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MalT180717

ID: 1501589650 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 901 (880)
Sequences: 4948 (3733.9)
Seq/Len: 5.623
Nf(neff/√len): 125.9

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: 5.623).

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
665_D668_A7.4591.00
585_R588_E7.2921.00
624_D627_N6.1711.00
344_H363_H6.0681.00
49_I158_L5.5141.00
543_F546_T5.3511.00
703_E706_P4.6101.00
464_N467_E4.4871.00
191_A222_L4.2551.00
424_R427_E3.8371.00
503_E506_R3.6391.00
590_E622_R3.4991.00
629_R663_T3.3021.00
187_T190_E3.2801.00
130_Y157_V3.2611.00
851_Y859_E3.1811.00
743_R746_D3.1311.00
871_I875_Y3.1241.00
839_R842_Q3.1161.00
548_W552_E3.0101.00
277_L347_A2.9701.00
847_I856_I2.9441.00
548_W583_W2.8701.00
39_S43_Y2.8391.00
348_A364_A2.8001.00
49_I126_V2.7711.00
580_L588_E2.7581.00
264_D300_E2.7531.00
53_A126_V2.7471.00
274_S320_Y2.7261.00
552_E576_R2.7111.00
195_F226_A2.7001.00
188_H209_S2.6661.00
27_S55_G2.6111.00
37_I49_I2.5881.00
841_W845_G2.5461.00
267_T300_E2.5301.00
535_S551_Q2.5091.00
191_A212_C2.4821.00
26_L52_W2.4701.00
50_S61_W2.4141.00
47_T51_Q2.4041.00
128_D158_L2.3901.00
264_D267_T2.3771.00
840_E877_K2.3301.00
58_D121_S2.3291.00
352_M372_M2.3131.00
712_E734_L2.2811.00
577_A593_A2.2731.00
580_L592_S2.2711.00
580_L585_R2.2591.00
41_A160_R2.2501.00
619_S627_N2.2271.00
16_T47_T2.2241.00
22_L48_L2.2221.00
325_G329_R2.1501.00
211_I222_L2.1401.00
660_W665_D2.1191.00
844_L874_L2.1061.00
51_Q54_A2.0411.00
587_D622_R2.0221.00
252_S330_Q2.0131.00
590_E615_L1.9911.00
865_T872_R1.9871.00
190_E193_Q1.9641.00
268_R272_L1.9291.00
224_L259_V1.9261.00
545_Q583_W1.9191.00
26_L35_A1.9171.00
660_W668_A1.9001.00
627_N631_Q1.8981.00
594_R615_L1.8941.00
275_A329_R1.8861.00
559_N595_S1.8801.00
576_R592_S1.8761.00
193_Q197_C1.8751.00
538_L543_F1.8711.00
847_I871_I1.8641.00
657_V673_L1.8521.00
698_Q703_E1.8451.00
619_S631_Q1.8431.00
862_V867_I1.8371.00
854_E858_G1.8261.00
538_L546_T1.8091.00
272_L339_E1.8071.00
593_A618_C1.8011.00
719_R753_D1.7961.00
495_G511_M1.7761.00
548_W576_R1.7521.00
345_R349_E1.7481.00
288_V350_S1.7391.00
271_L328_L1.7351.00
46_T50_S1.7301.00
508_L512_Q1.7291.00
192_K208_S1.7281.00
728_N754_A1.7221.00
267_T301_I1.7221.00
573_V595_S1.7031.00
345_R369_D1.6971.00
130_Y139_H1.6941.00
269_H339_E1.6921.00
875_Y880_V1.6911.00
125_L155_L1.6821.00
171_R178_E1.6821.00
19_R22_L1.6721.00
844_L886_A1.6701.00
276_I343_I1.6641.00
188_H212_C1.6571.00
204_E207_E1.6551.00
209_S213_D1.6541.00
265_L268_R1.6531.00
735_N754_A1.6521.00
548_W580_L1.6521.00
849_S859_E1.6471.00
844_L890_A1.6320.99
415_Q419_M1.6310.99
881_A885_D1.6290.99
619_S624_D1.6280.99
37_I158_L1.6050.99
618_C622_R1.6030.99
847_I853_N1.5970.99
625_L663_T1.5950.99
627_N630_S1.5920.99
271_L301_I1.5910.99
590_E594_R1.5870.99
53_A124_Y1.5770.99
276_I329_R1.5740.99
697_A701_L1.5660.99
735_N751_L1.5620.99
708_E712_E1.5600.99
547_A579_L1.5580.99
