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scEMC1 1-380

ID: 1505235215 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 380 (338)
Sequences: 4152 (2975.9)
Seq/Len: 12.284
Nf(neff/√len): 161.9

HHblits Results: (2016_02)
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: 12.284).

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
153_L189_L2.9371.00
58_I72_F2.7321.00
329_E349_F2.5301.00
315_D319_K2.4921.00
145_Q187_L2.4731.00
304_V314_L2.4591.00
189_L199_F2.3551.00
251_A255_R2.3201.00
112_W146_V2.3111.00
116_D119_D2.3081.00
188_V198_G2.2861.00
73_N76_S2.2321.00
303_I347_V2.1521.00
60_S66_S2.1321.00
57_L101_A2.1201.00
134_T147_S2.1031.00
57_L94_L2.0501.00
86_P104_C2.0371.00
91_E105_V2.0171.00
284_L304_V1.9961.00
129_N146_V1.9671.00
336_M350_S1.9521.00
27_S30_A1.9201.00
94_L137_P1.9011.00
66_S70_S1.8861.00
102_M114_K1.8421.00
69_V104_C1.8221.00
303_I313_G1.8221.00
148_I152_E1.8211.00
57_L71_S1.7831.00
354_H358_I1.7751.00
102_M144_D1.7651.00
215_W219_V1.7611.00
157_D160_S1.7391.00
271_Q274_P1.7151.00
315_D318_N1.6811.00
146_V156_L1.6651.00
256_L304_V1.6581.00
349_F360_V1.6351.00
154_H166_K1.6311.00
50_S94_L1.6161.00
135_I146_V1.6121.00
348_V359_E1.5901.00
100_N114_K1.5671.00
197_M211_Q1.5461.00
129_N150_N1.5351.00
102_M137_P1.5081.00
145_Q155_I1.5021.00
55_R80_L1.4891.00
104_C115_Y1.4801.00
204_T207_I1.4781.00
293_D305_L1.4621.00
200_S204_T1.4541.00
329_E354_H1.4531.00
116_D123_L1.4231.00
40_L58_I1.4070.99
24_A33_T1.4050.99
102_M135_I1.4040.99
221_D250_N1.3930.99
188_V226_D1.3910.99
48_P137_P1.3840.99
137_P340_D1.3810.99
55_R71_S1.3790.99
109_S113_Q1.3770.99
142_L345_E1.3720.99
139_S184_P1.3540.99
284_L308_D1.3460.99
45_K59_L1.3430.99
170_P189_L1.3220.99
146_V150_N1.3180.99
70_S82_R1.3130.99
124_E165_W1.3060.99
135_I144_D1.3000.99
24_A36_Q1.2990.99
57_L92_I1.2810.99
196_Y249_W1.2700.99
70_S79_I1.2680.99
71_S83_N1.2650.99
281_L314_L1.2580.99
95_D98_D1.2570.99
351_H354_H1.2560.99
301_I346_L1.2490.99
297_G344_D1.2390.98
303_I340_D1.2340.98
311_I349_F1.2300.98
303_I337_F1.2260.98
248_L302_L1.2190.98
54_N300_K1.2170.98
113_Q122_L1.2170.98
23_Q58_I1.2130.98
95_D100_N1.2090.98
191_V195_Q1.2080.98
122_L366_I1.2040.98
122_L208_P1.2010.98
113_Q125_E1.1960.98
366_I369_S1.1930.98
208_P366_I1.1920.98
33_T79_I1.1910.98
303_I311_I1.1860.98
187_L201_A1.1830.98
124_E161_K1.1820.98
59_L89_I1.1770.98
202_N318_N1.1750.98
137_P180_H1.1750.98
341_K344_D1.1720.98
99_H345_E1.1700.97
51_R98_D1.1680.97
79_I163_A1.1670.97
230_S245_S1.1660.97
358_I366_I1.1660.97
56_V101_A1.1600.97
104_C107_S1.1590.97
104_C113_Q1.1550.97
124_E279_T1.1500.97
79_I322_L1.1460.97
215_W253_W1.1460.97
60_S68_L1.1420.97
56_V74_V1.1370.97
33_T122_L1.1370.97
277_V322_L1.1350.97
121_F162_L1.1330.97
301_I313_G1.1220.97
255_R262_R1.1170.96
245_S249_W1.1150.96
188_V199_F1.1140.96
58_I70_S1.1080.96
249_W253_W1.1080.96
35_W77_G1.1070.96
54_N142_L1.1070.96
163_A208_P1.0990.96
83_N115_Y1.0980.96
306_T310_F1.0960.96
284_L306_T1.0940.96
129_N148_I1.0930.96
71_S114_K1.0900.96
79_I208_P1.0860.96
250_N254_L1.0790.95
32_I162_L1.0760.95
59_L92_I1.0730.95
141_Y147_S1.0700.95
54_N345_E1.0680.95
210_W279_T1.0590.95
33_T36_Q1.0570.95
79_I277_V1.0550.95
122_L322_L1.0540.95
169_L172_G1.0540.95
250_N291_V1.0490.94
155_I198_G1.0470.94
78_Q121_F1.0460.94
94_L340_D1.0450.94
306_T312_G1.0400.94
334_V349_F1.0340.94
262_R269_E1.0310.94
26_F33_T1.0290.94
312_G325_K1.0280.94
215_W249_W1.0260.94
181_R184_P1.0260.94
118_H159_Q1.0240.93
122_L125_E1.0230.93
122_L163_A1.0200.93
186_A346_L1.0170.93
86_P107_S1.0160.93
143_N346_L1.0100.93
50_S57_L1.0090.93
79_I366_I1.0070.93
143_N301_I1.0050.93
300_K315_D1.0050.93
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  
4nsxA10.88161000.378Contact Map
1vyhC100.79211000.38Contact Map
3sfzA10.87371000.383Contact Map
4noxA10.851000.391Contact Map
4wjuA20.83421000.396Contact Map
4ci8A20.84741000.401Contact Map
1flgA20.87891000.403Contact Map
1yiqA10.89471000.407Contact Map
4wjsA10.83681000.413Contact Map
4u1eI10.79741000.414Contact 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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