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T0793 -force run

ID: 1401131644 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 595 (536)
Sequences: 470 (390.7)
Seq/Len: 0.877
Nf(neff/√len): 16.9

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: 0.877).

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
206_F403_I3.1861.00
227_A356_L3.0911.00
241_W307_S3.0031.00
213_S395_R2.9831.00
180_A208_F2.9561.00
171_V181_V2.9281.00
168_I355_V2.8751.00
212_S321_D2.8351.00
162_N351_N2.7941.00
257_G302_G2.6270.99
179_L403_I2.5430.99
247_A287_Q2.4990.99
246_N289_S2.4810.99
160_F354_H2.4690.99
207_S309_S2.4390.99
351_N354_H2.3980.99
185_I355_V2.3520.98
182_I407_A2.3300.98
217_S308_T2.2870.98
204_I399_R2.2410.97
411_G415_S2.1830.97
222_L344_I2.1750.97
177_L219_A2.1290.96
176_L426_Y2.1120.96
125_Y258_I2.0970.96
246_N288_R2.0800.96
47_S60_N2.0620.95
220_A308_T2.0480.95
362_Y413_V2.0460.95
160_F358_L2.0340.95
184_G226_V2.0260.95
220_A306_I1.9820.94
328_I396_M1.9700.94
249_E285_G1.9640.93
37_A40_I1.9340.93
252_L260_I1.9050.92
125_Y128_S1.8970.92
411_G414_L1.8940.92
452_V486_I1.8910.92
242_N286_R1.8720.91
266_S320_N1.8640.91
224_V261_V1.8560.91
289_S293_G1.8000.89
445_I515_F1.7850.88
208_F306_I1.7360.86
249_E288_R1.7290.86
185_I359_V1.7110.85
207_S307_S1.7070.85
123_F126_L1.6980.85
522_R529_V1.6860.84
451_F472_Y1.6820.84
221_A345_K1.6270.81
358_L361_K1.6010.80
207_S264_E1.5980.79
538_S541_F1.5840.79
408_K419_D1.5380.76
278_Y322_G1.5280.75
490_V494_M1.5250.75
162_N354_H1.5170.74
459_F473_G1.5050.73
160_F355_V1.5040.73
310_E322_G1.4840.72
25_K29_D1.4840.72
321_D392_T1.4830.72
181_V185_I1.4790.72
531_D534_G1.4580.70
521_G528_S1.4370.68
261_V308_T1.4340.68
357_P364_I1.4320.68
278_Y310_E1.4300.68
346_K375_Y1.4280.68
161_D164_F1.4270.68
246_N250_G1.4140.67
459_F486_I1.4060.66
537_Q541_F1.3980.65
212_S264_E1.3740.63
166_M351_N1.3670.63
207_S400_Y1.3640.63
70_S83_K1.3520.62
163_W355_V1.3430.61
354_H358_L1.3410.61
220_A243_A1.3180.59
158_G163_W1.3090.58
203_G267_S1.3060.58
81_L353_G1.3040.57
14_D19_K1.3030.57
38_S86_Y1.3030.57
213_S341_A1.2980.57
264_E278_Y1.2950.57
392_T440_L1.2840.56
359_V362_Y1.2810.55
220_A261_V1.2790.55
278_Y301_W1.2790.55
243_A248_L1.2780.55
217_S343_N1.2690.54
253_S508_N1.2680.54
81_L85_G1.2600.54
217_S261_V1.2570.53
219_A222_L1.2550.53
179_L206_F1.2520.53
206_F328_I1.2490.53
265_L273_T1.2490.53
215_G353_G1.2440.52
515_F541_F1.2360.51
204_I304_S1.2330.51
28_G31_E1.2320.51
140_Q143_P1.2280.51
228_G241_W1.2270.51
203_G303_T1.2240.50
64_K333_Q1.2120.49
250_G289_S1.2100.49
452_V459_F1.2080.49
280_I305_V1.2070.49
527_R530_K1.2070.49
344_I358_L1.2050.49
10_P14_D1.2050.49
85_G353_G1.2020.48
212_S392_T1.2000.48
44_A57_I1.1980.48
245_R272_D1.1960.48
118_I473_G1.1910.47
116_V331_N1.1880.47
187_A303_T1.1860.47
