GREMLIN.BAKERLAB.org
Powered by OPENSEQ.org
Welcome: casp11@openseq.org My Submissions
T0840 1-540

ID: 1404413550 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 540 (519)
Sequences: 1015 (577.3)
Seq/Len: 1.956
Nf(neff/√len): 25.3

Jackhmmer Results: (2014_04_16)
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: 1.956).

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
94_G98_T4.5511.00
96_T101_L3.9011.00
96_T99_K3.4351.00
98_T101_L2.7561.00
94_G101_L2.5801.00
98_T103_L2.5661.00
94_G99_K2.5361.00
299_L326_G2.5151.00
395_S400_C2.4031.00
395_S398_T2.3941.00
98_T102_V2.3641.00
96_T114_G2.3461.00
394_L400_C2.3001.00
426_V442_M2.2371.00
96_T103_L2.1630.99
441_H522_G2.1020.99
101_L107_L2.0870.99
393_A398_T2.0510.99
96_T107_L2.0360.99
95_D98_T2.0350.99
394_L398_T2.0270.99
397_N400_C2.0220.99
96_T102_V2.0190.99
394_L397_N1.9900.99
94_G103_L1.9880.99
426_V450_L1.9700.99
96_T104_D1.8570.98
514_C523_C1.8550.98
403_F406_L1.8260.98
449_I487_L1.8250.98
256_T300_Q1.8030.97
98_T104_D1.8020.97
114_G121_C1.7710.97
514_C525_W1.7650.97
52_I57_H1.7590.97
200_K203_A1.7540.97
98_T107_L1.7540.97
243_Q257_R1.7530.97
442_M452_V1.7260.96
525_W530_C1.7250.96
99_K102_V1.6930.96
523_C530_C1.6810.96
288_G296_Y1.6710.95
519_H522_G1.6360.95
394_L399_S1.6200.94
448_R466_N1.6130.94
94_G97_D1.5900.94
49_F110_L1.5840.93
98_T105_P1.5810.93
432_T522_G1.5750.93
347_F410_S1.5640.93
54_N95_D1.5600.93
505_C514_C1.5390.92
101_L104_D1.5390.92
273_E277_D1.5360.92
50_V59_L1.5320.92
514_C530_C1.5170.91
521_M524_G1.4970.91
101_L105_P1.4970.91
199_L202_D1.4900.90
95_D101_L1.4900.90
392_E400_C1.4790.90
393_A396_P1.4660.89
96_T105_P1.4640.89
323_V346_A1.4620.89
42_D47_A1.4590.89
225_I243_Q1.4360.88
428_A443_G1.4320.88
241_T259_A1.4210.87
500_I522_G1.4190.87
284_L289_S1.4070.87
526_C536_C1.4060.87
505_C511_C1.3930.86
256_T299_L1.3880.86
272_R276_L1.3850.86
96_T106_A1.3820.85
415_D439_V1.3820.85
99_K104_D1.3700.85
46_S52_I1.3640.84
396_P399_S1.3610.84
215_V220_L1.3570.84
96_T100_V1.3520.84
417_F452_V1.3520.84
82_C85_C1.3450.83
94_G102_V1.3450.83
392_E396_P1.3450.83
401_R406_L1.3390.83
178_A522_G1.3300.82
56_L60_G1.3280.82
111_V154_D1.3270.82
95_D99_K1.3240.82
98_T114_G1.3230.82
505_C523_C1.3210.82
396_P400_C1.3180.81
93_P98_T1.3180.81
242_V256_T1.3140.81
210_F227_Y1.3060.81
393_A397_N1.3040.80
100_V426_V1.2900.79
101_L106_A1.2820.79
511_C514_C1.2770.79
93_P96_T1.2750.78
393_A400_C1.2730.78
273_E276_L1.2730.78
240_L258_L1.2680.78
210_F216_L1.2610.77
94_G107_L1.2580.77
97_D101_L1.2550.77
182_D187_G1.2550.77
104_D107_L1.2540.77
347_F375_G1.2540.77
82_C86_G1.2400.76
380_Q383_S1.2370.75
505_C525_W1.2320.75
42_D45_E1.2240.74
282_P287_R1.2240.74
395_S399_S1.2200.74
390_G394_L1.2180.74
94_G105_P1.2130.73
429_L440_A1.2090.73
