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BmdB_Cy

ID: 1501514306 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 746 (739)
Sequences: 12841 (10767.1)
Seq/Len: 17.376
Nf(neff/√len): 396.1

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: 17.376).

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
712_T729_I5.0071.00
635_R661_V3.8421.00
633_G711_D3.7421.00
395_R426_D3.5891.00
678_N717_Y3.3671.00
663_I672_Q3.2851.00
191_V201_L3.1701.00
738_T742_I3.0981.00
164_E257_T2.9321.00
433_Q441_Q2.9061.00
615_D655_K2.8991.00
619_N655_K2.7271.00
624_F628_R2.6621.00
731_T734_A2.6461.00
590_I615_D2.5651.00
615_D702_D2.5531.00
612_S616_Q2.5431.00
637_G681_C2.5381.00
390_W543_Q2.5271.00
368_A378_L2.5131.00
592_Q596_T2.5091.00
344_I533_D2.4991.00
621_V648_I2.4981.00
738_T741_D2.4911.00
737_N742_I2.4571.00
386_V547_L2.4271.00
630_I658_A2.4071.00
435_F551_L2.3981.00
325_K445_T2.3851.00
634_D682_K2.3561.00
592_Q595_R2.3101.00
179_Q183_Q2.2981.00
621_V652_A2.2971.00
583_A591_D2.2901.00
632_R711_D2.2761.00
525_W537_M2.2581.00
534_A538_E2.2411.00
635_R715_V2.2251.00
318_A452_H2.2071.00
619_N623_R2.2041.00
181_V284_Y2.2031.00
371_K436_F2.1711.00
674_Y724_R2.1611.00
596_T599_Q2.1511.00
184_R280_D2.1151.00
166_E257_T2.0901.00
384_G427_M2.0711.00
634_D658_A2.0681.00
630_I634_D2.0601.00
600_V608_W2.0531.00
525_W541_F2.0341.00
264_Y269_M2.0331.00
397_A424_L2.0001.00
175_S179_Q1.9931.00
710_E731_T1.9911.00
618_S655_K1.9591.00
145_M149_N1.9521.00
407_P411_E1.9471.00
585_L735_A1.9451.00
364_L375_P1.9191.00
631_G634_D1.9001.00
584_T587_Q1.8991.00
676_L681_C1.8781.00
95_G98_D1.8721.00
383_Y478_I1.8711.00
638_V649_N1.8711.00
277_V416_V1.8661.00
570_I573_Y1.8611.00
395_R428_D1.8551.00
54_T83_I1.8511.00
144_Y147_G1.8491.00
667_H675_I1.8451.00
615_D619_N1.8431.00
734_A737_N1.8401.00
617_R645_E1.8321.00
609_L648_I1.8291.00
245_L268_L1.8191.00
181_V281_L1.8191.00
708_E711_D1.8161.00
174_L281_L1.8011.00
635_R659_A1.8011.00
191_V243_W1.8011.00
604_F644_V1.7811.00
460_F464_Y1.7801.00
319_K455_Y1.7791.00
598_D612_S1.7761.00
674_Y717_Y1.7681.00
70_F75_G1.7671.00
710_E733_Q1.7641.00
514_V523_V1.7361.00
279_Q414_Q1.7341.00
144_Y148_R1.7181.00
623_R703_L1.7071.00
739_I742_I1.7051.00
652_A656_A1.7001.00
436_F556_D1.6921.00
434_P437_T1.6881.00
180_K183_Q1.6851.00
51_L87_L1.6621.00
649_N685_L1.6561.00
609_L644_V1.6491.00
687_S690_Y1.6471.00
590_I655_K1.6381.00
586_H732_H1.6361.00
399_N476_M1.6361.00
615_D618_S1.6311.00
638_V650_L1.6201.00
735_A738_T1.6161.00
669_Y673_T1.6121.00
589_F593_A1.6101.00
178_F248_L1.6081.00
738_T746_F1.6061.00
550_Q563_S1.6011.00
604_F607_E1.5961.00
591_D595_R1.5961.00
457_G461_I1.5941.00
390_W540_M1.5931.00
730_I738_T1.5911.00
185_H280_D1.5871.00
633_G712_T1.5861.00
381_T438_K1.5791.00
377_A443_Q1.5731.00
