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human syx

ID: 1502376483 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 288 (256)
Sequences: 2313 (1475.6)
Seq/Len: 9.035
Nf(neff/√len): 92.2

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: 9.035).

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
50_N82_I2.8101.00
260_K264_K2.3361.00
48_A133_E2.0161.00
267_M271_C1.9881.00
264_K267_M1.9771.00
37_V123_L1.8301.00
52_E133_E1.8031.00
94_K97_E1.7611.00
270_I273_V1.7541.00
227_G230_I1.7301.00
54_V75_L1.7091.00
41_R126_K1.6661.00
261_A265_K1.6461.00
44_I130_V1.6271.00
161_T164_E1.5831.00
270_I274_I1.5711.00
254_A258_Q1.5511.00
200_S203_I1.5471.00
231_D235_Y1.5351.00
275_L279_I1.5251.00
263_R267_M1.5191.00
97_E124_S1.5171.00
32_E35_E1.5131.00
54_V82_I1.4881.00
274_I278_V1.4661.00
33_F96_I1.4571.00
246_R249_S1.4561.00
227_G231_D1.4420.99
214_D218_D1.4420.99
43_F89_V1.4320.99
232_R235_Y1.4120.99
36_Q92_K1.4040.99
198_R216_F1.3770.99
276_G279_I1.3650.99
138_Q208_S1.3560.99
193_S197_T1.3540.99
55_K59_S1.3420.99
237_V240_A1.3370.99
47_I50_N1.3350.99
200_S207_N1.3340.99
268_I272_C1.3320.99
256_K260_K1.3180.99
187_I191_A1.3030.99
234_E238_E1.3000.99
197_T200_S1.2950.99
36_Q99_S1.2840.99
86_A131_M1.2820.99
261_A264_K1.2810.99
100_I116_R1.2790.98
225_S228_E1.2770.98
30_M34_F1.2700.98
246_R250_D1.2700.98
249_S253_K1.2670.98
229_M232_R1.2620.98
258_Q261_A1.2570.98
124_S128_V1.2500.98
89_V93_L1.2490.98
257_Y261_A1.2480.98
58_H209_I1.2430.98
251_T255_V1.2270.98
273_V277_I1.2250.98
47_I89_V1.2250.98
262_R267_M1.2200.98
244_V247_A1.2200.98
209_I229_M1.2200.98
119_Q123_L1.2190.98
220_A224_E1.2140.98
195_I251_T1.2140.98
275_L278_V1.2140.98
89_V138_Q1.2090.98
264_K268_I1.2090.98
209_I216_F1.2080.98
240_A243_Y1.2010.97
48_A130_V1.1970.97
53_E56_R1.1950.97
126_K129_E1.1930.97
188_S192_L1.1920.97
218_D221_M1.1910.97
132_S136_A1.1770.97
50_N85_T1.1690.97
257_Y260_K1.1680.97
213_H217_M1.1650.97
276_G280_A1.1500.96
58_H141_Y1.1430.96
88_K91_S1.1420.96
82_I85_T1.1420.96
89_V127_F1.1350.96
273_V279_I1.1300.96
33_F230_I1.1280.96
216_F222_L1.1260.96
144_R147_G1.1260.96
205_L233_I1.1250.96
95_S98_Q1.1220.96
236_N239_H1.1200.96
202_I240_A1.1150.96
253_K257_Y1.1150.96
266_I270_I1.1120.96
130_V133_E1.1060.95
58_H76_E1.1030.95
250_D253_K1.1020.95
221_M224_E1.0940.95
210_R213_H1.0870.95
248_V252_K1.0870.95
90_R94_K1.0750.94
118_T124_S1.0730.94
45_D48_A1.0720.94
239_H243_Y1.0710.94
203_I206_E1.0700.94
250_D257_Y1.0610.94
43_F85_T1.0610.94
72_K76_E1.0600.94
258_Q266_I1.0600.94
174_P179_S1.0580.94
146_K206_E1.0580.94
204_K214_D1.0540.94
245_E248_V1.0500.93
90_R212_L1.0470.93
193_S196_E1.0440.93
268_I271_C1.0420.93
187_I190_Q1.0420.93
218_D222_L1.0420.93
124_S138_Q1.0410.93
246_R259_S1.0330.93
122_T202_I1.0290.92
218_D240_A1.0290.92
131_M135_N1.0220.92
34_F37_V1.0210.92
181_I185_S1.0210.92
131_M195_I1.0210.92
83_K124_S1.0190.92
52_E55_K1.0150.92
77_E81_D1.0150.92
46_K49_E1.0050.91
257_Y264_K1.0030.91
179_S183_M1.0020.91
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  
3c98B10.79861000.194Contact Map
4jehB10.76741000.269Contact Map
2xheB10.73961000.279Contact Map
1fioA10.64931000.488Contact Map
2m8rA10.378599.90.546Contact Map
1s94A20.416799.90.581Contact Map
1jthB20.232699.90.619Contact Map
1sfcB30.263999.80.64Contact Map
2npsB10.236199.80.655Contact Map
3b5nB30.239699.70.666Contact 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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