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T0835 21-424 -force run

ID: 1406431991 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 404 (352)
Sequences: 267 (233.1)
Seq/Len: 0.759
Nf(neff/√len): 12.4

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: 0.759).

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
353_I368_S2.4310.98
48_I81_I2.1760.96
310_V379_T2.1560.96
124_T188_A2.1520.95
51_V54_A2.0070.93
267_D325_Y1.9290.91
266_L316_A1.9210.90
262_A325_Y1.8860.89
8_L377_L1.8540.88
359_D363_T1.8040.86
250_G262_A1.7370.83
15_V99_H1.6630.80
334_L339_N1.6560.79
91_F99_H1.6430.78
14_K99_H1.6160.77
103_K106_K1.6040.76
84_Q95_I1.5510.73
280_N341_P1.5370.72
192_A199_P1.5330.71
121_W124_T1.5320.71
86_A103_K1.5180.70
101_I268_H1.5030.69
279_L305_I1.4830.68
209_A258_M1.4740.67
244_Y332_L1.4670.66
220_T223_P1.4610.66
217_V257_D1.4580.66
247_L262_A1.4550.66
43_E47_A1.4540.65
54_A77_L1.4430.65
226_G233_N1.4180.63
19_N40_D1.4150.62
314_I329_A1.4050.62
232_Q304_Y1.3930.61
20_K305_I1.3870.60
40_D43_E1.3780.59
250_G253_L1.3680.58
346_M354_A1.3670.58
280_N301_Q1.3670.58
80_F300_S1.3620.58
78_V140_R1.3520.57
73_K269_F1.3490.57
342_A358_I1.3450.57
39_K226_G1.3350.56
10_A368_S1.3340.56
122_A210_A1.3150.54
193_Q375_E1.3140.54
250_G259_I1.3110.54
247_L319_I1.3090.53
274_I341_P1.3080.53
21_T34_D1.3050.53
20_K43_E1.2970.52
77_L368_S1.2950.52
12_Y77_L1.2940.52
308_P375_E1.2920.52
99_H273_L1.2900.52
11_L321_R1.2870.52
94_F106_K1.2790.51
281_E300_S1.2790.51
243_A262_A1.2760.51
47_A274_I1.2750.51
20_K106_K1.2700.50
210_A258_M1.2660.50
178_A230_S1.2650.50
47_A57_F1.2620.49
180_D183_S1.2620.49
7_H373_T1.2500.48
248_V315_K1.2450.48
96_Y102_N1.2400.47
20_K99_H1.2390.47
213_M261_A1.2380.47
288_G297_K1.2260.46
355_F366_K1.2220.46
48_I119_A1.2150.45
106_K124_T1.2120.45
309_M332_L1.2120.45
47_A232_Q1.2110.45
275_S278_L1.2100.45
45_V302_I1.2040.44
95_I106_K1.2010.44
73_K281_E1.1970.44
92_Y103_K1.1950.44
337_F343_Q1.1910.43
15_V20_K1.1890.43
145_I358_I1.1880.43
300_S316_A1.1830.43
216_Q265_E1.1810.42
244_Y315_K1.1760.42
348_Y351_T1.1750.42
55_A77_L1.1730.42
51_V354_A1.1720.42
117_W188_A1.1660.41
268_H273_L1.1640.41
306_I345_Q1.1600.41
135_N150_D1.1580.41
83_Y99_H1.1560.40
306_I329_A1.1550.40
225_N253_L1.1540.40
281_E305_I1.1530.40
20_K94_F1.1480.40
120_L145_I1.1450.39
99_H106_K1.1410.39
129_T189_L1.1410.39
47_A268_H1.1330.38
180_D188_A1.1330.38
310_V375_E1.1300.38
266_L312_A1.1300.38
54_A208_L1.1300.38
56_I122_A1.1290.38
47_A101_I1.1280.38
56_I299_F1.1250.38
13_Q300_S1.1250.38
95_I306_I1.1180.37
224_V242_Q1.1070.36
265_E375_E1.1050.36
13_Q16_T1.1040.36
255_D258_M1.1010.36
336_F377_L1.1000.36
11_L205_M1.0980.36
147_A154_K1.0970.36
231_W302_I1.0950.35
189_L208_L1.0910.35
13_Q20_K1.0900.35
15_V107_T1.0890.35
186_L208_L1.0890.35
19_N94_F1.0880.35
94_F103_K1.0840.35
98_D327_E1.0800.34
180_D226_G1.0760.34
19_N102_N1.0730.34
121_W188_A1.0670.33
39_K45_V1.0660.33
315_K318_E1.0630.33
306_I346_M1.0630.33
278_L341_P1.0580.33
243_A265_E1.0580.33
125_Q191_D1.0580.33
333_S337_F1.0580.33
102_N106_K1.0550.32
266_L300_S1.0510.32
95_I101_I1.0500.32
213_M258_M1.0480.32
7_H377_L1.0460.32
8_L57_F1.0460.32
268_H274_I1.0440.32
47_A51_V1.0430.31
110_A347_Y1.0410.31
119_A140_R1.0410.31
41_P83_Y1.0400.31
300_S359_D1.0380.31
301_Q360_S1.0370.31
54_A122_A1.0340.31
186_L249_A1.0320.31
84_Q316_A1.0320.31
181_Q184_V1.0310.31
288_G300_S1.0310.31
294_I297_K1.0290.30
184_V193_Q1.0280.30
43_E101_I1.0280.30
87_D254_G1.0270.30
16_T231_W1.0260.30
293_L353_I1.0260.30
12_Y353_I1.0250.30
127_Y376_A1.0230.30
101_I273_L1.0230.30
76_S214_L1.0230.30
39_K180_D1.0210.30
19_N379_T1.0210.30
344_A364_V1.0200.30
301_Q341_P1.0200.30
262_A301_Q1.0180.30
107_T283_T1.0170.30
13_Q283_T1.0160.29
45_V231_W1.0150.29
179_G184_V1.0150.29
244_Y355_F1.0140.29
16_T45_V1.0140.29
333_S379_T1.0130.29
336_F364_V1.0090.29
366_K375_E1.0080.29
8_L17_V1.0080.29
101_I311_F1.0070.29
189_L249_A1.0070.29
98_D194_A1.0050.29
281_E359_D1.0040.29
103_K107_T1.0030.29
57_F81_I1.0010.28
80_F352_G1.0000.28
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  
3vw5A30.863999.90.839Contact Map
3wkgA10.888699.90.84Contact Map
3gt5A10.863999.90.845Contact Map
1fp3A20.878799.90.845Contact Map
2gz6A20.821899.90.847Contact Map
2zblA60.881299.80.863Contact Map
4c1sA20.75599.30.909Contact Map
3wkxA10.7599.20.912Contact Map
3k7xA10.586699.20.913Contact Map
2ahfA20.730299.10.914Contact 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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