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4IGL_B

ID: 1380135944 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 690 (675)
Sequences: 935 (802.7)
Seq/Len: 1.385
Nf(neff/√len): 30.9

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: 1.385).

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
47_D51_F5.8301.00
94_D98_R4.9291.00
236_D240_A4.8311.00
284_S288_Q4.8201.00
73_D77_N4.5091.00
187_S191_K4.2921.00
257_D261_Q3.8141.00
481_W661_S3.6941.00
646_Y651_Y3.6621.00
637_K647_Y3.6441.00
587_Y598_V3.5541.00
665_A669_D3.3061.00
337_D341_N3.2931.00
465_T469_S3.2831.00
482_T486_E3.2051.00
516_K641_A2.9971.00
611_Y615_G2.7641.00
45_Q54_Q2.7421.00
234_R243_T2.7271.00
166_N170_Q2.7231.00
305_E310_R2.6171.00
637_K648_G2.5991.00
647_Y659_W2.5721.00
71_L80_Y2.5581.00
508_D512_Q2.4491.00
369_D373_Q2.4251.00
127_E134_R2.3700.99
613_Y679_N2.2070.99
635_S647_Y2.1220.99
480_I489_T2.1070.98
416_D420_N2.1000.98
638_E647_Y2.0960.98
599_D603_L2.0500.98
98_R133_G2.0000.98
367_R376_S1.9610.97
635_S659_W1.9570.97
680_N683_R1.9250.97
606_S647_Y1.9210.97
640_D651_Y1.9010.97
594_S647_Y1.8990.96
633_R645_Y1.8910.96
341_N680_N1.8860.96
341_N372_Y1.8780.96
686_D689_G1.8630.96
516_K651_Y1.8630.96
631_T638_E1.8280.95
186_V192_P1.8120.95
16_D20_L1.8100.95
467_S485_G1.7960.95
513_R516_K1.7840.95
637_K667_T1.7400.94
47_D53_A1.7370.93
469_S485_G1.7310.93
513_R651_Y1.7290.93
124_F135_P1.7160.93
637_K659_W1.7140.93
593_S610_Y1.6980.92
303_T313_G1.6930.92
593_S647_Y1.6870.92
490_V642_T1.6660.91
632_V638_E1.6610.91
481_W651_Y1.6530.91
635_S638_E1.6510.91
606_S638_E1.6470.91
463_L472_C1.6430.91
648_G651_Y1.6420.91
664_P690_M1.6180.90
640_D646_Y1.6180.90
593_S635_S1.6130.90
125_Q137_S1.6100.90
479_L487_L1.6080.89
437_L441_V1.5990.89
77_N97_G1.5960.89
255_A264_A1.5850.89
503_E518_S1.5790.88
594_S606_S1.5720.88
659_W673_L1.5620.88
516_K640_D1.5540.87
89_T102_A1.5520.87
647_Y667_T1.5460.87
659_W677_V1.5420.87
593_S606_S1.5400.87
658_R672_N1.5370.86
637_K645_Y1.5370.86
505_Y642_T1.5320.86
633_R647_Y1.5300.86
281_L289_K1.5290.86
593_S659_W1.5270.86
633_R638_E1.5120.85
593_S638_E1.5040.85
185_S194_S1.5030.85
441_V448_G1.4870.84
610_Y659_W1.4860.84
42_T58_P1.4640.83
660_L665_A1.4620.82
648_G659_W1.4540.82
516_K647_Y1.4520.82
665_A670_G1.4300.80
240_A260_G1.4290.80
284_S290_L1.4260.80
233_T241_V1.4220.80
91_V99_S1.4160.80
665_A673_L1.4160.80
335_E344_S1.4020.79
420_N658_R1.3950.78
649_F690_M1.3830.77
645_Y648_G1.3810.77
313_G331_D1.3750.77
57_D68_F1.3720.77
653_Q656_A1.3710.76
638_E645_Y1.3670.76
516_K646_Y1.3630.76
649_F659_W1.3570.75
261_Q283_Y1.3520.75
153_F156_A1.3500.75
635_S648_G1.3460.75
42_T94_D1.3450.74
637_K649_F1.3420.74
594_S637_K1.3410.74
513_R646_Y1.3410.74
584_R605_I1.3300.73
94_D133_G1.3280.73
513_R641_A1.3280.73
597_E648_G1.3270.73
83_S87_G1.3190.72
44_H52_L1.3180.72
96_E133_G1.3150.72
516_K637_K1.3100.72
659_W667_T1.3080.72
481_W487_L1.3040.71
220_W224_L1.3040.71
675_R679_N1.3030.71
11_S26_A1.2910.70
368_Y374_L1.2850.70
246_D252_Q1.2830.69
51_F76_G1.2810.69
644_L660_L1.2810.69
635_S645_Y1.2770.69
606_S635_S1.2760.69
666_G677_V1.2730.69
633_R651_Y1.2710.68
606_S633_R1.2700.68
42_T55_S1.2580.67
647_Y688_D1.2560.67
30_H34_P1.2520.67
637_K665_A1.2510.67
506_R515_L1.2490.66
