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T0808 19-330 -force run -force run

ID: 1405972752 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 312 (310)
Sequences: 83 (71.7)
Seq/Len: 0.268
Nf(neff/√len): 4.1

Jackhmmer Results: (2014_04_16)
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: 0.268).

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
43_F99_I2.3680.86
197_L240_Q2.0720.74
156_W272_Y1.9200.65
221_L287_F1.9150.65
172_S227_V1.8710.62
208_N211_E1.8070.58
202_S237_S1.8060.58
155_E258_Q1.7760.56
259_I296_Y1.7620.56
168_E171_H1.7230.53
243_L284_I1.6800.50
251_N275_A1.6530.48
157_F299_P1.6250.47
156_W298_R1.6210.46
257_M271_A1.6100.46
7_V39_V1.6010.45
131_D134_D1.5850.44
16_T265_G1.5720.43
234_N283_L1.5610.43
230_G234_N1.4820.38
101_L282_K1.4700.37
99_I134_D1.4500.36
7_V155_E1.3890.32
272_Y299_P1.3720.31
176_A255_F1.3700.31
202_S209_P1.3620.31
40_S100_D1.3620.31
296_Y299_P1.3130.28
157_F272_Y1.3070.28
16_T40_S1.3030.27
231_E269_Y1.3010.27
181_E294_T1.3010.27
202_S212_I1.2990.27
44_Y114_I1.2890.27
29_V300_H1.2610.25
15_V196_I1.2600.25
25_T63_I1.2570.25
220_L276_T1.2540.25
202_S206_T1.2540.25
43_F119_A1.2530.25
8_G132_F1.2520.25
188_Y296_Y1.2490.25
137_G202_S1.2440.24
229_I297_K1.2410.24
139_R289_R1.2350.24
168_E188_Y1.2330.24
38_I102_Q1.2300.24
171_H207_Q1.2280.24
136_W218_I1.2240.23
91_I186_M1.2110.23
243_L308_P1.2100.23
91_I94_A1.2050.23
10_S272_Y1.2020.22
147_Y159_N1.1990.22
140_G289_R1.1790.21
193_E305_N1.1790.21
14_Y310_Q1.1760.21
135_Y292_T1.1760.21
206_T213_P1.1740.21
162_T252_T1.1730.21
137_G212_I1.1690.21
186_M196_I1.1670.21
140_G203_P1.1610.21
26_Q274_Y1.1560.20
137_G287_F1.1500.20
141_P164_P1.1500.20
257_M296_Y1.1490.20
188_Y223_Q1.1490.20
171_H174_Y1.1460.20
87_G242_Y1.1460.20
195_R286_S1.1420.20
259_I266_N1.1410.20
108_G269_Y1.1400.20
103_G111_F1.1310.19
141_P240_Q1.1300.19
128_Y300_H1.1300.19
266_N288_L1.1230.19
272_Y298_R1.1220.19
12_N139_R1.1210.19
104_V170_M1.1180.19
141_P197_L1.1170.19
186_M214_D1.1160.19
270_T287_F1.1140.19
122_V161_I1.1140.19
74_V242_Y1.1120.19
212_I237_S1.1070.18
137_G303_L1.1030.18
64_K71_G1.1030.18
10_S99_I1.0990.18
164_P271_A1.0990.18
175_M197_L1.0930.18
189_N195_R1.0930.18
200_V284_I1.0920.18
161_I310_Q1.0920.18
175_M240_Q1.0890.18
108_G113_E1.0860.18
40_S98_R1.0860.18
204_F237_S1.0850.18
57_A76_L1.0840.18
7_V84_V1.0820.17
166_E252_T1.0820.17
209_P237_S1.0820.17
21_G33_T1.0810.17
218_I231_E1.0770.17
35_P191_P1.0770.17
87_G285_A1.0750.17
206_T209_P1.0750.17
146_G196_I1.0730.17
209_P213_P1.0720.17
237_S283_L1.0700.17
203_P289_R1.0680.17
194_R224_G1.0670.17
203_P239_G1.0660.17
218_I230_G1.0650.17
55_L76_L1.0650.17
36_K161_I1.0630.17
76_L191_P1.0560.17
206_T237_S1.0530.16
253_Y273_F1.0530.16
73_K149_L1.0510.16
139_R203_P1.0480.16
101_L204_F1.0470.16
39_V74_V1.0470.16
66_S125_K1.0440.16
14_Y295_W1.0440.16
7_V260_R1.0440.16
262_D265_G1.0430.16
16_T266_N1.0420.16
11_G252_T1.0420.16
57_A272_Y1.0400.16
181_E204_F1.0360.16
259_I295_W1.0340.16
166_E177_A1.0310.16
76_L167_G1.0310.16
14_Y40_S1.0300.16
166_E174_Y1.0290.16
40_S102_Q1.0290.16
117_L288_L1.0280.16
288_L296_Y1.0260.15
190_S194_R1.0230.15
28_G184_F1.0220.15
47_Q79_N1.0200.15
259_I299_P1.0190.15
270_T294_T1.0160.15
195_R241_S1.0150.15
197_L242_Y1.0150.15
50_T67_Y1.0150.15
13_G310_Q1.0150.15
101_L242_Y1.0130.15
202_S283_L1.0130.15
147_Y162_T1.0120.15
171_H257_M1.0120.15
209_P212_I1.0100.15
156_W299_P1.0080.15
137_G189_N1.0070.15
129_V300_H1.0060.15
155_E260_R1.0040.15
253_Y292_T1.0040.15
218_I234_N1.0030.15
28_G194_R1.0020.15
33_T46_H1.0020.15
231_E234_N1.0020.15
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: (12Jul14)
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  
2bgoA10.349497.60.937Contact Map
2vzsA2097.10.941Contact Map
4kmqA10.362297.10.942Contact Map
2vzpA20.355896.60.945Contact Map
2w87A20.394296.40.946Contact Map
2y8kA10.371896.10.948Contact Map
2w47A10.381496.10.948Contact Map
2cdpA40.37595.10.952Contact Map
2wz8A10.362294.60.953Contact Map
2w3jA10.39194.50.953Contact 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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