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jrfl

ID: 1502107875 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 847 (847)
Sequences: 2744 (337.2)
Seq/Len: 3.240
Nf(neff/√len): 11.6

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: 3.240).

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
280_T444_L4.6121.00
493_K598_A3.8031.00
623_E627_D3.6501.00
746_L749_V3.2361.00
738_R749_V3.2341.00
650_E653_E2.9011.00
649_Q653_E2.8891.00
290_E333_K2.8571.00
272_D275_T2.7821.00
344_K347_E2.7671.00
326_H330_S2.7001.00
611_D615_N2.6471.00
208_E374_G2.4911.00
61_D64_V2.3571.00
816_G820_I2.3331.00
662_N674_K2.3031.00
815_E820_I2.2401.00
113_Q199_T2.2281.00
653_E656_K2.2131.00
156_F171_A2.1721.00
64_V205_I2.1561.00
321_D410_R2.1361.00
646_K649_Q2.1311.00
632_E635_T2.1151.00
96_K272_D2.0681.00
792_Q816_G2.0661.00
267_V274_F2.0551.00
272_D276_N2.0481.00
328_N332_A2.0391.00
355_V456_T2.0271.00
227_D237_K2.0111.00
228_K264_E1.9861.00
158_I169_E1.9771.00
412_K415_I1.9591.00
216_A222_I1.9571.00
420_E423_K1.9521.00
737_G749_V1.9421.00
808_A812_A1.9411.00
91_H235_P1.9211.00
84_V226_N1.9211.00
621_E624_R1.9091.00
195_T199_T1.8630.99
788_W791_L1.8590.99
354_I606_S1.8550.99
276_N465_D1.8530.99
354_I605_W1.8380.99
723_G779_R1.8060.99
796_Q800_N1.7890.99
843_E846_L1.7800.99
24_L605_W1.7520.99
192_S197_V1.7250.99
840_Q843_E1.7200.99
302_K314_T1.7150.99
45_K627_D1.7090.99
164_D189_R1.7090.99
20_L23_I1.7070.99
792_Q815_E1.6890.99
220_F284_Q1.6860.99
766_L787_W1.6800.98
305_H311_A1.6760.98
642_N649_Q1.6700.98
208_E220_F1.6660.98
712_L747_I1.6480.98
804_S808_A1.6400.98
26_I605_W1.6370.98
824_L828_Y1.6360.98
342_V388_S1.6190.98
105_E171_A1.6120.98
806_L809_T1.6110.98
779_R783_V1.5960.98
656_K668_K1.5910.98
558_Q620_M1.5850.98
19_L23_I1.5780.97
713_P717_G1.5740.97
835_P840_Q1.5570.97
267_V342_V1.5560.97
738_R746_L1.5540.97
16_G19_L1.5520.97
48_T98_N1.5490.97
741_N747_I1.5480.97
691_T749_V1.5470.97
24_L606_S1.5460.97
807_N816_G1.5420.97
64_V67_V1.5310.97
828_Y831_I1.5290.97
789_N792_Q1.5260.97
229_T265_E1.5260.97
513_F704_S1.5240.97
45_K48_T1.5190.97
46_E620_M1.5050.96
462_G465_D1.4930.96
774_E777_G1.4900.96
20_L787_W1.4830.96
286_K340_Q1.4820.96
807_N815_E1.4800.96
835_P839_R1.4750.96
266_E344_K1.4700.96
836_T842_L1.4640.96
324_Q330_S1.4640.96
816_G824_L1.4620.95
796_Q844_R1.4590.95
840_Q846_L1.4590.95
329_I337_T1.4530.95
229_T237_K1.4530.95
828_Y832_L1.4490.95
364_P368_M1.4480.95
747_I766_L1.4450.95
555_R558_Q1.4300.95
837_R840_Q1.4250.95
355_V458_I1.4230.95
120_K420_E1.4220.95
91_H621_E1.4100.94
738_R745_A1.4060.94
1_M24_L1.4060.94
731_R737_G1.4050.94
606_S790_L1.4010.94
712_L741_N1.4010.94
821_I824_L1.3990.94
605_W790_L1.3880.94
287_E336_D1.3860.94
623_E631_S1.3860.94
61_D206_S1.3840.93
779_R792_Q1.3830.93
24_L27_C1.3800.93
7_R20_L1.3790.93
839_R843_E1.3770.93
13_L20_L1.3670.93
26_I606_S1.3600.93
229_T233_K1.3600.93
433_Q437_S1.3590.93
736_S739_L1.3470.92