586_S610_Y1.2410.66
606_S637_K1.2400.66
647_Y669_D1.2400.66
489_T502_S1.2380.65
508_D651_Y1.2370.65
284_S592_C1.2340.65
676_M687_P1.2180.64
94_D100_V1.2120.63
635_S676_M1.2100.63
669_D673_L1.2080.63
589_N593_S1.2030.62
637_K646_Y1.2020.62
606_S659_W1.1980.62
637_K641_A1.1930.61
135_P138_V1.1930.61
684_L688_D1.1910.61
103_M121_T1.1890.61
662_A673_L1.1880.61
482_T487_L1.1870.61
648_G662_A1.1860.61
641_A651_Y1.1850.60
632_V645_Y1.1840.60
256_F304_Y1.1820.60
613_Y637_K1.1810.60
21_S24_D1.1800.60
92_L101_I1.1780.60
639_R645_Y1.1760.60
305_E308_T1.1740.59
646_Y666_G1.1740.59
104_T111_N1.1700.59
593_S634_Y1.1700.59
85_D284_S1.1650.58
632_V647_Y1.1640.58
613_Y682_L1.1620.58
516_K642_T1.1590.58
594_S667_T1.1590.58
415_Y613_Y1.1590.58
512_Q647_Y1.1580.58
377_A612_P1.1530.57
282_T291_R1.1520.57
637_K670_G1.1500.57
676_M681_P1.1490.57
311_L334_Y1.1460.57
31_P34_P1.1450.57
81_T91_V1.1440.56
606_S645_Y1.1420.56
645_Y654_P1.1400.56
669_D672_N1.1390.56
594_S635_S1.1390.56
597_E608_E1.1370.56
15_F21_S1.1360.56
516_K633_R1.1350.56
86_A166_N1.1340.55
211_D214_G1.1320.55
55_S58_P1.1300.55
464_F468_G1.1240.54
511_S649_F1.1230.54
666_G669_D1.1230.54
633_R646_Y1.1190.54
647_Y651_Y1.1180.54
69_S82_Q1.1170.54
257_D263_S1.1160.54
630_K633_R1.1140.53
70_Y78_I1.1100.53
586_S598_V1.1060.53
594_S659_W1.1040.52
608_E633_R1.1040.52
45_Q53_A1.1040.52
608_E630_K1.1030.52
24_D28_R1.0990.52
82_Q88_N1.0970.52
13_T21_S1.0970.52
101_I121_T1.0950.51
104_T112_G1.0940.51
254_V262_L1.0920.51
612_P674_Y1.0910.51
57_D66_T1.0900.51
28_R32_D1.0870.51
591_T635_S1.0840.50
641_A647_Y1.0840.50
104_T119_A1.0830.50
314_I593_S1.0820.50
446_N658_R1.0790.50
608_E635_S1.0710.49
644_L664_P1.0670.49
285_A288_Q1.0660.49
663_D686_D1.0650.48
43_Y56_L1.0640.48
645_Y651_Y1.0630.48
602_G646_Y1.0610.48
635_S667_T1.0600.48
187_S193_L1.0600.48
646_Y667_T1.0600.48
411_R420_N1.0600.48
435_Y439_I1.0590.48
372_Y680_N1.0580.48
104_T469_S1.0570.48
344_S365_A1.0560.48
634_Y673_L1.0520.47
516_K638_E1.0490.47
339_V372_Y1.0440.46
505_Y591_T1.0430.46
479_L485_G1.0430.46
606_S670_G1.0420.46
466_A634_Y1.0410.46
664_P688_D1.0400.46
420_N447_R1.0380.46
594_S608_E1.0370.46
372_Y638_E1.0360.46
285_A417_S1.0350.45
68_F84_V1.0340.45
636_G666_G1.0330.45
611_Y648_G1.0320.45
330_Q377_A1.0310.45
219_A224_L1.0310.45
374_L377_A1.0290.45
632_V637_K1.0280.45
632_V680_N1.0270.45
584_R597_E1.0260.45
112_G119_A1.0250.44
241_V254_V1.0240.44
642_T651_Y1.0230.44
647_Y673_L1.0220.44
584_R633_R1.0210.44
648_G667_T1.0210.44
490_V503_E1.0200.44
80_Y88_N1.0190.44
606_S641_A1.0130.43
334_Y345_I1.0120.43
590_L637_K1.0090.43
608_E647_Y1.0080.43
439_I613_Y1.0070.43
51_F104_T1.0060.43
470_Q660_L1.0040.42
366_Y377_A1.0040.42
17_N24_D1.0020.42
594_S669_D1.0010.42
667_T670_G1.0010.42
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  
4iglB20.9711000.143Contact Map
4iglA20.488499.90.843Contact Map
4ghbA20.346496.70.952Contact Map
3hfqA20.426128.30.978Contact Map
2ymuA20.333326.40.978Contact Map
2ojhA10.346418.60.98Contact Map
4by2A30.17113.10.981Contact Map
1ri6A10.410.10.982Contact Map
3u4yA20.33337.90.983Contact Map
3fvzA10.19427.70.983Contact 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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