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T0835 -force run

ID: 1403893222 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 424 (370)
Sequences: 285 (250.3)
Seq/Len: 0.770
Nf(neff/√len): 13.0

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: 0.770).

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
144_T208_A2.9801.00
373_I388_S2.5010.99
68_I101_I2.2170.96
330_V399_T2.0990.95
286_L336_A2.0340.94
287_D345_Y1.9960.93
282_A345_Y1.9580.92
270_G282_A1.9440.91
28_L397_L1.9340.91
142_A230_A1.8770.89
71_V74_A1.8260.88
379_D383_T1.8110.87
177_N198_A1.7330.84
35_V119_H1.6410.79
270_G273_L1.6090.77
354_L359_N1.6090.77
366_M374_A1.5990.76
177_N304_V1.5810.75
237_V277_D1.5800.75
63_E67_A1.5530.73
111_F119_H1.5200.71
221_I225_M1.5120.70
27_H393_T1.5020.70
308_G317_K1.4980.69
267_L282_A1.4820.68
34_K119_H1.4760.68
100_F320_S1.4480.65
375_F386_K1.4470.65
334_I349_A1.4320.64
270_G279_I1.4260.64
303_T325_I1.4120.63
74_A97_L1.4070.62
259_G324_Y1.3810.60
263_A282_A1.3790.60
267_L339_I1.3690.59
141_W144_T1.3660.59
200_D253_N1.3510.57
303_T320_S1.3500.57
113_N260_N1.3430.57
264_Y352_L1.3320.56
201_Q207_M1.3320.56
65_V322_I1.3260.55
27_H397_L1.3210.55
121_I288_H1.3200.55
328_P395_E1.3140.54
257_G308_G1.3090.54
357_F363_Q1.3080.54
313_L373_I1.2880.52
230_A278_M1.2850.52
32_Y97_L1.2790.51
30_A388_S1.2780.51
132_P263_A1.2770.51
60_D63_E1.2750.51
40_K63_E1.2660.50
98_V160_R1.2660.50
40_K325_I1.2600.50
165_I378_I1.2590.50
59_K253_N1.2550.49
40_K119_H1.2540.49
137_W249_L1.2530.49
123_K130_A1.2530.49
119_H293_L1.2510.49
201_Q204_V1.2470.49
40_K130_A1.2470.49
294_I361_P1.2390.48
295_S299_L1.2370.48
74_A142_A1.2350.48
39_N114_F1.2340.47
39_N60_D1.2320.47
200_D260_N1.2310.47
112_Y123_K1.2290.47
275_D278_M1.2250.47
39_N399_T1.2150.46
362_A378_I1.2140.46
40_K114_F1.2060.45
31_L341_R1.1950.44
143_L392_S1.1910.44
97_L388_S1.1890.44
103_Y119_H1.1860.43
286_L332_A1.1850.43
137_W208_A1.1840.43
199_G235_M1.1790.43
386_K395_E1.1780.43
100_F372_G1.1770.43
268_V335_K1.1730.42
229_A278_M1.1690.42
71_V374_A1.1690.42
106_A123_K1.1690.42
288_H293_L1.1670.42
93_K289_F1.1620.41
104_Q115_I1.1620.41
114_F130_A1.1610.41
28_L77_F1.1600.41
25_A397_L1.1600.41
137_W204_V1.1590.41
258_Y322_I1.1590.41
113_N138_R1.1590.41
28_L37_V1.1580.41
252_Q273_L1.1570.41
41_T368_Y1.1560.41
295_S298_L1.1540.41
269_A377_G1.1530.41
377_G392_S1.1520.40
67_A121_I1.1500.40
330_V395_E1.1430.40
118_D347_E1.1420.40
326_I366_M1.1400.39
76_I319_F1.1400.39
204_V345_Y1.1390.39
329_M352_L1.1380.39
298_L361_P1.1300.39
320_S336_A1.1290.39
141_W208_A1.1270.38
368_Y371_T1.1260.38
67_A294_I1.1240.38
33_Q320_S1.1230.38
155_N170_D1.1180.38
130_A208_A1.1180.38
147_Y396_A1.1160.37
230_A233_M1.1130.37
300_N321_Q1.1110.37
67_A259_G1.1090.37
249_L322_I1.1070.37
335_K338_E1.1060.37
32_Y289_F1.1020.36
76_I142_A1.1010.36
39_N322_I1.0960.36
236_Q285_E1.0890.35
27_H313_L1.0860.35
226_R275_D1.0810.35
326_I349_A1.0800.35
285_E395_E1.0780.34
68_I100_F1.0760.34
41_T60_D1.0730.34
202_A231_G1.0700.34
61_P103_Y1.0700.34
65_V133_N1.0680.34
253_N260_N1.0660.34
366_M375_F1.0650.33
60_D209_L1.0630.33
121_I325_I1.0610.33
385_N392_S1.0610.33
31_L214_A1.0590.33
288_H345_Y1.0580.33
67_A77_F1.0560.33
133_N258_Y1.0540.33
71_V139_A1.0540.33
246_G312_T1.0530.33
65_V258_Y1.0530.33
80_R264_Y1.0480.32
135_W208_A1.0480.32
267_L279_I1.0440.32
21_K357_F1.0420.32
40_K117_P1.0400.32
74_A374_A1.0390.31
286_L320_S1.0380.31
377_G391_E1.0370.31
27_H41_T1.0350.31
209_L212_A1.0340.31
68_I140_L1.0340.31
233_M266_L1.0310.31
298_L302_F1.0300.31
63_E121_I1.0280.31
314_I317_K1.0280.31
206_L269_A1.0280.31
32_Y139_A1.0270.31
69_D73_R1.0260.31
93_K303_T1.0260.31
139_A160_R1.0260.31
200_D322_I1.0250.30
28_L32_Y1.0220.30
142_A259_G1.0200.30
229_A232_I1.0190.30
233_M278_M1.0180.30
116_Y122_N1.0180.30
236_Q284_N1.0160.30
321_Q361_P1.0140.30
356_F397_L1.0140.30
364_A384_V1.0140.30
283_F345_Y1.0130.30
362_A379_D1.0120.29
68_I317_K1.0100.29
31_L38_A1.0070.29
59_K200_D1.0050.29
140_L209_L1.0050.29
340_S346_L1.0050.29
115_I326_I1.0030.29
23_V340_S1.0020.29
69_D385_N1.0010.29
63_E130_A1.0000.29
258_Y332_A1.0000.29
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  
3gt5A10.85381000.77Contact Map
3wkgA10.88681000.775Contact Map
2gz6A20.83491000.779Contact Map
3vw5A30.86791000.784Contact Map
1fp3A20.88681000.787Contact Map
2zblA60.88681000.79Contact Map
3k11A10.905799.60.876Contact Map
4c1sA20.719399.50.88Contact Map
3pmmA10.724199.50.883Contact Map
4mu9A20.806699.50.886Contact 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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