667_T674_K1.3400.92
1_M5_G1.3390.92
292_N437_S1.3390.92
146_M149_G1.3390.92
179_V189_R1.3380.92
64_V284_Q1.3340.92
220_F481_K1.3320.92
772_I787_W1.3320.92
416_N423_K1.3320.92
48_T623_E1.3300.92
841_G846_L1.3280.91
827_T830_A1.3280.91
713_P816_G1.3260.91
833_H844_R1.3240.91
509_V544_N1.3240.91
653_E667_T1.3230.91
171_A558_Q1.3210.91
367_V498_Q1.3200.91
713_P815_E1.3190.91
84_V620_M1.3190.91
303_S314_T1.3190.91
305_H310_R1.3170.91
779_R804_S1.3170.91
556_M637_I1.3160.91
91_H624_R1.3160.91
199_T416_N1.3150.91
132_D136_T1.3130.91
837_R843_E1.3130.91
1_M605_W1.3070.91
765_L772_I1.3050.91
788_W800_N1.3040.90
189_R192_S1.3030.90
147_E151_I1.3020.90
10_Y19_L1.2990.90
226_N229_T1.2990.90
832_L844_R1.2950.90
765_L788_W1.2940.90
175_K192_S1.2900.90
544_N642_N1.2810.89
839_R846_L1.2800.89
658_A665_D1.2780.89
749_V755_C1.2780.89
324_Q328_N1.2700.89
783_V792_Q1.2680.89
787_W807_N1.2650.89
788_W795_S1.2580.88
161_S192_S1.2560.88
417_M420_E1.2550.88
331_R403_N1.2540.88
731_R787_W1.2510.88
772_I779_R1.2510.88
24_L717_G1.2510.88
761_R764_D1.2500.88
731_R747_I1.2490.88
20_L48_T1.2480.88
689_V696_V1.2480.88
61_D598_A1.2470.88
658_A662_N1.2470.88
423_K558_Q1.2450.88
775_L778_R1.2420.87
2_R612_R1.2420.87
772_I795_S1.2400.87
747_I795_S1.2360.87
714_A747_I1.2300.87
274_F348_Q1.2290.87
10_Y23_I1.2290.87
287_E340_Q1.2280.87
3_V24_L1.2260.86
423_K433_Q1.2200.86
667_T820_I1.2160.86
374_G435_R1.2150.86
13_L64_V1.2140.86
330_S437_S1.2130.86
835_P846_L1.2130.86
21_L28_S1.2120.86
435_R483_E1.2120.86
319_I606_S1.2100.85
24_L354_I1.2080.85
135_A138_T1.2050.85
413_Q421_V1.2040.85
302_K316_G1.2040.85
834_I840_Q1.2030.85
326_H406_T1.2030.85
637_I689_V1.2010.85
418_W426_Y1.1980.85
113_Q195_T1.1980.85
747_I765_L1.1960.85
7_R25_M1.1950.85
493_K726_E1.1940.84
131_K689_V1.1920.84
267_V388_S1.1920.84
787_W803_V1.1920.84
287_E333_K1.1910.84
462_G467_R1.1910.84
803_V807_N1.1880.84
712_L723_G1.1870.84
812_A824_L1.1850.84
526_M544_N1.1850.84
835_P843_E1.1810.84
64_V208_E1.1810.84
714_A816_G1.1810.84
791_L844_R1.1730.83
178_V189_R1.1710.83
755_C758_S1.1710.83
844_R847_L1.1690.83
781_W786_Y1.1670.83
431_R435_R1.1650.82
319_I605_W1.1640.82
712_L731_R1.1520.81
1_M606_S1.1480.81
620_M623_E1.1470.81
1_M26_I1.1430.81
772_I800_N1.1410.81
268_V274_F1.1370.80
26_I354_I1.1370.80
27_C605_W1.1360.80
501_K513_F1.1340.80
10_Y20_L1.1340.80
341_I749_V1.1310.80
4_K8_K1.1290.80
731_R795_S1.1280.80
161_S197_V1.1280.80
228_K265_E1.1250.79
364_P423_K1.1240.79
233_K272_D1.1240.79
64_V374_G1.1230.79
61_D67_V1.1220.79
757_F764_D1.1210.79
574_V623_E1.1200.79
766_L769_V1.1200.79
169_E302_K1.1160.79
637_I659_S1.1160.79
766_L788_W1.1100.78
789_N796_Q1.1080.78
310_R498_Q1.1050.78
48_T650_E1.1040.77
46_E84_V1.1030.77
623_E626_I1.1020.77
290_E294_T1.0990.77
1_M27_C1.0990.77
297_N433_Q1.0990.77
447_R450_G1.0950.77
14_W20_L1.0940.77
149_G152_K1.0940.77
10_Y635_T1.0930.76
45_K623_E1.0930.76
342_V390_W1.0920.76
779_R816_G1.0920.76
