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T0835 -force run

ID: 1403892678 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 424 (361)
Sequences: 265 (229.4)
Seq/Len: 0.734
Nf(neff/√len): 12.1

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: 0.734).

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
373_I388_S2.4890.98
68_I101_I2.2280.96
144_T208_A2.1610.95
330_V399_T2.1270.95
286_L336_A1.9680.91
71_V74_A1.9430.91
282_A345_Y1.9240.90
287_D345_Y1.9230.90
28_L397_L1.7980.85
270_G282_A1.7940.85
379_D383_T1.7180.82
229_A278_M1.6830.80
354_L359_N1.6700.79
366_M374_A1.6320.77
111_F119_H1.6240.76
35_V119_H1.6110.76
243_P303_T1.6070.75
34_K119_H1.5800.74
123_K126_K1.5390.71
27_H393_T1.5120.69
300_N361_P1.4720.66
142_A230_A1.4710.66
264_Y352_L1.4500.64
237_V277_D1.4430.64
212_A219_P1.4400.63
141_W144_T1.4350.63
104_Q115_I1.4340.63
299_L325_I1.4240.62
63_E67_A1.4210.62
106_A123_K1.4200.62
59_K246_G1.4170.61
334_I349_A1.4140.61
74_A97_L1.4110.61
270_G273_L1.4080.61
246_G253_N1.4060.61
40_K325_I1.4050.61
40_K119_H1.3980.60
267_L339_I1.3970.60
121_I288_H1.3900.59
198_A250_S1.3830.59
267_L282_A1.3750.58
300_N321_Q1.3690.58
97_L388_S1.3680.57
40_K63_E1.3660.57
263_A282_A1.3540.56
98_V160_R1.3500.56
375_F386_K1.3390.55
252_Q324_Y1.3350.55
93_K289_F1.3210.53
60_D63_E1.3200.53
119_H293_L1.3190.53
32_Y97_L1.3160.53
294_I361_P1.3130.53
100_F320_S1.3040.52
328_P395_E1.3000.52
270_G279_I1.2980.52
233_M281_A1.2890.51
39_N60_D1.2870.51
155_N170_D1.2850.50
275_D278_M1.2700.49
230_A278_M1.2640.49
40_K126_K1.2590.48
103_Y119_H1.2510.48
30_A388_S1.2470.47
27_H397_L1.2440.47
41_T368_Y1.2410.47
329_M352_L1.2400.47
93_K301_E1.2380.46
198_A201_Q1.2370.46
301_E320_S1.2350.46
114_F126_K1.2330.46
357_F363_Q1.2330.46
308_G317_K1.2220.45
362_A378_I1.2210.45
40_K114_F1.2130.44
320_S336_A1.2120.44
65_V322_I1.2120.44
200_D203_S1.2100.44
326_I366_M1.2090.44
268_V335_K1.2020.43
165_I378_I1.2000.43
165_I302_F1.1990.43
149_T209_L1.1910.42
251_W322_I1.1900.42
295_S298_L1.1890.42
67_A77_F1.1850.42
326_I365_Q1.1830.42
126_K144_T1.1790.41
122_N126_K1.1780.41
67_A294_I1.1720.41
245_N273_L1.1670.40
213_Q395_E1.1620.40
67_A252_Q1.1610.40
71_V374_A1.1600.40
115_I126_K1.1600.40
112_Y123_K1.1580.40
39_N399_T1.1580.40
330_V395_E1.1570.40
118_D347_E1.1550.39
140_L165_I1.1520.39
288_H293_L1.1480.39
137_W208_A1.1450.39
368_Y371_T1.1440.39
27_H41_T1.1400.38
68_I139_A1.1340.38
116_Y122_N1.1340.38
74_A142_A1.1310.38
75_A97_L1.1300.37
28_L77_F1.1280.37
31_L341_R1.1280.37
200_D246_G1.1240.37
33_Q320_S1.1240.37
76_I142_A1.1220.37
285_E395_E1.1170.36
200_D208_A1.1130.36
25_A397_L1.1110.36
206_L269_A1.1100.36
326_I349_A1.1080.36
114_F123_K1.1060.36
209_L228_L1.1050.35
264_Y335_K1.0990.35
313_L373_I1.0990.35
335_K338_E1.0990.35
21_K357_F1.0980.35
139_A160_R1.0950.35
250_S306_Q1.0950.35
206_L228_L1.0940.35
314_I317_K1.0880.34
40_K117_P1.0870.34
65_V251_W1.0870.34
147_Y396_A1.0840.34
202_A231_G1.0810.34
100_F372_G1.0740.33
206_L225_M1.0730.33
118_D214_A1.0700.33
130_A367_Y1.0660.32
167_A174_K1.0660.32
32_Y289_F1.0660.32
233_M278_M1.0650.32
141_W208_A1.0640.32
59_K65_V1.0630.32
139_A204_V1.0630.32
140_L209_L1.0630.32
286_L332_A1.0630.32
356_F397_L1.0630.32
127_T303_T1.0620.32
76_I319_F1.0580.32
145_Q211_D1.0570.32
164_T267_L1.0560.32
61_P103_Y1.0540.32
115_I326_I1.0500.31
298_L361_P1.0480.31
33_Q336_A1.0450.31
77_F101_I1.0410.31
107_D274_G1.0410.31
39_N322_I1.0390.30
39_N114_F1.0370.30
225_M273_L1.0370.30
67_A288_H1.0340.30
263_A285_E1.0320.30
286_L320_S1.0290.30
353_S357_F1.0290.30
143_L392_S1.0290.30
36_T251_W1.0280.30
68_I317_K1.0280.30
96_S234_L1.0280.30
32_Y373_I1.0270.30
59_K200_D1.0230.29
38_A63_E1.0200.29
204_V213_Q1.0180.29
236_Q285_E1.0150.29
301_E325_I1.0130.29
67_A121_I1.0120.29
293_L361_P1.0100.28
225_M338_E1.0080.28
321_Q361_P1.0070.28
32_Y139_A1.0060.28
115_I121_I1.0050.28
225_M269_A1.0040.28
321_Q380_S1.0040.28
288_H294_I1.0020.28
82_Y91_L1.0020.28
201_Q204_V1.0010.28
31_L88_A1.0000.28
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: (12Jul14)
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  
3vw5A30.851499.90.847Contact Map
3wkgA10.867999.90.848Contact Map
3gt5A10.827899.90.85Contact Map
1fp3A20.865699.90.851Contact Map
2gz6A20.820899.90.852Contact Map
2zblA60.877499.80.869Contact Map
4c1sA20.719399.30.91Contact Map
3wkxA10.790199.20.912Contact Map
4mu9A20.797299.10.916Contact Map
3pmmA10.606199.10.917Contact 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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