115_S156_V1.2080.73
288_G294_Q1.2050.73
358_E361_E1.2010.72
522_G529_M1.1960.72
511_C523_C1.1910.71
268_L287_R1.1860.71
469_L491_S1.1840.71
437_V443_G1.1830.71
99_K107_L1.1830.71
392_E395_S1.1820.71
441_H451_Q1.1750.70
300_Q425_Q1.1750.70
510_T513_R1.1730.70
36_M52_I1.1720.70
377_D380_Q1.1710.70
112_S124_H1.1710.70
190_S239_F1.1710.70
508_F517_A1.1640.69
56_L124_H1.1640.69
99_K103_L1.1630.69
82_C88_G1.1610.69
391_L395_S1.1510.68
95_D107_L1.1470.67
298_V331_G1.1470.67
405_L408_S1.1460.67
258_L327_V1.1460.67
268_L280_F1.1440.67
120_R176_Y1.1420.67
447_G511_C1.1360.66
102_V213_L1.1330.66
402_H407_V1.1290.65
392_E398_T1.1220.65
227_Y243_Q1.1220.65
519_H523_C1.1140.64
162_T178_A1.1110.64
432_T500_I1.1080.63
382_P385_C1.1040.63
262_S265_E1.1030.63
94_G104_D1.0990.62
184_A191_P1.0970.62
428_A480_V1.0960.62
47_A58_V1.0960.62
227_Y241_T1.0940.62
311_L315_L1.0920.62
451_Q522_G1.0920.62
21_K26_S1.0900.61
99_K105_P1.0890.61
94_G106_A1.0830.61
451_Q521_M1.0820.61
59_L526_C1.0780.60
302_A324_L1.0770.60
390_G395_S1.0760.60
222_S227_Y1.0750.60
363_C368_V1.0740.60
216_L219_H1.0720.60
247_V251_P1.0700.59
197_R308_G1.0690.59
514_C519_H1.0680.59
518_W521_M1.0670.59
312_A315_L1.0640.59
439_V451_Q1.0630.59
283_K287_R1.0610.58
199_L488_L1.0590.58
103_L107_L1.0580.58
514_C521_M1.0570.58
93_P97_D1.0560.58
51_A265_E1.0560.58
119_G278_C1.0510.57
376_L379_F1.0510.57
505_C530_C1.0490.57
63_L71_T1.0490.57
98_T106_A1.0480.57
444_T450_L1.0470.57
150_D168_E1.0460.57
429_L442_M1.0450.57
265_E268_L1.0440.56
288_G522_G1.0420.56
58_V129_Q1.0390.56
79_C82_C1.0340.55
48_V495_V1.0340.55
60_G65_S1.0340.55
246_S251_P1.0340.55
495_V521_M1.0300.55
256_T298_V1.0290.55
258_L352_L1.0280.55
447_G451_Q1.0280.55
511_C525_W1.0270.55
210_F213_L1.0240.54
391_L394_L1.0240.54
451_Q487_L1.0230.54
237_V263_A1.0220.54
326_G440_A1.0190.54
404_P407_V1.0190.54
256_T413_R1.0180.54
165_T320_G1.0160.53
442_M450_L1.0160.53
99_K106_A1.0150.53
187_G190_S1.0130.53
240_L243_Q1.0120.53
477_Q492_G1.0120.53
504_G522_G1.0120.53
56_L130_G1.0100.53
416_L510_T1.0060.52
500_I521_M1.0050.52
94_G116_S1.0040.52
222_S225_I1.0040.52
178_A189_F1.0030.52
41_G45_E1.0030.52
401_R408_S1.0030.52
49_F58_V1.0010.52
378_F381_S1.0010.52
488_L497_Q1.0000.52
50_V110_L1.0000.52
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: (28Jun14)
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  
4fwwA10.93151000.216Contact Map
3al9A20.87781000.266Contact Map
3okyA10.87961000.28Contact Map
4gz8A20.89811000.288Contact Map
2uzxB20.80191000.29Contact Map
3ol2B10.8631000.303Contact Map
1olzA20.87781000.308Contact Map
3okyB10.88891000.324Contact Map
3nvqA20.84441000.345Contact Map
1q47A20.85741000.362Contact 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.

Page generated in 0.0332 seconds.