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iker2

ID: 1518192240 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 300 (271)
Sequences: 5869 (3845.2)
Seq/Len: 21.657
Nf(neff/√len): 233.6

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: 21.657).

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
159_P164_A3.2811.00
92_Y98_D3.2191.00
197_H202_Y3.1531.00
277_I281_W3.1231.00
210_V235_G2.9901.00
92_Y95_R2.8861.00
18_S23_A2.7821.00
89_D92_Y2.7421.00
206_L239_F2.7021.00
242_I246_F2.6991.00
95_R98_D2.6341.00
28_G32_L2.5371.00
237_G272_I2.3981.00
83_F87_M2.3531.00
230_G278_M2.1901.00
125_F129_S2.1561.00
241_I245_F2.0681.00
227_A283_Y2.0661.00
230_G275_G2.0521.00
116_I120_R2.0331.00
157_V194_L2.0311.00
145_L204_L2.0271.00
234_I275_G2.0231.00
57_E121_T1.9921.00
68_G113_V1.9661.00
234_I272_I1.9161.00
85_Q89_D1.9111.00
47_N55_K1.8961.00
109_G113_V1.8731.00
72_G109_G1.8571.00
17_F24_L1.7951.00
87_M90_P1.7871.00
118_A128_V1.7731.00
42_A135_L1.7631.00
54_T57_E1.7531.00
138_F211_L1.7361.00
129_S229_S1.7251.00
16_I29_L1.7211.00
82_N85_Q1.6971.00
161_F164_A1.6901.00
44_R47_N1.6531.00
45_R219_I1.6521.00
104_H264_G1.6371.00
18_S21_P1.6311.00
227_A279_M1.6211.00
141_G208_G1.6121.00
90_P94_F1.6001.00
140_L232_F1.5781.00
46_A58_V1.5611.00
16_I24_L1.5461.00
130_D226_G1.5371.00
224_P227_A1.5361.00
126_F226_G1.5291.00
78_V93_L1.5261.00
127_Q225_M1.5051.00
64_A68_G1.4901.00
85_Q92_Y1.4811.00
164_A195_P1.4741.00
68_G109_G1.4671.00
168_P171_R1.4401.00
124_S225_M1.4351.00
148_F165_M1.4231.00
234_I276_V1.4131.00
40_W44_R1.4060.99
154_W196_R1.4020.99
245_F265_Q1.3980.99
206_L243_V1.3900.99
241_I265_Q1.3860.99
61_L128_V1.3780.99
14_P25_H1.3760.99
115_I119_R1.3630.99
206_L210_V1.3600.99
30_M146_G1.3520.99
205_L209_V1.3380.99
117_F121_T1.3350.99
45_R48_R1.3110.99
208_G212_F1.3000.99
37_F142_A1.2970.99
230_G279_M1.2840.99
57_E123_R1.2820.99
166_L195_P1.2750.99
147_N152_E1.2740.99
134_P137_P1.2660.99
38_A65_G1.2640.99
91_L94_F1.2610.99
148_F201_L1.2600.99
231_L279_M1.2530.99
230_G282_A1.2520.99
201_L205_L1.2380.98
199_S243_V1.2350.98
44_R48_R1.2260.98
43_T59_E1.2220.98
43_T47_N1.2220.98
115_I125_F1.2110.98
39_M62_L1.2090.98
137_P210_V1.2090.98
124_S127_Q1.2080.98
12_F149_I1.2050.98
234_I279_M1.1870.98
79_L83_F1.1830.98
91_L95_R1.1790.98
211_L215_L1.1780.98
64_A113_V1.1770.98
35_F66_F1.1770.98
96_V99_G1.1720.98
253_F263_M1.1720.98
171_R193_V1.1650.97
145_L149_I1.1640.97
137_P211_L1.1560.97
276_V280_V1.1560.97
61_L65_G1.1480.97
160_N164_A1.1400.97
231_L235_G1.1310.97
141_G204_L1.1120.96
35_F69_V1.1100.96
30_M33_V1.1020.96
239_F243_V1.0980.96
16_I26_W1.0960.96
85_Q88_A1.0910.96
89_D95_R1.0910.96
269_I273_V1.0900.96
238_A272_I1.0850.96
218_Y231_L1.0800.95
60_N121_T1.0790.95
224_P283_Y1.0530.95
241_I272_I1.0470.94
123_R128_V1.0400.94
45_R134_P1.0380.94
56_N59_E1.0280.94
108_I112_V1.0230.93
69_V110_V1.0220.93
156_R248_Q1.0200.93
238_A242_I1.0140.93
273_V277_I1.0040.93
165_M168_P1.0010.92
31_Y34_G1.0000.92
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  
2kluA10.1760.969Contact Map
2m20A20.15334.90.97Contact Map
2l2tA20.14674.60.97Contact Map
2mfrA10.193.90.971Contact Map
2mofA10.143.70.972Contact Map
2i68A20.02673.40.972Contact Map
2m59A20.12333.20.973Contact Map
2rddB10.123330.973Contact Map
2jwaA20.13672.70.974Contact Map
4o6yA20.33332.60.974Contact 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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