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BuA3

ID: 1515265656 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 793 (749)
Sequences: 1717 (1239.7)
Seq/Len: 2.292
Nf(neff/√len): 45.3

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: 2.292).

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
635_V668_I4.9601.00
632_E639_S4.6201.00
101_V143_I4.6201.00
339_F553_L4.3491.00
326_R357_E3.9761.00
249_L284_F3.8791.00
634_F639_S3.8231.00
11_T172_Y3.7911.00
44_Q55_E3.6101.00
93_A169_L3.5891.00
635_V640_Q3.5691.00
98_E105_R3.5641.00
10_L75_L3.5231.00
631_V670_A3.4581.00
478_T546_M3.4321.00
256_S300_E3.2521.00
270_I275_T3.2421.00
604_I624_V3.0231.00
101_V106_I2.9541.00
74_M140_K2.9341.00
731_I778_D2.9171.00
107_A118_A2.9161.00
293_G296_Y2.8861.00
221_S268_E2.8271.00
224_V282_F2.7801.00
281_H357_E2.7741.00
181_V218_K2.7411.00
227_P261_A2.7041.00
225_F266_V2.6961.00
630_E642_R2.6571.00
628_C672_G2.6311.00
268_E277_R2.5681.00
265_C282_F2.5431.00
84_G179_P2.5301.00
329_M360_L2.4911.00
222_L267_A2.4841.00
10_L73_T2.4681.00
223_R268_E2.4381.00
391_E436_L2.4191.00
323_E708_E2.3971.00
593_Q601_M2.3721.00
93_A147_C2.3251.00
741_L763_I2.3221.00
106_I123_A2.3181.00
642_R673_Y2.3071.00
332_I579_V2.2881.00
90_F145_I2.2831.00
86_T177_Y2.2441.00
267_A280_Q2.2421.00
712_V776_A2.2121.00
253_Q259_S2.2031.00
390_I433_A2.1971.00
258_H300_E2.1761.00
629_P674_D2.1631.00
15_E30_P2.1581.00
183_F205_I2.1561.00
15_E45_K2.1351.00
716_L756_A2.1241.00
253_Q261_A2.0941.00
98_E108_S2.0881.00
622_I668_I2.0690.99
638_V662_R2.0680.99
70_W144_A2.0500.99
634_F671_T2.0450.99
430_H434_H2.0450.99
740_A766_N2.0420.99
739_E765_V2.0140.99
7_K174_N2.0080.99
221_S270_I1.9780.99
626_S655_L1.9680.99
323_E330_Q1.9650.99
640_Q668_I1.9430.99
86_T124_V1.9360.99
110_V381_Q1.9340.99
677_L684_Q1.9180.99
85_R119_D1.9150.99
264_T279_T1.9070.99
266_V277_R1.9030.99
739_E773_V1.8960.99
53_N167_G1.8830.99
101_V120_I1.8760.99
763_I776_A1.8720.99
77_I124_V1.8650.99
257_P361_L1.8630.99
688_Q722_I1.8570.99
100_Y105_R1.8550.99
72_R144_A1.8540.99
632_E642_R1.8480.99
76_N140_K1.8460.98
714_A733_F1.8330.98
383_R428_E1.8320.98
184_E208_G1.8300.98
88_L120_I1.8280.98
387_T436_L1.8230.98
102_Y141_I1.8130.98
183_F269_L1.7960.98
667_K688_Q1.7920.98
106_I118_A1.7920.98
222_L245_Y1.7790.98
734_G777_S1.7770.98
332_I337_A1.7760.98
311_E318_A1.7590.98
361_L400_I1.7540.98
222_L265_C1.7470.98
699_L715_E1.7380.98
632_E641_G1.7350.97
83_N180_A1.7330.97
697_R715_E1.7310.97
430_H442_T1.7310.97
331_Q579_V1.7290.97
593_Q599_K1.7200.97
181_V209_G1.7160.97
387_T435_R1.7110.97
626_S631_V1.7000.97
704_A708_E1.6870.97