354_T538_E1.5691.00
589_F651_M1.5671.00
146_L150_P1.5651.00
737_N741_D1.5631.00
734_A738_T1.5611.00
424_L460_F1.5601.00
558_N561_R1.5581.00
734_A742_I1.5551.00
384_G398_I1.5531.00
69_N72_A1.5531.00
512_N525_W1.5531.00
321_Y449_G1.5521.00
225_R228_E1.5511.00
741_D745_K1.5481.00
382_V548_L1.5471.00
47_V113_V1.5461.00
319_K463_D1.5371.00
661_V679_S1.5351.00
600_V603_V1.5341.00
741_D746_F1.5301.00
649_N653_V1.5231.00
444_S448_D1.5221.00
602_V647_I1.5191.00
630_I636_V1.5181.00
343_E536_V1.5171.00
673_T677_E1.5151.00
180_K288_P1.5151.00
318_A454_H1.5141.00
588_L736_S1.5131.00
366_R370_D1.5071.00
365_R516_E1.5071.00
469_Q472_P1.5061.00
674_Y678_N1.5061.00
104_T107_E1.5021.00
316_E320_A1.5011.00
545_V549_D1.4991.00
186_P298_T1.4941.00
590_I618_S1.4911.00
707_A711_D1.4871.00
352_L529_E1.4841.00
239_P242_Q1.4711.00
640_A649_N1.4701.00
323_T463_D1.4701.00
170_D173_R1.4691.00
320_A324_N1.4691.00
169_L258_Y1.4691.00
678_N724_R1.4681.00
174_L260_L1.4661.00
554_Q557_I1.4651.00
677_E724_R1.4651.00
742_I745_K1.4641.00
319_K323_T1.4591.00
538_E542_T1.4581.00
360_K549_D1.4581.00
739_I743_N1.4571.00
388_A429_M1.4461.00
602_V644_V1.4451.00
57_K86_A1.4451.00
427_M442_T1.4361.00
645_E687_S1.4341.00
192_I268_L1.4321.00
383_Y512_N1.4301.00
352_L534_A1.4281.00
738_T743_N1.4201.00
543_Q564_Q1.4181.00
171_I250_A1.4040.99
144_Y149_N1.4010.99
157_I162_Y1.4010.99
600_V610_T1.4000.99
215_V255_E1.3990.99
65_G68_D1.3850.99
583_A587_Q1.3840.99
659_A712_T1.3820.99
69_N103_P1.3820.99
586_H707_A1.3780.99
229_E251_F1.3760.99
730_I734_A1.3740.99
735_A742_I1.3740.99
46_P49_Q1.3710.99
459_E462_R1.3670.99
679_S717_Y1.3610.99
539_S543_Q1.3540.99
44_R66_I1.3530.99
588_L740_Q1.3530.99
527_Y537_M1.3510.99
367_L552_V1.3510.99
55_W105_I1.3490.99
430_D433_Q1.3490.99
145_M148_R1.3410.99
180_K284_Y1.3400.99
737_N745_K1.3250.99
164_E259_L1.3220.99
455_Y463_D1.3190.99
212_E249_K1.3170.99
428_D433_Q1.3150.99
382_V551_L1.3140.99
324_N327_P1.3110.99
381_T442_T1.3100.99
363_K553_E1.3080.99
385_E438_K1.3080.99
337_L472_P1.3080.99
363_K549_D1.2980.99
742_I746_F1.2970.99
641_K687_S1.2960.99
568_A573_Y1.2960.99
299_F302_Y1.2950.99
66_I105_I1.2910.99
157_I160_Q1.2890.99
714_Y730_I1.2870.99
190_A200_I1.2850.99
213_S252_Q1.2810.99
147_G150_P1.2800.99
233_M236_H1.2780.99
481_T484_L1.2720.99
45_N66_I1.2680.99
375_P521_L1.2660.99
533_D536_V1.2630.99
429_M433_Q1.2620.99
669_Y693_M1.2600.99
357_T360_K1.2590.99
610_T613_E1.2490.99
357_T549_D1.2490.99
250_A260_L1.2460.98
386_V544_F1.2420.98
532_F537_M1.2420.98
589_F615_D1.2410.98
173_R288_P1.2410.98
334_S397_A1.2340.98
568_A572_Q1.2330.98
233_M263_R1.2330.98
607_E617_R1.2270.98
233_M249_K1.2240.98
11_V14_I1.2230.98
380_C398_I1.2160.98
168_E256_H1.2130.98
371_K440_E1.2120.98
624_F627_S1.2100.98
321_Y325_K1.2070.98
385_E547_L1.2070.98