43_Y219_A1.5520.99
329_R340_L1.5460.99
49_I53_A1.5450.99
270_F297_R1.5440.99
698_Q706_P1.5410.99
577_A589_A1.5280.99
589_A618_C1.5180.99
731_L750_V1.5160.99
869_T873_N1.5160.99
855_Q858_G1.5120.99
186_F194_F1.5120.99
731_L753_D1.5090.99
75_A78_L1.5020.99
284_L350_S1.4890.99
429_N433_A1.4880.99
715_N734_L1.4840.99
852_S855_Q1.4780.99
287_R353_A1.4730.99
708_E741_A1.4700.99
548_W579_L1.4700.99
748_Q752_L1.4610.99
512_Q534_Q1.4590.99
854_E864_A1.4580.99
573_V592_S1.4480.98
389_E392_L1.4470.98
576_R580_L1.4460.98
27_S52_W1.4450.98
276_I347_A1.4440.98
188_H192_K1.4400.98
149_Q153_L1.4350.98
51_Q55_G1.4210.98
307_F324_F1.4200.98
52_W156_V1.4200.98
667_A701_L1.4160.98
36_L159_S1.4150.98
279_S317_W1.4150.98
593_A615_L1.4130.98
734_L750_V1.4130.98
708_E734_L1.4080.98
738_Y750_V1.4070.98
660_W672_W1.4010.98
58_D123_L1.3980.98
615_L619_S1.3970.98
746_D749_R1.3920.98
128_D131_H1.3810.98
590_E618_C1.3810.98
847_I874_L1.3680.98
49_I156_V1.3680.98
159_S163_P1.3680.98
20_E24_A1.3620.97
873_N876_Q1.3600.97
588_E591_A1.3590.97
40_P43_Y1.3540.97
854_E869_T1.3510.97
844_L847_I1.3510.97
843_V870_H1.3500.97
160_R321_H1.3500.97
35_A154_T1.3460.97
332_C343_I1.3440.97
880_V889_H1.3370.97
629_R633_N1.3370.97
419_M431_L1.3350.97
356_F359_E1.3340.97
416_A432_L1.3320.97
847_I872_R1.3300.97
342_E346_A1.3300.97
734_L738_Y1.3290.97
210_R213_D1.3260.97
419_M427_E1.3240.97
653_N672_W1.3210.97
844_L880_V1.3100.97
866_T877_K1.3080.97
130_Y133_I1.3030.96
594_R598_E1.3010.96
41_A323_L1.3000.96
62_Y77_Y1.2980.96
853_N875_Y1.2980.96
555_F576_R1.2970.96
546_T550_T1.2960.96
738_Y746_D1.2900.96
263_V267_T1.2870.96
731_L757_L1.2830.96
671_N675_H1.2820.96
552_E556_Q1.2810.96
210_R214_D1.2780.96
670_A674_R1.2780.96
889_H893_L1.2780.96
21_R25_K1.2740.96
853_N868_K1.2740.96
870_H873_N1.2740.96
746_D750_V1.2680.96
322_P325_G1.2670.96
277_L288_V1.2640.96
866_T870_H1.2640.96
531_L557_L1.2620.96
506_R509_A1.2600.95
53_A59_I1.2590.95
865_T869_T1.2540.95
579_L583_W1.2510.95
853_N856_I1.2460.95
360_A364_A1.2460.95
626_D663_T1.2440.95
416_A435_A1.2440.95
20_E190_E1.2430.95
719_R727_L1.2430.95
46_T128_D1.2420.95
851_Y855_Q1.2420.95
224_L227_L1.2360.95
220_T321_H1.2360.95
694_I710_V1.2360.95
837_T877_K1.2350.95
34_L146_I1.2270.95
511_M534_Q1.2230.94
25_K183_Q1.2220.94
362_H366_A1.2200.94
882_H885_D1.2200.94
590_E619_S1.2190.94
144_F148_H1.2170.94
16_T19_R1.2160.94
216_S322_P1.2130.94
853_N883_R1.2090.94
18_V23_L1.2080.94
636_E656_R1.2080.94
196_D208_S1.2070.94
531_L553_K1.2060.94
556_Q560_E1.2060.94
16_T51_Q1.2030.94
711_L730_N1.2000.94
695_A707_A1.1990.94
552_E580_L1.1990.94
192_K205_A1.1970.94
756_K759_N1.1960.94
508_L534_Q1.1960.94
449_A475_A1.1910.93
47_T223_Q1.1900.93
846_L859_E1.1900.93
24_A28_G1.1870.93
670_A701_L1.1850.93
270_F285_I1.1850.93
364_A376_I1.1820.93
306_L324_F1.1770.93
546_T549_E1.1760.93
123_L153_L1.1750.93
885_D888_Q1.1710.93
519_R553_K1.1690.92
57_N124_Y1.1670.92
666_K697_A1.1660.92