777_S787_L1.6860.97
268_E275_T1.6850.97
30_P72_R1.6840.97
5_D178_T1.6780.97
88_L143_I1.6630.97
340_I360_L1.6610.97
554_F578_V1.6550.96
585_P589_Y1.6540.96
639_S642_R1.6440.96
715_E723_R1.6380.96
29_R32_T1.6280.96
669_T684_Q1.6220.96
293_G301_R1.6220.96
205_I245_Y1.6180.96
43_W72_R1.6160.96
188_I280_Q1.6150.96
84_G177_Y1.6140.96
266_V279_T1.6110.96
481_I548_R1.6050.96
109_H114_D1.5770.95
323_E326_R1.5620.95
88_L118_A1.5590.95
290_E293_G1.5500.94
401_L456_V1.5430.94
330_Q334_E1.5370.94
52_F69_G1.5370.94
188_I282_F1.5360.94
288_R296_Y1.5300.94
695_P717_I1.5200.94
89_E117_K1.5190.93
364_E389_M1.5140.93
262_L281_H1.5120.93
183_F267_A1.4940.93
621_E658_N1.4850.92
93_A97_T1.4800.92
72_R142_P1.4700.92
12_E769_H1.4610.92
352_L396_H1.4590.92
307_T557_F1.4560.91
427_G431_D1.4550.91
257_P302_L1.4520.91
43_W70_W1.4450.91
667_K686_E1.4430.91
304_L400_I1.4370.91
641_G657_W1.4360.91
172_Y350_I1.4340.91
46_V55_E1.4330.91
101_V123_A1.4240.90
371_G379_K1.4140.90
220_F267_A1.4130.90
183_F278_T1.3990.89
233_N247_I1.3960.89
99_V145_I1.3960.89
224_V265_C1.3920.89
89_E174_N1.3920.89
320_L325_M1.3840.88
309_R332_I1.3740.88
28_M144_A1.3700.88
90_F93_A1.3690.88
99_V116_W1.3620.87
297_L361_L1.3590.87
20_D146_R1.3520.87
307_T337_A1.3480.87
68_P146_R1.3460.87
104_T123_A1.3440.86
501_H530_S1.3420.86
226_S261_A1.3410.86
223_R266_V1.3390.86
204_D244_S1.3350.86
70_W146_R1.3330.86
730_F755_Q1.3280.86
106_I143_I1.3270.85
289_F550_T1.3200.85
5_D276_L1.3200.85
387_T432_L1.3140.85
349_G353_R1.3140.85
489_H492_W1.3140.85
191_T202_S1.3110.85
289_F400_I1.3090.84
322_E354_L1.3080.84
366_I389_M1.3080.84
639_S657_W1.3010.84
313_H328_E1.2980.84
309_R328_E1.2890.83
28_M72_R1.2870.83
290_E296_Y1.2850.83
206_A391_E1.2810.83
630_E644_K1.2790.82
313_H327_T1.2680.82
733_F778_D1.2670.82
188_I265_C1.2660.82
329_M354_L1.2660.82
8_Q177_Y1.2630.81
204_D242_I1.2620.81
331_Q558_K1.2570.81
181_V269_L1.2540.81
304_L363_W1.2540.81
30_P144_A1.2520.81
97_T118_A1.2510.81
634_F641_G1.2460.80
316_V324_M1.2390.80
296_Y301_R1.2370.80
74_M142_P1.2370.80
705_Q708_E1.2350.79
305_R598_S1.2320.79
390_I436_L1.2320.79
323_E702_Q1.2290.79
590_Y593_Q1.2280.79
98_E146_R1.2240.79
224_V249_L1.2220.78
50_H71_Y1.2220.78
589_Y593_Q1.2200.78
738_S768_Q1.2190.78
257_P297_L1.2170.78
747_T750_G1.2160.78
690_R722_I1.2150.78
600_P627_N1.2110.77
321_T324_M1.2060.77
386_L390_I1.2040.77
172_Y348_S1.2010.77
109_H388_N1.2000.77
302_L338_N1.1960.76
105_R108_S1.1950.76
356_D396_H1.1930.76
459_P480_G1.1920.76
342_L347_Q1.1900.76
364_E399_V1.1890.76
696_S716_L1.1850.75
85_R180_A1.1810.75
634_F640_Q1.1800.75
288_R299_G1.1790.75
114_D346_Q1.1780.75