20_L796_Q1.0910.76
2_R24_L1.0900.76
199_T620_M1.0890.76
583_L605_W1.0890.76
46_E229_T1.0880.76
11_Q25_M1.0870.76
284_Q586_I1.0840.76
691_T755_C1.0840.76
48_T171_A1.0830.76
765_L787_W1.0830.76
714_A722_E1.0820.75
292_N435_R1.0810.75
4_K29_A1.0790.75
586_I593_L1.0780.75
152_K208_E1.0770.75
834_I841_G1.0760.75
772_I788_W1.0760.75
284_Q288_S1.0750.75
3_V605_W1.0750.75
1_M354_I1.0740.75
46_E610_L1.0740.75
721_P844_R1.0730.75
447_R457_E1.0730.75
779_R815_E1.0720.75
21_L481_K1.0720.75
631_S637_I1.0710.74
45_K483_E1.0680.74
714_A815_E1.0680.74
662_N665_D1.0680.74
548_R555_R1.0670.74
715_P718_P1.0650.74
783_V816_G1.0650.74
20_L714_A1.0640.74
779_R807_N1.0630.74
781_W785_K1.0620.74
778_R816_G1.0610.73
175_K191_I1.0610.73
681_G684_V1.0600.73
164_D312_F1.0600.73
721_P796_Q1.0570.73
836_T839_R1.0570.73
509_V653_E1.0560.73
745_A749_V1.0550.73
766_L791_L1.0540.73
280_T285_L1.0540.73
638_E645_E1.0540.73
401_E404_T1.0530.73
481_K642_N1.0510.72
342_V435_R1.0510.72
178_V182_D1.0510.72
736_S740_V1.0510.72
307_G310_R1.0500.72
40_G44_W1.0490.72
98_N431_R1.0470.72
481_K649_Q1.0460.72
365_E379_Y1.0460.72
195_T416_N1.0440.72
796_Q807_N1.0440.72
830_A835_P1.0430.72
7_R747_I1.0420.72
36_T40_G1.0410.71
399_N404_T1.0400.71
744_L753_S1.0400.71
83_V642_N1.0390.71
737_G766_L1.0390.71
574_V665_D1.0380.71
837_R846_L1.0380.71
794_W797_E1.0380.71
3_V606_S1.0370.71
713_P737_G1.0370.71
605_W716_R1.0340.71
329_I344_K1.0330.71
156_F558_Q1.0320.70
15_K29_A1.0320.70
8_K20_L1.0320.70
731_R738_R1.0320.70
832_L847_L1.0310.70
714_A731_R1.0310.70
779_R796_Q1.0310.70
134_N137_N1.0310.70
8_K787_W1.0300.70
272_D279_K1.0290.70
747_I788_W1.0270.70
418_W421_V1.0270.70
132_D138_T1.0260.70
603_A711_L1.0260.70
788_W831_I1.0250.70
763_R767_L1.0250.70
267_V769_V1.0240.70
834_I837_R1.0220.69
809_T815_E1.0220.69
574_V579_G1.0220.69
411_I428_P1.0220.69
731_R766_L1.0200.69
220_F274_F1.0180.69
59_A64_V1.0170.69
154_C159_T1.0170.69
789_N800_N1.0150.69
731_R741_N1.0150.69
12_Y20_L1.0140.69
1_M6_I1.0140.69
290_E437_S1.0140.69
101_E722_E1.0140.69
7_R24_L1.0120.68
768_T772_I1.0100.68
171_A420_E1.0100.68
159_T164_D1.0100.68
266_E275_T1.0100.68
836_T840_Q1.0090.68
794_W801_S1.0090.68
284_Q374_G1.0080.68
189_R417_M1.0080.68
773_V776_L1.0060.68
747_I791_L1.0060.68
423_K435_R1.0060.68
725_E761_R1.0050.68
208_E342_V1.0040.67
276_N279_K1.0030.67
837_R841_G1.0030.67
199_T493_K1.0030.67
653_E714_A1.0020.67
775_L782_E1.0010.67
679_I684_V1.0000.67
413_Q418_W1.0000.67
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  
4tvpG10.53251000.435Contact Map
4r4hA10.39671000.481Contact Map
4jzzA10.39551000.559Contact Map
3lqaG10.33881000.632Contact Map
2bf1A10.34711000.642Contact Map
4i3sG10.21021000.819Contact Map
4tvpB10.14881000.823Contact Map
3tygA10.1831000.846Contact Map
1qbzA30.14171000.859Contact Map
4jpkA10.18891000.876Contact 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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