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F r3 -end -force run

ID: 1516357929 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 404 (402)
Sequences: 398 (248.7)
Seq/Len: 0.990
Nf(neff/√len): 12.4

Jackhmmer Results: (2016_04)
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: 0.990).

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
228_V263_W3.1491.00
116_R146_D2.8841.00
291_E308_K2.7241.00
265_I290_L2.3200.99
269_L284_V2.1500.97
106_F154_G2.1490.97
225_S268_G2.1300.97
165_D207_G1.9780.95
212_F224_V1.9780.95
12_L16_Q1.8460.92
31_R36_E1.8430.92
111_G151_D1.7690.90
76_Y80_L1.7670.90
381_P398_L1.6900.87
14_L28_L1.6760.86
321_V331_M1.5960.82
280_L369_M1.5610.80
383_L396_F1.5520.80
365_F385_I1.5290.78
335_V394_F1.5100.77
112_I148_W1.4990.76
220_P324_A1.4870.76
166_V204_V1.4780.75
39_P44_P1.4720.75
335_V363_G1.4670.74
77_G80_L1.4660.74
213_L222_A1.4640.74
355_I358_S1.4460.73
334_S366_N1.4340.72
337_D361_N1.4160.70
229_K260_N1.4120.70
24_A29_E1.3910.68
11_L32_V1.3910.68
389_D393_D1.3690.67
61_V66_G1.3690.67
318_G324_A1.3630.66
116_R124_L1.3600.66
13_E16_Q1.3440.65
5_E24_A1.3290.63
158_L208_I1.3280.63
216_S219_M1.3220.63
22_Q26_A1.3170.62
235_E238_G1.3160.62
29_E38_Q1.3150.62
108_F154_G1.3130.62
285_S316_Q1.3130.62
124_L128_L1.3080.61
283_S318_G1.3070.61
264_S287_T1.3060.61
175_S283_S1.3020.61
367_V383_L1.2930.60
54_F57_S1.2880.60
217_A220_P1.2790.59
168_V350_G1.2770.59
120_R142_R1.2770.59
230_A263_W1.2770.59
9_Q13_E1.2700.58
93_L268_G1.2650.58
128_L131_D1.2650.58
129_A134_F1.2550.57
387_M394_F1.2520.56
93_L207_G1.2510.56
115_A299_S1.2430.56
29_E33_R1.2420.56
67_T70_A1.2360.55
6_T25_L1.2340.55
124_L253_P1.2230.54
99_G107_S1.2220.54
53_D56_Q1.2210.54
45_K50_S1.2200.54
4_I12_L1.2180.53
131_D322_A1.2160.53
280_L329_M1.2140.53
108_F201_I1.2100.53
28_L31_R1.2050.52
158_L206_F1.2050.52
231_P235_E1.2020.52
46_R65_S1.2000.52
231_P263_W1.1990.52
158_L164_F1.1940.51
286_Y313_D1.1940.51
41_T45_K1.1930.51
41_T58_G1.1920.51
379_I400_F1.1850.50
110_T170_V1.1840.50
363_G387_M1.1760.49
142_R174_E1.1730.49
146_D201_I1.1710.49
300_D387_M1.1640.48
45_K49_K1.1640.48
19_E33_R1.1630.48
201_I204_V1.1630.48
83_D86_P1.1610.48
79_S90_V1.1590.48
162_W210_Y1.1570.48
373_A379_I1.1510.47
49_K61_V1.1460.47
95_N394_F1.1420.46
49_K53_D1.1400.46
273_K387_M1.1390.46
241_L247_N1.1350.46
275_F280_L1.1300.45
208_I264_S1.1280.45
127_F209_A1.1270.45
45_K52_A1.1270.45
55_K59_S1.1260.45
10_E15_K1.1260.45
161_R258_T1.1240.45
53_D63_A1.1240.45
124_L358_S1.1230.45
102_G262_V1.1200.44
22_Q27_V1.1170.44
24_A27_V1.1160.44
370_T373_A1.1160.44
163_Q272_V1.1140.44
107_S270_S1.1130.44
43_A46_R1.1110.43
5_E278_A1.1100.43
160_N221_D1.1000.42
253_P358_S1.0980.42
63_A67_T1.0960.42
278_A338_L1.0950.42
25_L30_Q1.0950.42
311_L319_V1.0940.42
30_Q34_Q1.0930.42
228_V265_I1.0910.42
215_E274_T1.0890.41
74_S201_I1.0880.41
16_Q28_L1.0860.41
128_L134_F1.0860.41
223_V228_V1.0840.41
6_T19_E1.0830.41
48_A56_Q1.0800.41
224_V267_P1.0770.40
61_V69_G1.0750.40
364_Y384_A1.0700.40
11_L162_W1.0680.40
47_L51_P1.0670.40
234_K345_L1.0670.40
50_S54_F1.0650.39
365_F383_L1.0650.39
64_S201_I1.0640.39
20_A23_K1.0630.39
115_A321_V1.0630.39
95_N175_S1.0610.39
284_V315_F1.0610.39
329_M391_A1.0600.39
27_V162_W1.0590.39
58_G62_A1.0580.39
204_V290_L1.0550.38
47_L52_A1.0540.38
132_S379_I1.0530.38
45_K48_A1.0490.38
237_F282_G1.0490.38
48_A61_V1.0490.38
4_I8_K1.0490.38
363_G400_F1.0470.38
165_D227_R1.0430.37
101_F274_T1.0420.37
38_Q212_F1.0420.37
26_A30_Q1.0420.37
237_F323_F1.0410.37
31_R35_V1.0390.37
377_L400_F1.0390.37
235_E370_T1.0380.37
46_R50_S1.0380.37
168_V204_V1.0380.37
51_P64_S1.0370.37
104_G264_S1.0350.37
319_V369_M1.0350.37
163_Q340_Q1.0320.36
8_K19_E1.0310.36
52_A56_Q1.0290.36
10_E34_Q1.0270.36
76_Y79_S1.0260.36
130_L372_A1.0260.36
52_A68_G1.0250.36
48_A54_F1.0240.36
8_K13_E1.0240.36
9_Q43_A1.0240.36
89_S237_F1.0240.36
150_L283_S1.0200.35
207_G268_G1.0190.35
220_P286_Y1.0190.35
27_V33_R1.0170.35
109_E136_G1.0150.35
120_R173_R1.0120.35
182_A192_E1.0120.35
10_E28_L1.0120.35
91_S282_G1.0100.35
388_T393_D1.0090.35
145_A175_S1.0080.34
313_D375_E1.0080.34
127_F134_F1.0060.34
148_W158_L1.0050.34
40_A64_S1.0050.34
131_D135_L1.0040.34
59_S62_A1.0040.34
71_T162_W1.0030.34
93_L97_A1.0000.34
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  
4rl8A4099.90.796Contact Map
3pguA10.821893.10.956Contact Map
2x27X10.485190.70.959Contact Map
2yy0A40.089189.80.96Contact Map
1ormA10.356489.30.96Contact Map
3iynQ40.118888.60.961Contact Map
1qjpA10.339188.40.961Contact Map
3kvnX20.759988.30.961Contact Map
3qraA10.346587.40.961Contact Map
2f1vA60.445586.90.962Contact 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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