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OPENSEQ.org

RA

ID: 1379164819 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 830 (815)
Sequences: 4712 (252.1)
Seq/Len: 5.782
Nf(neff/√len): 8.8

HHblits Results: (2013_03)
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: 5.782).

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
270_N422_I5.8661.00
468_K574_T5.2481.00
345_K348_D4.9141.00
280_S322_E4.9011.00
598_D602_R4.6901.00
714_R725_E3.9861.00
86_E267_H3.7811.00
74_L221_N3.6571.00
223_G260_D3.6491.00
311_D391_R3.5631.00
624_K628_E3.5591.00
277_E325_S3.4841.00
722_L725_E3.2911.00
316_Y320_S3.2671.00
277_E322_E3.2211.00
223_G259_T3.1881.00
333_K336_R3.1631.00
345_K349_K3.1401.00
211_A217_I3.1311.00
224_N260_D2.9831.00
277_E329_K2.9231.00
81_Y230_S2.8841.00
607_V610_D2.8341.00
222_E232_T2.8301.00
625_A628_E2.8181.00
789_L792_T2.7121.00
373_R389_P2.7061.00
54_A200_T2.7051.00
791_T795_V2.6871.00
666_A725_E2.6301.00
596_Q599_R2.6271.00
807_A811_G2.6151.00
713_V725_E2.6041.00
640_D643_K2.5801.00
331_K377_E2.5451.00
295_Q301_T2.4951.00
621_T624_K2.4821.00
228_N267_H2.4711.00
819_R825_L2.4531.00
276_N329_K2.4131.00
184_R397_L2.3801.00
633_A640_D2.3771.00
157_D184_R2.3511.00
178_T181_N2.3351.00
343_T431_N2.3301.00
637_N649_K2.3201.00
168_V187_N2.2691.00
287_G412_N2.2231.00
555_R612_I2.2131.00
51_S54_A2.2051.00
343_T433_T2.1851.00
139_L142_R2.1751.00
38_E88_K2.1581.00
144_M287_G2.1541.00
811_G815_L2.1511.00
261_D333_K2.1261.00
125_G128_A2.0941.00
393_K396_V2.0901.00
321_E384_K2.0861.00
631_Q643_K2.0861.00
316_Y387_I2.0781.00
690_A693_G2.0611.00
466_K586_Y2.0601.00
151_I162_V2.0421.00
331_K379_E2.0231.00
598_D606_G2.0111.00
134_N138_D1.9991.00
295_Q300_M1.9871.00
296_I300_M1.9831.00
628_E631_Q1.9771.00
155_I184_R1.9751.00
332_K335_K1.9731.00
322_E325_S1.9581.00
637_N643_K1.9571.00
772_G775_A1.9301.00
737_R740_D1.9111.00
811_G814_I1.9021.00
328_N331_K1.9011.00
168_V186_I1.8971.00
265_R447_Q1.8801.00
103_Q194_T1.8751.00
224_N232_T1.8711.00
224_N228_N1.8691.00
815_L830_L1.8651.00
169_E184_R1.8611.00
325_S329_K1.8591.00
262_I331_K1.8551.00
274_Q278_T1.8461.00
296_I302_F1.8321.00
643_K649_K1.8301.00
771_W774_I1.8101.00
550_I555_R1.8101.00
799_G803_F1.8091.00
110_K400_R1.8031.00
825_L828_A1.8021.00
814_I819_R1.8011.00
787_S791_T1.7921.00
614_Q621_T1.7881.00
688_P693_G1.7681.00
717_S725_E1.7651.00
280_S284_T1.7571.00
293_Q307_K1.7471.00
156_R159_K1.7461.00
74_L222_E1.7421.00
76_T232_T1.7381.00
717_S721_A1.7381.00
482_L485_L1.7211.00
698_E703_G1.7201.00
779_K783_D1.7191.00
321_E373_R1.7051.00
721_A725_E1.6991.00
293_Q309_V1.6971.00
331_K335_K1.6931.00
160_K168_V1.6911.00
142_R145_K1.6831.00
149_F164_S1.6821.00
307_K410_R1.6781.00
713_V717_S1.6711.00
606_G610_D1.6661.00
634_S643_K1.6631.00
162_V292_G1.6551.00
803_F810_I1.6491.00
633_A637_N1.6461.00
