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T0793

ID: 1401132758 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 595 (545)
Sequences: 593 (501.5)
Seq/Len: 1.088
Nf(neff/√len): 21.5

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: 1.088).

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
241_W307_S3.0421.00
247_A287_Q3.0011.00
180_A208_F2.9071.00
213_S395_R2.8331.00
168_I355_V2.8271.00
206_F403_I2.8241.00
220_A308_T2.7371.00
246_N289_S2.6781.00
47_S60_N2.6261.00
227_A356_L2.6091.00
257_G302_G2.4450.99
207_S309_S2.4340.99
162_N351_N2.4160.99
179_L403_I2.3410.99
212_S321_D2.3160.99
217_S308_T2.3080.99
204_I399_R2.2840.99
160_F354_H2.2640.99
252_L260_I2.2600.99
182_I407_A2.2310.98
125_Y258_I2.2190.98
246_N288_R2.2000.98
362_Y413_V2.1440.98
411_G415_S2.1300.98
351_N354_H2.0570.97
185_I355_V2.0320.97
171_V181_V2.0040.96
249_E285_G1.9940.96
310_E322_G1.9910.96
278_Y310_E1.9620.96
278_Y322_G1.9490.95
222_L344_I1.9240.95
160_F358_L1.8930.94
176_L426_Y1.8840.94
220_A306_I1.8800.94
208_F306_I1.8740.94
289_S293_G1.8710.94
181_V185_I1.8190.93
411_G414_L1.8120.92
37_A40_I1.7850.92
177_L219_A1.7720.91
185_I359_V1.7640.91
452_V541_F1.7280.90
184_G226_V1.7180.90
328_I396_M1.6640.87
212_S310_E1.6610.87
452_V486_I1.6020.85
491_F495_L1.5950.84
346_K375_Y1.5830.84
522_R529_V1.5700.83
266_S320_N1.5670.83
187_A303_T1.5520.82
224_V261_V1.5330.81
207_S307_S1.5140.80
444_A506_V1.5130.80
246_N250_G1.4910.78
158_G353_G1.4910.78
358_L361_K1.4890.78
531_D534_G1.4700.77
459_F473_G1.4690.77
408_K419_D1.4610.76
220_A243_A1.4540.76
249_E288_R1.4500.76
221_A345_K1.4400.75
357_P364_I1.4310.74
278_Y301_W1.4270.74
451_F472_Y1.4210.73
342_D345_K1.4200.73
321_D392_T1.4170.73
250_G289_S1.4090.73
521_G528_S1.4070.72
486_I541_F1.3980.72
163_W264_E1.3980.72
212_S264_E1.3840.71
163_W278_Y1.3720.70
417_D420_I1.3700.70
392_T440_L1.3690.69
207_S264_E1.3680.69
179_L206_F1.3610.69
242_N286_R1.3580.69
338_A342_D1.3550.68
158_G278_Y1.3490.68
445_I515_F1.3430.67
226_V356_L1.3370.67
215_G264_E1.3360.67
161_D164_F1.3310.66
54_E60_N1.3280.66
176_L332_E1.3210.65
55_K407_A1.3180.65
460_S471_N1.2950.63
243_A248_L1.2890.63
225_S353_G1.2880.63
225_S278_Y1.2880.63
404_T408_K1.2850.62
175_L426_Y1.2840.62
542_Y545_K1.2830.62
334_F343_N1.2830.62
158_G225_S1.2790.62
162_N354_H1.2710.61
490_V494_M1.2710.61
204_I304_S1.2660.61
278_Y353_G1.2650.61
455_N459_F1.2580.60
213_S341_A1.2570.60
289_S295_V1.2560.60
85_G353_G1.2540.60
525_T529_V1.2540.60
321_D440_L1.2490.59
46_F112_L1.2480.59
58_I68_F1.2430.59
193_L402_V1.2410.58
160_F355_V1.2330.58
518_A521_G1.2330.58
133_L360_A1.2320.57
515_F541_F1.2260.57
208_F537_Q1.2200.56
170_E334_F1.2190.56
527_R530_K1.2130.56
70_S83_K1.2130.56
85_G406_S1.2100.55
176_L204_I1.2090.55
163_W301_W1.1920.54
253_S508_N1.1900.54
166_M351_N1.1880.53
203_G267_S1.1870.53
261_V308_T1.1860.53
96_L357_P1.1840.53
118_I473_G1.1840.53
54_E407_A1.1810.53
206_F328_I1.1790.53