661_Q697_A1.1650.92
580_L583_W1.1630.92
880_V886_A1.1600.92
290_G346_A1.1600.92
473_K477_E1.1590.92
573_V599_V1.1580.92
847_I865_T1.1510.92
549_E553_K1.1450.91
47_T50_S1.1430.91
41_A321_H1.1420.91
272_L332_C1.1390.91
467_E470_R1.1380.91
43_Y218_W1.1350.91
869_T872_R1.1340.91
695_A714_L1.1310.91
843_V860_L1.1270.91
126_V156_V1.1250.90
134_T138_I1.1220.90
273_K347_A1.1190.90
850_G853_N1.1180.90
52_W124_Y1.1170.90
308_L319_C1.1160.90
498_L506_R1.1150.90
378_L410_Q1.1130.90
474_L477_E1.1120.90
866_T878_L1.1120.90
831_I835_P1.1110.90
322_P326_N1.1090.90
24_A27_S1.1090.90
670_A697_A1.1080.90
257_D331_R1.1060.89
198_R223_Q1.1060.89
792_Q796_Q1.1030.89
280_M318_F1.1030.89
865_T868_K1.1000.89
515_E534_Q1.0990.89
550_T553_K1.0980.89
508_L538_L1.0970.89
141_S145_F1.0960.89
257_D327_F1.0950.89
160_R323_L1.0950.89
333_Q339_E1.0940.89
749_R753_D1.0930.89
188_H213_D1.0900.89
182_Q185_A1.0900.89
127_I157_V1.0880.88
633_N656_R1.0870.88
37_I179_I1.0870.88
513_Q517_M1.0870.88
750_V753_D1.0850.88
872_R876_Q1.0850.88
837_T873_N1.0840.88
272_L331_R1.0840.88
509_A513_Q1.0830.88
862_V870_H1.0800.88
586_L618_C1.0780.88
473_K494_L1.0760.88
299_E303_R1.0760.88
195_F208_S1.0750.88
712_E716_E1.0750.88
215_V225_I1.0750.88
695_A711_L1.0740.88
581_W586_L1.0730.87
573_V596_G1.0700.87
694_I698_Q1.0700.87
738_Y743_R1.0670.87
850_G884_Q1.0660.87
577_A592_S1.0630.87
300_E304_Q1.0620.87
38_T159_S1.0610.87
469_E473_K1.0610.87
889_H892_Q1.0610.87
753_D757_L1.0600.87
394_E398_K1.0590.87
42_G45_K1.0580.86
45_K160_R1.0580.86
552_E588_E1.0570.86
548_W585_R1.0570.86
871_I874_L1.0560.86
40_P185_A1.0550.86
592_S595_S1.0520.86
544_L579_L1.0520.86
472_A493_V1.0500.86
358_S383_S1.0470.86
62_Y127_I1.0460.86
597_I615_L1.0460.86
340_L344_H1.0450.86
279_S359_E1.0430.85
298_L302_E1.0430.85
360_A376_I1.0410.85
37_I156_V1.0410.85
339_E342_E1.0390.85
551_Q575_I1.0380.85
129_D132_L1.0380.85
270_F294_G1.0360.85
393_L396_S1.0330.85
796_Q799_L1.0320.85
656_R672_W1.0320.85
765_S769_I1.0310.84
538_L550_T1.0290.84
224_L228_S1.0280.84
557_L560_E1.0190.84
555_F572_L1.0190.84
868_K872_R1.0180.83
593_A611_C1.0180.83
77_Y133_I1.0170.83
577_A614_M1.0160.83
629_R656_R1.0160.83
192_K196_D1.0120.83
329_R344_H1.0110.83
555_F569_H1.0110.83
133_I139_H1.0070.83
498_L510_L1.0060.82
25_K29_A1.0060.82
214_D326_N1.0050.82
61_W126_V1.0030.82
394_E415_Q1.0030.82
875_Y882_H1.0020.82
375_D379_N1.0020.82
668_A672_W1.0020.82
274_S327_F1.0010.82
222_L416_A1.0010.82
559_N569_H1.0010.82
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  
1z6tA40.4751000.721Contact Map
2a5yB20.38291000.767Contact Map
1hz4A10.40621000.777Contact Map
2qenA10.34521000.801Contact Map
3sf4A30.375199.90.812Contact Map
2fnaA20.340799.90.816Contact Map
1w3bA20.428499.90.821Contact Map
4ui9O1099.90.823Contact Map
3ro2A10.34399.90.823Contact Map
4a1sA20.344199.90.824Contact 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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