13_L18_W1.1850.47
252_L280_I1.1820.47
171_V222_L1.1770.46
308_T538_S1.1740.46
342_D345_K1.1720.46
448_I524_T1.1720.46
325_V392_T1.1700.45
26_K29_D1.1700.45
227_A328_I1.1650.45
58_I68_F1.1640.45
374_F405_T1.1630.45
167_Y540_V1.1590.44
182_I185_I1.1560.44
288_R310_E1.1550.44
360_A364_I1.1530.44
157_K229_N1.1520.44
193_L402_V1.1490.44
179_L212_S1.1480.44
363_L406_S1.1470.43
446_D492_K1.1430.43
44_A58_I1.1430.43
185_I410_L1.1380.43
217_S222_L1.1370.43
217_S221_A1.1320.42
58_I73_L1.1270.42
48_D51_T1.1260.42
460_S471_N1.1250.41
402_V408_K1.1250.41
280_I313_I1.1220.41
187_A259_P1.1220.41
269_T272_D1.1170.41
242_N246_N1.1170.41
508_N512_D1.1160.41
176_L332_E1.1160.41
203_G283_G1.1140.41
26_K30_S1.1130.40
126_L402_V1.1110.40
266_S281_A1.1080.40
158_G353_G1.1050.40
78_L88_I1.1020.40
542_Y545_K1.1000.39
538_S542_Y1.0980.39
215_G278_Y1.0970.39
187_A203_G1.0970.39
182_I328_I1.0930.39
64_K535_K1.0890.38
538_S544_L1.0880.38
54_E60_N1.0870.38
290_N293_G1.0830.38
54_E407_A1.0820.38
291_V295_V1.0820.38
213_S391_N1.0770.37
525_T530_K1.0770.37
492_K503_V1.0720.37
174_H247_A1.0720.37
176_L204_I1.0690.37
212_S341_A1.0690.37
246_N249_E1.0680.37
322_G353_G1.0650.36
156_P354_H1.0640.36
161_D193_L1.0590.36
202_A213_S1.0590.36
58_I78_L1.0550.36
81_L322_G1.0550.36
166_M170_E1.0530.35
202_A395_R1.0490.35
366_R413_V1.0490.35
83_K189_V1.0470.35
392_T435_V1.0460.35
167_Y171_V1.0440.35
212_S310_E1.0430.35
277_L292_H1.0420.35
268_T273_T1.0410.34
417_D420_I1.0400.34
360_A518_A1.0400.34
170_E347_A1.0390.34
170_E343_N1.0370.34
444_A506_V1.0360.34
154_L258_I1.0350.34
207_S265_L1.0350.34
85_G158_G1.0340.34
374_F377_E1.0340.34
168_I185_I1.0340.34
96_L357_P1.0330.34
192_F217_S1.0280.33
293_G516_I1.0280.33
356_L359_V1.0280.33
519_D529_V1.0270.33
159_T354_H1.0270.33
455_N459_F1.0260.33
163_W264_E1.0250.33
125_Y256_Y1.0240.33
228_G237_L1.0240.33
46_F112_L1.0230.33
245_R305_V1.0230.33
306_I420_I1.0210.33
175_L426_Y1.0180.33
264_E301_W1.0170.33
158_G215_G1.0140.32
337_N341_A1.0140.32
519_D522_R1.0130.32
325_V395_R1.0130.32
136_I352_Y1.0100.32
207_S278_Y1.0100.32
133_L360_A1.0100.32
45_R217_S1.0080.32
25_K28_G1.0070.32
163_W353_G1.0060.32
321_D440_L1.0060.32
287_Q315_N1.0060.32
273_T443_K1.0040.31
354_H357_P1.0010.31
444_A509_A1.0000.31
404_T408_K1.0000.31
73_L77_N1.0000.31
212_S308_T1.0000.31
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  
1g41A10.450498.10.934Contact Map
1um8A10.460597.80.938Contact Map
1ofhA30.457197.70.939Contact Map
1tueA60.337897.60.94Contact Map
3hwsA60.435397.60.94Contact Map
2r44A10.482497.60.941Contact Map
1ojlA60.448797.50.942Contact Map
3sylA20.452197.50.942Contact Map
3bosA20.378297.50.942Contact Map
4qhsA70.354697.50.942Contact 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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