715_E760_R1.1770.75
634_F669_T1.1750.74
47_T73_T1.1740.74
68_P148_D1.1730.74
352_L364_E1.1720.74
264_T281_H1.1720.74
729_Q780_K1.1680.74
87_C119_D1.1680.74
355_C362_V1.1680.74
207_F269_L1.1660.74
442_T454_V1.1660.74
624_V657_W1.1640.73
191_T199_G1.1640.73
90_F116_W1.1620.73
87_C117_K1.1580.73
335_M589_Y1.1550.73
322_E353_R1.1540.73
289_F295_F1.1520.72
775_S789_S1.1520.72
386_L429_L1.1520.72
602_L631_V1.1510.72
205_I222_L1.1510.72
170_Y311_E1.1490.72
295_F400_I1.1470.72
125_E139_G1.1440.72
729_Q756_A1.1430.72
205_I267_A1.1430.72
93_A99_V1.1430.72
734_G779_S1.1420.71
91_E172_Y1.1400.71
640_Q643_K1.1380.71
622_I659_V1.1370.71
602_L670_A1.1360.71
733_F741_L1.1350.71
258_H333_K1.1340.71
540_L591_V1.1310.70
700_L710_I1.1310.70
541_K545_T1.1250.70
631_V657_W1.1240.70
671_T677_L1.1220.69
13_H45_K1.1220.69
256_S259_S1.1160.69
716_L783_L1.1160.69
363_W401_L1.1160.69
9_R174_N1.1120.68
696_S731_I1.1120.68
330_Q358_L1.1110.68
115_E349_G1.1090.68
87_C182_H1.1070.68
226_S232_V1.1060.68
202_S246_Q1.1050.68
9_R172_Y1.1040.68
632_E640_Q1.1000.67
109_H381_Q1.0980.67
256_S333_K1.0980.67
295_F302_L1.0900.66
172_Y322_E1.0880.66
66_Q167_G1.0850.66
89_E176_V1.0830.66
11_T48_L1.0820.65
697_R717_I1.0790.65
11_T73_T1.0750.65
773_V776_A1.0730.64
431_D434_H1.0730.64
773_V778_D1.0720.64
326_R330_Q1.0720.64
289_F401_L1.0710.64
709_T742_L1.0700.64
231_E234_S1.0700.64
622_I633_L1.0680.64
10_L48_L1.0670.64
669_T686_E1.0670.64
332_I557_F1.0660.64
30_P43_W1.0660.64
632_E673_Y1.0650.64
287_F295_F1.0630.63
383_R387_T1.0620.63
325_M354_L1.0620.63
161_S165_L1.0600.63
352_L393_H1.0560.63
574_N581_R1.0480.62
325_M348_S1.0480.62
347_Q352_L1.0410.61
432_L435_R1.0400.61
326_R354_L1.0390.61
640_Q657_W1.0380.61
18_R65_Y1.0370.61
324_M327_T1.0370.61
75_L88_L1.0360.60
706_D769_H1.0360.60
731_I761_A1.0320.60
87_C178_T1.0250.59
147_C169_L1.0240.59
404_L454_V1.0210.59
202_S244_S1.0180.58
602_L679_L1.0180.58
91_E350_I1.0180.58
206_A242_I1.0110.58
688_Q720_N1.0080.57
119_D124_V1.0080.57
735_C741_L1.0070.57
477_E489_H1.0070.57
602_L672_G1.0070.57
778_D786_A1.0060.57
706_D767_K1.0050.57
584_T762_S1.0050.57
601_M672_G1.0040.57
323_E701_T1.0000.56
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  
4cu7A10.92561000.319Contact Map
3gm8A10.90161000.32Contact Map
4ypjA201000.32Contact Map
3fn9A40.81081000.418Contact Map
3cmgA10.7971000.422Contact Map
1yq2A60.81971000.567Contact Map
1jz7A40.83231000.576Contact Map
3bgaA20.82851000.585Contact Map
3obaA40.83861000.585Contact Map
4jklA20.67841000.591Contact 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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