603_V608_W1.2030.98
145_M150_P1.2000.98
667_H672_Q1.1980.98
686_D690_Y1.1920.98
39_P67_H1.1910.98
607_E645_E1.1870.98
140_V143_A1.1870.98
432_K560_L1.1860.98
457_G460_F1.1810.98
670_E674_Y1.1750.98
557_I561_R1.1720.98
98_D111_R1.1720.98
630_I656_A1.1720.98
325_K448_D1.1710.98
279_Q283_H1.1690.97
593_A615_D1.1680.97
566_D570_I1.1640.97
590_I619_N1.1600.97
446_L450_L1.1590.97
670_E724_R1.1580.97
628_R683_I1.1580.97
144_Y150_P1.1570.97
228_E232_R1.1550.97
302_Y305_I1.1540.97
67_H106_A1.1520.97
547_L562_I1.1510.97
730_I741_D1.1470.97
131_L135_F1.1440.97
460_F463_D1.1420.97
618_S652_A1.1400.97
364_L378_L1.1350.97
50_K53_Q1.1350.97
373_V439_V1.1320.97
572_Q575_A1.1310.97
459_E463_D1.1300.97
248_L260_L1.1280.97
169_L174_L1.1260.97
373_V377_A1.1240.97
193_L199_Q1.1230.97
546_E550_Q1.1210.97
654_L713_A1.1170.96
383_Y480_F1.1160.96
170_D285_Y1.1150.96
636_V658_A1.1150.96
215_V252_Q1.1130.96
607_E644_V1.1120.96
617_R648_I1.1110.96
102_Y111_R1.1110.96
633_G731_T1.1100.96
54_T87_L1.1100.96
637_G676_L1.1080.96
226_L259_L1.1070.96
573_Y576_T1.1050.96
361_W521_L1.1040.96
240_L267_L1.1030.96
306_Y310_K1.1020.96
570_I574_N1.1000.96
585_L654_L1.0960.96
617_R620_Q1.0930.96
354_T541_F1.0930.96
712_T731_T1.0880.96
252_Q258_Y1.0860.96
614_L651_M1.0850.96
175_S208_E1.0840.96
187_M190_A1.0770.95
586_H654_L1.0750.95
155_S158_S1.0740.95
350_Q530_E1.0730.95
512_N523_V1.0720.95
284_Y288_P1.0710.95
367_L371_K1.0700.95
644_V648_I1.0680.95
455_Y460_F1.0560.95
134_P197_K1.0550.95
363_K552_V1.0550.95
566_D571_D1.0530.95
639_L672_Q1.0510.94
662_P716_I1.0500.94
176_R288_P1.0470.94
379_L521_L1.0460.94
587_Q590_I1.0450.94
48_E66_I1.0450.94
321_Y448_D1.0440.94
388_A391_S1.0440.94
159_P162_Y1.0420.94
437_T440_E1.0420.94
361_W365_R1.0400.94
734_A739_I1.0380.94
251_F261_C1.0360.94
354_T534_A1.0340.94
328_D426_D1.0320.94
511_D526_N1.0270.94
254_Q257_T1.0250.93
659_A715_V1.0250.93
377_A447_L1.0220.93
639_L663_I1.0200.93
380_C384_G1.0170.93
192_I267_L1.0170.93
380_C446_L1.0170.93
175_S211_V1.0140.93
142_T307_D1.0130.93
148_R194_P1.0100.93
619_N702_D1.0080.93
614_L648_I1.0080.93
456_D459_E1.0070.93
626_Q707_A1.0070.93
596_T612_S1.0070.93
441_Q445_T1.0050.93
640_A685_L1.0050.93
88_R93_K1.0050.93
361_W375_P1.0040.93
191_V244_P1.0040.93
137_L267_L1.0040.93
373_V378_L1.0020.92
138_T299_F1.0000.92
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  
2vsqA10.8111000.325Contact Map
2jgpA10.6811000.444Contact Map
4tx3B10.57241000.584Contact Map
1l5aA30.56171000.584Contact Map
4znmA201000.591Contact Map
4jn3A20.5671000.593Contact Map
4hvmA40.5081000.598Contact Map
2xhgA10.5671000.621Contact Map
1q9jA20.49061000.68Contact Map
3fotA10.57771000.701Contact 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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