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bbs_7_full -force run

ID: 1505241655 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 50% gaps before running GREMLIN.
Length: 712 (670)
Sequences: 299 (218.7)
Seq/Len: 0.446
Nf(neff/√len): 8.4

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: 0.446).

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 > 50% 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
245_D250_G3.0240.99
249_D253_D2.8390.98
245_D249_D2.5160.96
206_F214_G2.2810.92
245_D253_D2.0060.84
247_V253_D1.9110.79
30_Q35_G1.7780.72
166_D170_R1.7670.71
256_V264_E1.6830.66
30_Q42_M1.6590.64
687_K705_L1.6540.64
164_C172_L1.6470.63
46_M51_A1.6440.63
512_F516_E1.6410.63
564_S570_I1.6020.60
245_D257_G1.5690.58
32_V43_C1.5540.57
264_E349_L1.5490.56
626_L647_L1.5400.56
43_C79_I1.5380.56
32_V81_I1.5330.55
151_P159_V1.5330.55
459_E491_H1.5120.54
211_G214_G1.5070.53
33_V79_I1.5010.53
96_Q119_F1.4870.52
309_G342_L1.4700.51
41_V303_V1.4680.50
393_L421_S1.4640.50
145_N165_Q1.4560.50
33_V43_C1.4540.49
371_S374_P1.4520.49
144_I160_P1.4340.48
80_F92_K1.4170.47
358_E395_L1.4100.46
207_G211_G1.4060.46
110_A122_A1.3990.45
30_Q258_R1.3820.44
540_F612_Y1.3750.44
310_W314_L1.3690.43
98_L132_C1.3680.43
121_S130_C1.3530.42
264_E452_E1.3450.41
210_D227_W1.3340.41
142_D245_D1.3270.40
450_R490_L1.3270.40
30_Q36_D1.3260.40
334_E338_K1.3230.40
66_L206_F1.3210.40
41_V88_R1.3190.39
245_D255_L1.3190.39
229_I393_L1.3160.39
77_E90_F1.3090.39
617_A620_V1.3070.39
504_N593_E1.3060.39
163_A187_P1.3040.38
89_G94_G1.3040.38
41_V90_F1.2960.38
229_I262_M1.2960.38
92_K106_E1.2800.37
55_F79_I1.2800.37
47_K50_E1.2720.36
71_A74_T1.2700.36
123_S130_C1.2690.36
255_L291_G1.2670.36
485_I489_S1.2660.36
148_I154_R1.2660.36
138_Y172_L1.2640.36
98_L101_E1.2580.35
610_L618_K1.2570.35
282_L302_I1.2540.35
531_K604_K1.2540.35
32_V79_I1.2480.34
257_G261_G1.2480.34
650_A654_Q1.2460.34
373_V376_F1.2450.34
502_P565_D1.2430.34
253_D257_G1.2420.34
663_H671_I1.2410.34
78_K82_A1.2380.34
204_L230_R1.2380.34
653_L676_I1.2350.34
303_V306_T1.2340.34
614_L646_I1.2330.33
164_C170_R1.2270.33
67_E246_I1.2230.33
169_L209_S1.2220.33
104_L134_D1.2210.33
454_K465_L1.2210.33
208_T214_G1.2200.33
163_A173_Q1.2180.32
91_T98_L1.2110.32
140_S143_K1.2110.32
652_H655_E1.2110.32
105_T108_I1.2100.32
80_F90_F1.2040.32
667_L676_I1.2030.32
44_F49_G1.2020.31
113_I122_A1.1990.31
306_T310_W1.1990.31
118_L125_I1.1960.31
414_L420_N1.1890.31
172_L207_G1.1880.31
521_V552_E1.1880.31
100_F132_C1.1880.31
306_T610_L1.1870.30
456_R673_D1.1870.30
127_N134_D1.1840.30
669_G673_D1.1840.30
177_V265_V1.1830.30
139_L163_A1.1820.30
140_S164_C1.1820.30
