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iker2

ID: 1518192250 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 294 (270)
Sequences: 5893 (3929.6)
Seq/Len: 21.826
Nf(neff/√len): 239.1

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: 21.826).

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
197_H202_Y3.3461.00
159_P164_A3.3311.00
92_Y98_D3.1981.00
277_I281_W3.1441.00
210_V235_G2.9621.00
92_Y95_R2.8881.00
89_D92_Y2.7571.00
206_L239_F2.7231.00
18_S23_A2.6981.00
242_I246_F2.6931.00
95_R98_D2.6121.00
28_G32_L2.5731.00
237_G272_I2.4651.00
83_F87_M2.4401.00
230_G278_M2.2011.00
125_F129_S2.1191.00
230_G275_G2.1091.00
145_L204_L2.0901.00
241_I245_F2.0691.00
157_V194_L2.0351.00
234_I275_G2.0111.00
116_I120_R2.0021.00
68_G113_V1.9801.00
57_E121_T1.9751.00
227_A283_Y1.9521.00
72_G109_G1.9241.00
234_I272_I1.9191.00
47_N55_K1.8981.00
85_Q89_D1.8611.00
109_G113_V1.8471.00
118_A128_V1.7631.00
87_M90_P1.7561.00
42_A135_L1.7541.00
138_F211_L1.7441.00
17_F24_L1.7391.00
54_T57_E1.7391.00
161_F164_A1.7071.00
16_I29_L1.7011.00
129_S229_S1.6901.00
104_H264_G1.6841.00
82_N85_Q1.6571.00
44_R47_N1.6571.00
130_D226_G1.6551.00
227_A279_M1.6401.00
45_R219_I1.6361.00
90_P94_F1.6251.00
141_G208_G1.6151.00
140_L232_F1.6141.00
18_S21_P1.5821.00
46_A58_V1.5631.00
126_F226_G1.5581.00
16_I24_L1.5321.00
224_P227_A1.5301.00
64_A68_G1.4971.00
164_A195_P1.4891.00
78_V93_L1.4721.00
127_Q225_M1.4711.00
154_W196_R1.4641.00
14_P25_H1.4611.00
68_G109_G1.4531.00
85_Q92_Y1.4391.00
148_F165_M1.4311.00
147_N152_E1.4191.00
241_I265_Q1.4070.99
124_S225_M1.4010.99
30_M146_G1.3920.99
117_F121_T1.3860.99
245_F265_Q1.3810.99
206_L243_V1.3760.99
61_L128_V1.3750.99
40_W44_R1.3710.99
206_L210_V1.3680.99
234_I276_V1.3580.99
134_P137_P1.3530.99
45_R48_R1.3270.99
57_E123_R1.3140.99
115_I119_R1.3050.99
230_G282_A1.3000.99
37_F142_A1.3000.99
91_L94_F1.2950.99
230_G279_M1.2920.99
231_L279_M1.2910.99
208_G212_F1.2760.99
166_L195_P1.2700.99
160_N164_A1.2690.99
205_L209_V1.2680.99
38_A65_G1.2670.99
44_R48_R1.2370.98
148_F201_L1.2300.98
137_P210_V1.2290.98
199_S243_V1.2290.98
234_I279_M1.2220.98
43_T47_N1.2150.98
211_L215_L1.2140.98
115_I125_F1.2100.98
91_L95_R1.2030.98
124_S127_Q1.2010.98
35_F66_F1.1930.98
39_M62_L1.1920.98
201_L205_L1.1910.98
145_L149_I1.1850.98
171_R193_V1.1830.98
168_P171_R1.1780.98
141_G204_L1.1700.97
64_A113_V1.1640.97
276_V280_V1.1630.97
43_T59_E1.1540.97
35_F69_V1.1500.97
89_D95_R1.1470.97
253_F263_M1.1470.97
79_L83_F1.1440.97
61_L65_G1.1380.97
12_F149_I1.1250.97
137_P211_L1.1100.96
231_L235_G1.1020.96
30_M33_V1.0940.96
16_I26_W1.0910.96
269_I273_V1.0890.96
239_F243_V1.0820.96
60_N121_T1.0810.95
238_A272_I1.0700.95
241_I272_I1.0690.95
96_V99_G1.0600.95
45_R134_P1.0490.94
224_P283_Y1.0460.94
123_R128_V1.0350.94
238_A242_I1.0340.94
56_N59_E1.0240.93
212_F216_N1.0180.93
273_V277_I1.0170.93
156_R248_Q1.0010.92
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  
2kluA10.153112.80.965Contact Map
4px7A10.72795.40.971Contact Map
2l9uA20.13614.10.972Contact Map
2zxeA10.299340.973Contact Map
2mofA10.14293.90.973Contact Map
3ixzA10.30953.80.973Contact Map
2ks1B10.14293.80.973Contact Map
2m20A20.13613.60.973Contact Map
2m59A20.12593.20.974Contact Map
2ls4A10.08163.20.974Contact 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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