45_R54_E1.1770.52
337_N341_A1.1770.52
73_L262_F1.1750.52
355_V410_L1.1740.52
38_S86_Y1.1730.52
212_S341_A1.1680.51
140_Q143_P1.1660.51
203_G303_T1.1640.51
290_N293_G1.1630.51
46_F55_K1.1620.51
267_S427_F1.1530.50
322_G353_G1.1510.50
265_L273_T1.1510.50
8_I11_F1.1510.50
354_H357_P1.1510.50
264_E301_W1.1480.50
189_V359_V1.1440.49
381_F405_T1.1430.49
213_S241_W1.1360.48
217_S261_V1.1350.48
81_L163_W1.1320.48
190_T308_T1.1310.48
85_G278_Y1.1300.48
187_A259_P1.1280.48
207_S400_Y1.1280.48
222_L308_T1.1280.48
264_E278_Y1.1260.47
269_T524_T1.1220.47
203_G283_G1.1210.47
257_G510_L1.1210.47
382_E397_F1.1200.47
133_L222_L1.1190.47
158_G322_G1.1160.47
163_W355_V1.1120.46
12_A19_K1.1110.46
158_G307_S1.1080.46
483_E495_L1.1060.46
252_L280_I1.1050.46
217_S221_A1.1040.45
130_D294_E1.1030.45
14_D19_K1.1030.45
248_L280_I1.0990.45
41_I59_T1.0960.45
192_F217_S1.0940.44
57_I237_L1.0940.44
188_L264_E1.0910.44
325_V392_T1.0910.44
58_I288_R1.0890.44
359_V362_Y1.0880.44
212_S392_T1.0880.44
280_I305_V1.0870.44
209_T502_D1.0860.44
455_N458_K1.0820.43
116_V331_N1.0800.43
252_L262_F1.0790.43
85_G159_T1.0790.43
46_F57_I1.0780.43
160_F202_A1.0780.43
359_V413_V1.0770.43
13_L18_W1.0750.43
397_F427_F1.0710.42
213_S391_N1.0670.42
225_S301_W1.0660.42
288_R310_E1.0660.42
459_F486_I1.0650.42
508_N512_D1.0650.42
81_L158_G1.0620.42
204_I310_E1.0620.42
85_G158_G1.0540.41
26_K29_D1.0520.41
220_A261_V1.0510.40
254_N439_S1.0500.40
523_Q529_V1.0500.40
301_W353_G1.0470.40
44_A58_I1.0470.40
81_L278_Y1.0460.40
385_L424_R1.0440.40
366_R413_V1.0440.40
174_H247_A1.0430.40
487_I494_M1.0430.40
78_L322_G1.0400.39
180_A219_A1.0400.39
213_S322_G1.0400.39
265_L282_E1.0400.39
332_E340_N1.0390.39
125_Y227_A1.0380.39
118_I364_I1.0360.39
37_A86_Y1.0350.39
47_S54_E1.0350.39
374_F377_E1.0340.39
245_R272_D1.0340.39
291_V295_V1.0340.39
517_L525_T1.0330.39
263_D310_E1.0320.39
163_W185_I1.0310.39
360_A364_I1.0310.39
228_G241_W1.0280.38
474_L538_S1.0270.38
402_V408_K1.0250.38
158_G241_W1.0250.38
28_G31_E1.0220.38
188_L359_V1.0220.38
202_A213_S1.0220.38
212_S278_Y1.0200.38
206_F306_I1.0170.37
247_A289_S1.0160.37
277_L344_I1.0150.37
308_T538_S1.0130.37
158_G283_G1.0110.37
241_W325_V1.0090.37
125_Y268_T1.0080.37
44_A57_I1.0070.37
267_S278_Y1.0070.37
165_N169_D1.0050.36
522_R537_Q1.0030.36
506_V510_L1.0030.36
225_S322_G1.0030.36
212_S240_S1.0020.36
182_I403_I1.0010.36
166_M170_E1.0010.36
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: (24May14)
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  
1tueA60.3429980.921Contact Map
1ofhA30.452197.80.925Contact Map
3bosA20.376597.80.925Contact Map
2r44A10.480797.70.927Contact Map
3sylA20.450497.70.927Contact Map
2chgA40.351397.60.928Contact Map
3co5A20.221897.60.929Contact Map
3n70A80.228697.60.929Contact Map
1um8A10.423597.50.93Contact Map
3hwsA60.44297.40.931Contact 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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