447_N468_Y1.1810.30
577_L622_L1.1790.30
238_I253_D1.1780.30
175_S262_M1.1780.30
453_L508_L1.1770.30
21_L30_Q1.1760.30
681_F684_T1.1750.30
29_T87_I1.1730.30
40_I57_T1.1730.30
32_V51_A1.1720.30
700_Y708_F1.1710.29
112_H151_P1.1680.29
387_D591_S1.1660.29
137_Y180_E1.1650.29
479_Q486_K1.1620.29
673_D677_D1.1620.29
161_V194_N1.1620.29
249_D257_G1.1590.29
287_T294_V1.1590.29
205_L208_T1.1520.28
237_G275_V1.1510.28
542_F565_D1.1500.28
165_Q263_V1.1460.28
156_L159_V1.1450.28
345_E370_K1.1450.28
293_C298_G1.1430.28
656_E705_L1.1430.28
85_S140_S1.1420.28
521_V641_P1.1420.28
513_S586_I1.1420.28
609_K687_K1.1420.28
376_F479_Q1.1390.28
444_C491_H1.1390.28
536_E576_V1.1360.27
87_I306_T1.1350.27
201_G219_T1.1350.27
57_T63_I1.1330.27
77_E138_Y1.1320.27
116_S130_C1.1320.27
213_L250_G1.1320.27
215_L257_G1.1310.27
225_H228_E1.1290.27
99_S124_Y1.1270.27
54_V78_K1.1260.27
102_T108_I1.1250.27
439_L444_C1.1250.27
119_F130_C1.1240.27
22_P30_Q1.1220.27
677_D680_K1.1220.27
672_T681_F1.1220.27
121_S124_Y1.1200.26
266_Y274_P1.1200.26
476_K627_K1.1190.26
201_G254_L1.1140.26
90_F286_V1.1130.26
437_F453_L1.1130.26
246_I249_D1.1120.26
62_K160_P1.1120.26
82_A120_L1.1120.26
56_K63_I1.1110.26
409_D415_L1.1110.26
454_K473_I1.1110.26
145_N166_D1.1100.26
263_V392_S1.1090.26
210_D231_N1.1070.26
18_M139_L1.1070.26
172_L188_T1.1070.26
445_Q448_T1.1060.26
568_S611_E1.1050.26
20_L49_G1.1050.26
47_K146_D1.1040.26
256_V265_V1.1030.25
175_S183_V1.1030.25
528_V608_P1.1030.25
565_D648_E1.1030.25
57_T78_K1.1010.25
213_L244_F1.1000.25
159_V163_A1.0980.25
450_R564_S1.0980.25
62_K125_I1.0970.25
86_E96_Q1.0970.25
214_G227_W1.0970.25
684_T696_I1.0960.25
34_V213_L1.0930.25
141_G164_C1.0910.25
375_S453_L1.0900.25
510_G586_I1.0900.25
496_F521_V1.0900.25
55_F138_Y1.0890.25
653_L667_L1.0880.25
261_G309_G1.0880.25
44_F231_N1.0850.24
166_D169_L1.0850.24
452_E467_A1.0850.24
78_K89_G1.0840.24
163_A174_G1.0840.24
238_I255_L1.0840.24
292_G626_L1.0840.24
513_S516_E1.0820.24
573_L588_L1.0820.24
493_R581_A1.0810.24
460_G463_G1.0800.24
124_Y137_Y1.0790.24
295_G311_I1.0790.24
241_V301_E1.0780.24
77_E92_K1.0770.24
669_G680_K1.0770.24
63_I265_V1.0760.24
77_E80_F1.0760.24
98_L105_T1.0760.24
311_I701_D1.0760.24
610_L671_I1.0760.24
87_I207_G1.0760.24
622_L628_E1.0760.24
510_G516_E1.0750.24
661_P673_D1.0740.24
79_I95_K1.0730.24
21_L204_L1.0730.24
55_F66_L1.0730.24
277_R671_I1.0710.24
491_H572_I1.0700.24
601_H608_P1.0690.24
643_Y676_I1.0690.24
80_F93_R1.0680.24
44_F145_N1.0660.23
183_V225_H1.0650.23
510_G628_E1.0640.23
64_A188_T1.0630.23
127_N137_Y1.0630.23
303_V422_A1.0630.23
510_G513_S1.0630.23
255_L292_G1.0630.23
169_L291_G1.0620.23
108_I129_Y1.0620.23