157_D397_L1.6421.00
585_S588_T1.6411.00
827_R830_L1.6260.99
276_N280_S1.6220.99
325_S328_N1.6210.99
221_N224_N1.6200.99
737_R750_E1.6060.99
328_N332_K1.6060.99
437_S440_N1.5930.99
468_K473_S1.5900.99
35_R38_E1.5830.99
304_N307_K1.5810.99
73_V617_E1.5810.99
714_R722_L1.5790.99
332_K336_R1.5700.99
291_G307_K1.5680.99
586_Y596_Q1.5670.99
804_I807_A1.5640.99
532_L601_V1.5530.99
642_T649_K1.5500.99
258_D261_D1.5490.99
755_S758_R1.5470.99
617_E624_K1.5360.99
278_T329_K1.5360.99
168_V173_P1.5090.99
270_N437_S1.5070.99
810_I813_G1.5050.99
151_I184_R1.5050.99
222_E226_S1.4980.99
335_K379_E1.4950.99
790_N798_E1.4760.99
321_E324_G1.4750.99
224_N261_D1.4710.99
293_Q301_T1.4700.99
345_K431_N1.4640.99
123_S144_M1.4610.99
689_T693_G1.4600.99
737_R741_S1.4470.99
725_E729_N1.4440.99
610_D614_Q1.4410.98
666_A672_A1.4380.98
289_N293_Q1.4340.98
142_R171_V1.4340.98
81_Y599_R1.4330.98
287_G309_V1.4320.98
260_D276_N1.4250.98
293_Q306_E1.4220.98
222_E228_N1.4200.98
717_S723_I1.4190.98
290_T293_Q1.4170.98
524_R532_L1.4150.98
819_R828_A1.4120.98
748_T770_L1.4100.98
532_L612_I1.4010.98
81_Y596_Q1.3980.98
683_L687_I1.3950.98
713_V723_I1.3920.98
172_V184_R1.3900.98
503_T506_V1.3890.98
686_L690_A1.3890.98
775_A799_G1.3880.98
156_R296_I1.3800.98
154_E187_N1.3760.98
163_Y292_G1.3750.98
799_G807_A1.3730.98
151_I160_K1.3720.98
122_N145_K1.3710.98
340_N343_T1.3660.98
602_R640_D1.3640.98
397_L400_R1.3580.98
262_I274_Q1.3550.97
717_S722_L1.3500.97
625_A631_Q1.3490.97
172_V395_I1.3480.97
122_N142_R1.3460.97
91_E442_V1.3450.97
287_G389_P1.3440.97
282_N414_S1.3410.97
54_A57_I1.3370.97
462_V612_I1.3360.97
335_K377_E1.3350.97
155_I187_N1.3310.97
311_D314_Q1.3310.97
666_A713_V1.3250.97
74_L232_T1.3220.97
531_H534_Q1.3220.97
356_V360_M1.3210.97
122_N141_D1.3110.97
588_T596_Q1.3090.97
290_T309_V1.3080.97
157_D302_F1.3080.97
12_L16_L1.3040.97
151_I155_I1.3030.97
144_M308_I1.3010.97
331_K378_S1.3000.97
502_I506_V1.2920.96
631_Q642_T1.2910.96
319_V322_E1.2900.96
54_A201_T1.2870.96
825_L830_L1.2870.96
725_E731_L1.2860.96
823_Q826_E1.2830.96
653_M657_G1.2830.96
35_R598_D1.2820.96
194_T402_K1.2800.96
783_D798_E1.2790.96
437_S442_V1.2770.96
790_N795_V1.2700.96
294_V301_T1.2680.96
354_L358_H1.2670.96
586_Y612_I1.2570.96
51_S201_T1.2560.96
230_S596_Q1.2560.96
301_T304_N1.2560.96
481_G485_L1.2550.96
211_A222_E1.2550.96
716_V721_A1.2530.96
766_L775_A1.2530.96
534_Q595_Q1.2490.95
344_F416_S1.2480.95
21_D466_K1.2470.95
750_E753_G1.2460.95
809_R819_R1.2440.95
664_I671_I1.2400.95
148_S163_Y1.2370.95
606_G614_Q1.2370.95
184_R187_N1.2320.95
719_F723_I1.2280.95
810_I814_I1.2270.95
163_Y168_V1.2190.95
226_S230_S1.2180.95
162_V193_V1.2160.94
826_E829_L1.2150.94
345_K433_T1.2130.94
262_I326_M1.2120.94
133_T137_E1.2100.94
692_R710_G1.2060.94
524_R534_Q1.2020.94
282_N322_E1.1980.94
775_A798_E1.1960.94
139_L144_M1.1950.94
