_V252_I1.1580.50
192_I318_W1.1570.50
11_H343_R1.1560.49
61_F65_Q1.1560.49
564_V572_A1.1560.49
446_V460_G1.1540.49
790_L793_T1.1530.49
258_V336_P1.1520.49
257_S284_L1.1510.49
220_F256_N1.1490.49
837_S842_A1.1480.49
20_L91_M1.1480.49
52_A55_A1.1480.49
676_P681_G1.1460.48
285_S317_I1.1460.48
256_N297_L1.1460.48
188_T207_V1.1450.48
840_Q845_P1.1420.48
649_P653_L1.1410.48
234_E237_R1.1410.48
206_A214_L1.1400.48
308_A320_N1.1400.48
257_S285_S1.1390.48
217_Y257_S1.1390.48
23_A186_W1.1380.48
86_A122_L1.1360.48
259_P318_W1.1350.47
192_I214_L1.1340.47
220_F318_W1.1340.47
294_P318_W1.1330.47
188_T317_I1.1310.47
649_P652_L1.1280.47
188_T285_S1.1250.47
862_Q871_N1.1250.47
561_R565_Q1.1230.46
191_E207_V1.1210.46
973_V981_L1.1210.46
191_E258_V1.1210.46
700_F711_Y1.1190.46
239_D297_L1.1180.46
215_S260_V1.1180.46
312_A344_Q1.1180.46
189_I289_I1.1180.46
191_E318_W1.1170.46
216_V318_W1.1170.46
65_Q120_F1.1140.45
221_G257_S1.1140.45
412_L431_I1.1140.45
309_M312_A1.1120.45
238_R309_M1.1120.45
752_A779_S1.1120.45
191_E342_A1.1110.45
230_V246_L1.1100.45
97_Y216_V1.1100.45
216_V221_G1.1100.45
361_A400_L1.1100.45
967_T982_S1.1080.45
977_I983_L1.1070.45
162_L181_T1.1070.45
876_A880_K1.1040.45
315_A318_W1.1030.44
221_G254_L1.1020.44
964_L982_S1.1010.44
860_V863_A1.1000.44
198_V217_Y1.1000.44
692_R763_S1.0990.44
367_G371_V1.0980.44
208_S284_L1.0950.44
217_Y319_S1.0950.44
934_E952_M1.0940.44
191_E196_Y1.0930.44
838_F843_A1.0930.44
236_S242_K1.0930.44
378_D381_L1.0910.43
188_T258_V1.0900.43
984_G988_D1.0890.43
460_G892_F1.0890.43
192_I309_M1.0880.43
966_A990_P1.0870.43
166_I318_W1.0870.43
257_S261_L1.0850.43
712_T755_Y1.0840.43
649_P658_F1.0800.42
733_H742_E1.0790.42
191_E289_I1.0790.42
221_G227_G1.0790.42
319_S335_I1.0780.42
196_Y283_M1.0780.42
205_L232_I1.0770.42
623_D634_V1.0770.42
926_F949_R1.0770.42
461_Y914_P1.0750.42
348_V364_L1.0730.42
751_E754_Q1.0730.42
312_A337_Y1.0720.42
215_S220_F1.0720.42
564_V568_L1.0710.42
669_M788_I1.0690.41
255_W285_S1.0680.41
198_V307_V1.0670.41
964_L980_E1.0670.41
187_N202_D1.0660.41
371_V392_G1.0660.41
188_T257_S1.0650.41
222_L256_N1.0650.41
257_S319_S1.0640.41
557_L564_V1.0620.41
365_W371_V1.0580.40
208_S221_G1.0580.40
838_F841_V1.0560.40
828_A831_Q1.0550.40
52_A56_L1.0550.40
966_A989_K1.0550.40
206_A258_V1.0550.40
252_I319_S1.0550.40
221_G255_W1.0540.40
992_I995_L1.0540.40
204_V208_S1.0520.40
851_T855_G1.0520.40
261_L319_S1.0510.40
973_V989_K1.0500.40
900_L906_V1.0500.40
257_S312_A1.0480.39
461_Y911_L1.0480.39
973_V990_P1.0480.39
82_E124_D1.0480.39
191_E370_G1.0480.39
188_T316_S1.0470.39
76_S100_V1.0470.39
252_I257_S1.0470.39
462_L892_F1.0460.39
72_P96_C1.0440.39
310_G337_Y1.0440.39
964_L989_K1.0440.39
193_N285_S1.0430.39
662_R665_L1.0390.39
192_I257_S1.0380.39
687_L755_Y1.0380.39
830_W834_L1.0370.38
259_P262_L1.0370.38
762_D766_R1.0360.38
194_R342_A1.0350.38
824_L827_Q1.0350.38
955_N990_P1.0350.38
112_I211_D1.0320.38
938_A952_M1.0310.38
237_R256_N1.0310.38
842_A845_P1.0300.38
961_G966_A1.0300.38
202_D257_S1.0300.38
247_V265_L1.0290.38
626_H631_T1.0290.38
255_W312_A1.0260.37
24_F52_A1.0260.37
220_F258_V1.0250.37
124_D127_H1.0240.37
848_H852_H1.0240.37
202_D256_N1.0230.37
216_V261_L1.0220.37
214_L261_L1.0210.37
47_T50_E1.0210.37
207_V317_I1.0210.37
749_G782_A1.0200.37
192_I207_V1.0160.37
96_C162_L1.0140.36
180_I316_S1.0140.36
262_L285_S1.0130.36
221_G284_L1.0120.36
188_T309_M1.0100.36
60_A153_E1.0080.36
188_T222_L1.0070.36
450_G454_G1.0050.36
854_F857_H1.0050.36
237_R258_V1.0040.36
436_K443_D1.0030.35
217_Y317_I1.0030.35
38_I250_H1.0030.35
115_K174_E1.0030.35
35_T47_T1.0020.35
187_N317_I1.0020.35
256_N282_G1.0020.35
115_K378_D1.0010.35
285_S315_A1.0010.35
312_A335_I1.0010.35
363_E401_G1.0010.35
837_S840_Q1.0000.35
450_G456_R1.0000.35
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  
2vsqA10.58761000.502Contact Map
4dg8A10.48951000.531Contact Map
4iz6A20.57661000.555Contact Map
4r0mB20.58961000.562Contact Map
4d4iA101000.61Contact Map
1amuA20.49951000.614Contact Map
3tsyA10.47751000.628Contact Map
3g7sA20.47151000.635Contact Map
3wvnA20.37541000.636Contact Map
3l8cA20.50351000.638Contact 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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