91_T141_G1.0610.23
579_K675_F1.0610.23
617_A632_H1.0610.23
449_T525_M1.0610.23
476_K686_V1.0600.23
643_Y667_L1.0590.23
108_I121_S1.0580.23
450_R459_E1.0580.23
243_S282_L1.0570.23
110_A121_S1.0550.23
212_K228_E1.0550.23
684_T694_L1.0550.23
138_Y164_C1.0540.23
45_G78_K1.0520.23
114_S120_L1.0520.23
562_F608_P1.0520.23
306_T309_G1.0500.23
380_D483_Y1.0500.23
672_T698_D1.0500.23
21_L116_S1.0490.23
254_L263_V1.0480.22
444_C448_T1.0470.22
57_T97_F1.0470.22
105_T109_K1.0460.22
31_K38_D1.0450.22
253_D305_S1.0440.22
255_L453_L1.0440.22
463_G490_L1.0440.22
50_E92_K1.0430.22
351_Y358_E1.0430.22
99_S130_C1.0420.22
608_P647_L1.0410.22
114_S126_Y1.0400.22
201_G239_L1.0400.22
635_N640_I1.0400.22
402_D408_S1.0390.22
656_E659_K1.0390.22
380_D481_R1.0370.22
385_N401_I1.0360.22
415_L420_N1.0350.22
416_D564_S1.0350.22
161_V318_P1.0350.22
64_A105_T1.0340.22
97_F100_F1.0340.22
151_P346_L1.0340.22
306_T444_C1.0330.22
84_G124_Y1.0310.22
420_N442_Y1.0310.22
477_T634_G1.0310.22
100_F103_N1.0300.22
250_G257_G1.0300.22
670_M680_K1.0300.22
620_V646_I1.0300.22
204_L225_H1.0290.21
641_P688_T1.0280.21
171_V176_D1.0280.21
445_Q478_C1.0280.21
238_I254_L1.0270.21
450_R476_K1.0270.21
443_R558_G1.0270.21
30_Q185_G1.0260.21
278_F292_G1.0250.21
664_L668_Y1.0250.21
408_S454_K1.0250.21
43_C52_V1.0240.21
21_L104_L1.0230.21
104_L122_A1.0230.21
518_H555_Y1.0230.21
34_V240_C1.0220.21
62_K98_L1.0220.21
204_L266_Y1.0220.21
35_G41_V1.0210.21
30_Q104_L1.0210.21
59_P78_K1.0200.21
137_Y183_V1.0190.21
416_D478_C1.0180.21
679_F682_K1.0180.21
89_G261_G1.0170.21
620_V633_E1.0170.21
627_K685_N1.0170.21
31_K77_E1.0160.21
678_K687_K1.0160.21
289_I393_L1.0150.21
566_N575_D1.0140.21
410_V419_K1.0130.21
675_F678_K1.0130.21
382_F385_N1.0110.21
99_S121_S1.0090.20
110_A117_D1.0080.20
490_L546_F1.0080.20
689_K693_L1.0080.20
82_A116_S1.0080.20
241_V244_F1.0080.20
81_I245_D1.0070.20
151_P156_L1.0070.20
80_F265_V1.0050.20
253_D265_V1.0050.20
81_I87_I1.0040.20
87_I229_I1.0040.20
122_A144_I1.0040.20
211_G261_G1.0040.20
374_P380_D1.0040.20
32_V88_R1.0030.20
241_V252_K1.0020.20
263_V283_S1.0020.20
82_A121_S1.0010.20
188_T581_A1.0000.20
55_F260_D1.0000.20
99_S104_L1.0000.20
459_E488_L1.0000.20
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  
3odtA20.400399.40.933Contact Map
4czxA10.401799.30.933Contact Map
2pbiB20.403199.30.936Contact Map
4u7aA1099.20.938Contact Map
3sfzA10.38999.10.94Contact Map
1gxrA20.345599.10.94Contact Map
4d0kA10.403199.10.941Contact Map
4pswB10.370899.10.941Contact Map
4zoxA10990.942Contact Map
4yvdA10.389990.943Contact 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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