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labeeba

ID: 1490313415 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 474 (420)
Sequences: 459 (251.9)
Seq/Len: 1.093
Nf(neff/√len): 12.3

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: 1.093).

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
435_C438_N3.6561.00
435_C440_E3.3161.00
434_Y438_N3.2661.00
434_Y440_E3.2421.00
436_Y440_E2.6701.00
438_N441_V2.5821.00
437_C440_E2.3920.99
435_C439_G2.2580.99
434_Y437_C2.2220.98
356_N359_R2.2100.98
435_C441_V2.2030.98
434_Y441_V2.1580.98
90_D94_C2.0790.97
85_C94_C1.9820.96
434_Y439_G1.9600.96
98_G104_L1.8630.94
436_Y441_V1.8520.93
85_C95_W1.8110.92
185_I203_M1.8010.92
385_S419_E1.7240.90
85_C90_D1.7020.89
173_G181_L1.6990.89
87_P97_R1.6900.89
266_Y278_E1.6820.88
319_R325_A1.6730.88
90_D109_P1.6600.87
94_C109_P1.6550.87
436_Y439_G1.6210.86
214_V218_I1.5540.82
188_I311_F1.5380.81
85_C109_P1.5290.81
90_D95_W1.5280.81
258_K324_D1.5190.80
195_H199_N1.4950.79
278_E282_L1.4770.78
95_W108_C1.4580.76
294_T297_L1.4580.76
275_I286_I1.4570.76
208_S271_N1.4360.75
199_N212_R1.4270.74
213_A219_K1.4250.74
196_C209_F1.4120.73
180_S428_F1.4050.72
257_C278_E1.4050.72
427_G430_V1.4000.72
271_N274_W1.3960.72
180_S415_R1.3900.71
95_W109_P1.3880.71
279_G283_H1.3800.70
93_I106_V1.3790.70
171_T220_D1.3690.70
384_K454_L1.3670.69
212_R219_K1.3610.69
354_F382_L1.3580.69
197_T201_I1.3570.69
279_G282_L1.3570.69
430_V438_N1.3520.68
278_E305_W1.3270.66
437_C441_V1.3230.66
198_R202_H1.3200.66
339_Y343_I1.3180.65
274_W278_E1.3170.65
74_I87_P1.3130.65
141_W147_C1.3050.64
351_F416_M1.3010.64
270_T300_F1.2910.63
101_G217_F1.2900.63
430_V440_E1.2890.63
174_Y184_A1.2820.62
199_N220_D1.2800.62
271_N396_H1.2780.62
444_E449_W1.2770.62
85_C96_P1.2660.61
275_I354_F1.2660.61
350_N364_K1.2640.61
273_Y303_T1.2570.60
218_I226_R1.2540.60
193_R354_F1.2520.59
276_L285_L1.2520.59
264_F393_F1.2470.59
382_L420_L1.2450.59
389_L394_G1.2440.59
280_L290_F1.2420.59
199_N219_K1.2400.58
337_W344_L1.2390.58
387_L391_L1.2390.58
199_N315_W1.2310.58
123_R212_R1.2260.57
399_V414_I1.2240.57
173_G177_S1.2230.57
385_S416_M1.2220.57
427_G438_N1.2190.56
94_C108_C1.2170.56
122_F146_E1.2120.56
173_G187_I1.2040.55
302_L349_L1.1930.54
188_I432_I1.1870.53
281_Y304_G1.1870.53
415_R420_L1.1860.53
260_I292_S1.1840.53
382_L385_S1.1750.52
386_T430_V1.1750.52
394_G426_Q1.1730.52
53_T56_M1.1690.52
210_M431_S1.1680.52
328_W342_P1.1680.52
125_C147_C1.1670.52
274_W282_L1.1670.52
89_W92_L1.1660.51
295_K398_I1.1650.51
266_Y282_L1.1620.51
277_V303_T1.1610.51
447_K450_T1.1600.51
266_Y305_W1.1570.51
266_Y274_W1.1550.50
199_N213_A1.1550.50
257_C281_Y1.1480.50
278_E304_G1.1470.50
214_V428_F1.1460.50
263_M428_F1.1450.49
382_L400_F1.1430.49
208_S319_R1.1420.49
90_D96_P1.1390.49
85_C108_C1.1380.49
90_D108_C1.1360.49
354_F444_E1.1330.48
194_L357_T1.1330.48
383_A390_I1.1320.48
188_I347_I1.1310.48
382_L444_E1.1290.48
285_L385_S1.1270.48
265_I270_T1.1220.47
200_Y220_D1.1210.47
199_N209_F1.1200.47
428_F432_I1.1180.47
283_H288_V1.1180.47
277_V382_L1.1140.46
197_T200_Y1.1110.46
44_Y47_D1.1080.46
353_L393_F1.1060.46
194_L266_Y1.1050.46
173_G184_A1.1000.45
354_F385_S1.0980.45
123_R380_R1.0970.45
275_I385_S1.0960.45
276_L390_I1.0950.45
257_C266_Y1.0910.44
388_V429_F1.0900.44
173_G191_F1.0870.44
427_G440_E1.0860.44
213_A220_D1.0850.44
212_R315_W1.0850.44
177_S181_L1.0820.43
275_I287_F1.0800.43
367_E433_I1.0770.43
96_P109_P1.0740.43
170_Y174_Y1.0730.43
183_V207_V1.0710.42
385_S444_E1.0710.42
123_R312_V1.0680.42
214_V446_K1.0680.42
184_A199_N1.0630.42
421_F429_F1.0600.41
389_L426_Q1.0590.41
279_G300_F1.0580.41
192_R286_I1.0570.41
327_C342_P1.0550.41
271_N305_W1.0540.41
355_L366_W1.0530.41
202_H205_L1.0520.41
195_H303_T1.0510.41
170_Y337_W1.0510.41
275_I360_V1.0490.40
278_E281_Y1.0490.40
217_F419_E1.0480.40
261_V269_A1.0470.40
337_W341_A1.0460.40
354_F396_H1.0460.40
177_S191_F1.0430.40
220_D354_F1.0430.40
415_R418_C1.0420.40
376_R380_R1.0420.40
271_N278_E1.0380.39
55_T62_L1.0360.39
279_G304_G1.0350.39
193_R199_N1.0350.39
131_W143_N1.0340.39
390_I405_H1.0320.39
198_R205_L1.0310.39
85_C89_W1.0300.39
266_Y357_T1.0290.39
188_I220_D1.0290.39
101_G326_R1.0280.39
354_F383_A1.0280.39
184_A193_R1.0260.38
427_G435_C1.0250.38
178_F208_S1.0240.38
264_F303_T1.0240.38
141_W360_V1.0220.38
59_Q62_L1.0210.38
171_T188_I1.0190.38
370_A376_R1.0180.38
383_A418_C1.0180.38
450_T453_N1.0160.37
96_P319_R1.0150.37
291_F300_F1.0150.37
228_G310_V1.0130.37
389_L392_V1.0130.37
257_C272_Y1.0120.37
209_F212_R1.0080.37
181_L361_L1.0060.37
365_I431_S1.0060.37
169_M414_I1.0010.36
184_A212_R1.0000.36
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  
4k5yA30.53161000.652Contact Map
4l6rA10.80591000.706Contact Map
3c5tA10.21311000.846Contact Map
4ersA10.19831000.852Contact Map
2qkhA10.19411000.852Contact Map
4rwfA101000.853Contact Map
4jkvA20.791199.90.854Contact Map
4hj0A20.187899.90.856Contact Map
4qinA10.683599.90.864Contact Map
3n94A10.299699.90.865Contact 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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