482_L486_F1.1930.94
268_G338_L1.1910.94
145_K171_V1.1880.94
177_G180_N1.1880.94
154_E160_K1.1880.94
287_G410_R1.1870.94
12_L17_T1.1870.94
314_Q320_S1.1840.93
119_L122_N1.1800.93
520_N555_R1.1770.93
187_N485_L1.1760.93
637_N640_D1.1700.93
282_N412_N1.1660.93
226_S267_H1.1660.93
295_Q302_F1.1640.93
274_Q447_Q1.1640.93
157_D167_Y1.1590.92
569_T617_E1.1560.92
157_D296_I1.1550.92
95_E164_S1.1510.92
824_G829_L1.1490.92
656_A659_I1.1460.92
694_P713_V1.1430.92
823_Q829_L1.1390.92
690_A694_P1.1380.91
167_Y184_R1.1370.91
122_N171_V1.1370.91
162_V192_A1.1310.91
687_I690_A1.1310.91
693_G703_G1.1270.91
171_V184_R1.1200.91
694_P699_E1.1170.90
81_Y228_N1.1130.90
811_G819_R1.1130.90
151_I156_R1.1120.90
344_F763_L1.1080.90
506_V511_L1.1080.90
260_D263_V1.1070.90
751_I754_Q1.1050.90
610_D617_E1.1040.90
162_V190_T1.1040.90
617_E621_T1.1030.90
35_R602_R1.1030.90
751_I774_I1.1010.90
292_G304_N1.1000.90
555_R640_D1.1000.90
329_K332_K1.0960.89
151_I159_K1.0940.89
666_A722_L1.0910.89
511_L617_E1.0900.89
758_R775_A1.0860.89
224_N230_S1.0850.89
76_T221_N1.0820.89
51_S57_I1.0820.89
187_N192_A1.0800.88
809_R815_L1.0790.88
319_V373_R1.0770.88
324_G331_K1.0750.88
293_Q304_N1.0740.88
267_H440_N1.0730.88
344_F767_R1.0700.88
139_L143_Q1.0690.88
270_N349_K1.0670.88
35_R458_E1.0660.88
187_N725_E1.0640.87
73_V482_L1.0590.87
340_N344_F1.0590.87
410_R414_S1.0560.87
230_S599_R1.0540.87
688_P798_E1.0520.87
110_K194_T1.0520.87
689_T694_P1.0510.87
349_K424_E1.0510.87
328_N377_E1.0510.87
320_S385_T1.0480.86
760_L768_I1.0480.86
584_T592_L1.0470.86
293_Q410_R1.0470.86
742_L770_L1.0440.86
290_T410_R1.0400.86
716_V725_E1.0390.86
274_Q277_E1.0360.85
306_E410_R1.0350.85
292_G306_E1.0350.85
90_A447_Q1.0340.85
13_L20_S1.0330.85
74_L224_N1.0330.85
783_D827_R1.0330.85
76_T222_E1.0300.85
316_Y389_P1.0280.85
156_R397_L1.0270.85
693_G699_E1.0260.85
666_A714_R1.0250.85
302_F307_K1.0250.85
103_Q400_R1.0240.85
272_L422_I1.0230.84
288_N309_V1.0220.84
13_L19_G1.0210.84
649_K653_M1.0210.84
416_S756_L1.0200.84
766_L783_D1.0190.84
755_S766_L1.0140.84
270_N275_W1.0120.84
598_D601_V1.0120.84
73_V545_A1.0090.83
659_I686_L1.0080.83
303_Y306_E1.0070.83
687_I697_P1.0070.83
814_I817_I1.0060.83
39_T545_A1.0040.83
349_K437_S1.0010.83
569_T620_N1.0010.83
14_I19_G1.0000.83
819_R830_L1.0000.83
339_G343_T1.0000.83
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: (08Feb14)
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  
4ncoA30.48671000.471Contact Map
4jzzA10.3881000.595Contact Map
3lqaG10.33011000.66Contact Map
2bf1A10.33491000.66Contact Map
4i3sG10.19521000.837Contact Map
1qbzA30.14341000.867Contact Map
3tygA10.16751000.876Contact Map
1envA10.13611000.896Contact Map
3k9aA10.09881000.9Contact Map
4jpkA10.17351000.9Contact 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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