OPENSEQ.org
GGDc

ID: 1518554737 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 435 (412)
Sequences: 3748 (2599.8)
Seq/Len: 9.097
Nf(neff/√len): 128.1

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: 9.097).

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
219_N260_I4.2341.00
252_K391_A3.8921.00
296_T301_V3.8181.00
354_M393_I3.6031.00
212_I286_P3.4181.00
358_D389_I3.3001.00
171_F266_L3.1371.00
86_T134_S3.0791.00
401_S404_S2.9861.00
49_G67_A2.9841.00
332_A353_V2.8991.00
129_R174_A2.8991.00
131_T135_L2.8321.00
341_H347_G2.7181.00
182_S316_R2.6971.00
26_F43_F2.6361.00
69_C89_F2.6331.00
23_A47_G2.5591.00
78_A158_H2.5421.00
110_E346_F2.5151.00
67_A166_F2.5081.00
294_E394_M2.4421.00
297_H301_V2.4271.00
314_L334_S2.4251.00
212_I263_D2.3811.00
70_A90_Q2.3681.00
248_A391_A2.3231.00
45_L166_F2.3111.00
73_L86_T2.2611.00
208_R267_H2.2491.00
267_H283_G2.2411.00
66_P90_Q2.2381.00
314_L330_T2.2011.00
392_Y409_C2.1831.00
79_P140_G2.1751.00
44_L167_S2.1261.00
285_V309_S2.0921.00
325_W329_Q2.0501.00
308_Q312_R1.9971.00
68_V162_A1.9451.00
300_S363_S1.9291.00
328_L353_V1.9281.00
354_M358_D1.9091.00
350_C396_A1.8941.00
323_R326_P1.8901.00
298_R362_H1.8821.00
132_S168_Y1.8691.00
185_R312_R1.8631.00
399_V405_L1.8611.00
130_V169_L1.8501.00
383_W387_Q1.8471.00
41_Y164_P1.8441.00
205_L283_G1.8411.00
213_L261_L1.8311.00
209_G264_S1.8091.00
30_C43_F1.8091.00
70_A130_V1.8011.00
70_A86_T1.8001.00
297_H382_T1.8001.00
76_S82_V1.7491.00
396_A405_L1.7431.00
69_C73_L1.7331.00
229_G247_T1.7301.00
245_W412_Y1.7291.00
318_V333_F1.7241.00
331_F334_S1.7231.00
249_G388_L1.7131.00
331_F359_Y1.6551.00
205_L267_H1.6461.00
164_P191_Q1.6451.00
183_F187_Q1.6381.00
135_L139_E1.6211.00
355_V390_I1.6141.00
84_R88_C1.6111.00
286_P289_D1.5931.00
105_E109_H1.5881.00
28_Y268_A1.5741.00
71_V75_C1.5721.00
189_R283_G1.5651.00
73_L82_V1.5461.00
106_Y110_E1.5391.00
61_V65_T1.5261.00
161_K164_P1.4931.00
350_C402_L1.4901.00
107_Y336_W1.4731.00
74_L77_L1.4721.00
300_S362_H1.4651.00
230_A398_E1.4611.00
162_A166_F1.4501.00
328_L356_E1.4430.99
74_L137_I1.4400.99
289_D308_Q1.4380.99
141_K184_Q1.4210.99
319_F326_P1.4130.99
324_A364_F1.4100.99
392_Y417_P1.4070.99
311_A315_R1.4030.99
299_I358_D1.4030.99
186_F190_V1.4030.99
396_A406_W1.4030.99
213_L268_A1.3980.99
386_T390_I1.3800.99
255_Y394_M1.3770.99
105_E108_L1.3690.99
91_M333_F1.3600.99
336_W349_V1.3570.99
72_A76_S1.3520.99
392_Y396_A1.3500.99
384_A388_L1.3470.99
249_G391_A1.3420.99
206_S268_A1.3320.99
108_L112_P1.3260.99
396_A409_C1.3250.99
96_L116_F1.3210.99
410_N414_S1.3070.99
406_W410_N1.3070.99
299_I386_T1.3000.99
390_I394_M1.2950.99
320_Q323_R1.2930.99
23_A269_A1.2880.99
320_Q326_P1.2870.99
239_E243_V1.2860.99
105_E115_R1.2800.99
83_H87_F1.2750.98
347_G399_V1.2720.98
334_S351_W1.2650.98
46_T50_A1.2620.98
77_L82_V1.2550.98
354_M389_I1.2530.98
15_Y265_L1.2520.98
395_L412_Y1.2400.98
53_V57_G1.2310.98
129_R181_C1.2250.98
395_L409_C1.2140.98
247_T408_L1.2090.98
87_F92_S1.2080.98
56_M60_A1.2050.98
248_A395_L1.2010.98
120_L176_L1.1910.97
346_F349_V1.1900.97
299_I355_V1.1900.97
290_I295_R1.1720.97
328_L360_L1.1710.97
49_G170_L1.1670.97
248_A412_Y1.1670.97
53_V60_A1.1670.97
88_C92_S1.1670.97
400_R404_S1.1660.97
130_V165_Y1.1620.97
309_S312_R1.1590.97
302_F394_M1.1580.97
74_L133_L1.1570.97
66_P93_W1.1470.96
174_A181_C1.1450.96
49_G64_F1.1400.96
355_V393_I1.1390.96
299_I390_I1.1390.96
220_V258_H1.1320.96
263_D286_P1.1290.96
319_F323_R1.1290.96
300_S304_R1.1260.96
242_Y246_T1.1240.96
65_T89_F1.1240.96
244_V408_L1.1170.96
105_E116_F1.1150.96
209_G268_A1.1150.96
331_F355_V1.1130.96
330_T334_S1.1110.96
322_S329_Q1.1100.96
50_A54_A1.1030.95
213_L265_L1.1010.95
311_A327_L1.0950.95
163_L167_S1.0940.95
208_R212_I1.0940.95
334_S359_Y1.0890.95
302_F390_I1.0860.95
387_Q391_A1.0830.95
402_L406_W1.0820.95
297_H383_W1.0780.94
248_A408_L1.0750.94
75_C160_C1.0650.94
407_L411_S1.0640.94
255_Y294_E1.0630.94
91_M318_V1.0610.94
207_W211_Q1.0600.94
327_L359_Y1.0590.94
70_A134_S1.0590.94
204_A208_R1.0570.94
273_P276_G1.0570.94
185_R285_V1.0550.94
45_L167_S1.0510.93
332_A349_V1.0440.93
351_W394_M1.0410.93
230_A248_A1.0390.93
95_T107_Y1.0340.93
104_T108_L1.0310.93
411_S414_S1.0270.92
43_F47_G1.0200.92
395_L405_L1.0200.92
320_Q351_W1.0190.92
66_P127_T1.0150.92
331_F356_E1.0130.92
136_D317_L1.0100.92
252_K387_Q1.0000.91
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  
3pfzA10.12181.90.981Contact Map
4n7wA20.30111.60.982Contact Map
3g14A20.1081.20.983Contact Map
3zuxA10.29891.10.983Contact Map
2i2jA10.04831.10.984Contact Map
4ogqE10.071310.984Contact Map
1q90L10.073610.984Contact Map
1sghB10.02990.90.985Contact Map
2l0lA10.06210.80.985Contact Map
1scfA400.80.985Contact 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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