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T0808 19-418 -force run

ID: 1406008802 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 400 (395)
Sequences: 82 (71.7)
Seq/Len: 0.208
Nf(neff/√len): 3.6

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: 0.208).

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_I2.3020.78
156_W272_Y2.0800.67
197_L240_Q1.9870.62
333_R383_C1.9700.61
335_T383_C1.9290.58
172_S227_V1.9250.58
202_S237_S1.8230.52
208_N211_E1.7890.50
156_W298_R1.7890.50
345_A353_Y1.7590.48
259_I296_Y1.7530.47
221_L287_F1.6830.43
145_L317_V1.6780.43
257_M271_A1.6660.42
155_E258_Q1.6610.42
157_F299_P1.6010.38
234_N283_L1.5870.38
243_L284_I1.5790.37
230_G234_N1.5460.35
202_S209_P1.5420.35
287_F349_V1.5170.34
16_T265_G1.5150.34
251_N275_A1.4940.32
76_L364_Y1.4620.31
156_W334_L1.4400.30
202_S212_I1.4390.30
101_L282_K1.4350.29
265_G365_L1.4340.29
344_T381_F1.4160.28
310_Q368_G1.3990.28
171_H367_M1.3970.28
272_Y334_L1.3920.27
168_E367_M1.3910.27
16_T40_S1.3870.27
49_T121_N1.3830.27
341_H377_M1.3760.27
136_W218_I1.3650.26
291_K368_G1.3330.25
272_Y299_P1.3310.24
147_Y159_N1.3180.24
202_S206_T1.3180.24
209_P237_S1.3020.23
44_Y114_I1.2850.22
140_G289_R1.2810.22
220_L276_T1.2740.22
335_T387_G1.2630.21
131_D375_V1.2620.21
136_W354_Q1.2600.21
181_E294_T1.2560.21
139_R289_R1.2500.21
186_M319_F1.2460.21
212_I237_S1.2420.21
25_T63_I1.2370.20
169_T368_G1.2370.20
128_Y300_H1.2320.20
140_G355_G1.2320.20
40_S100_D1.2320.20
186_M196_I1.2300.20
188_Y296_Y1.2240.20
7_V155_E1.2200.20
29_V300_H1.2190.20
296_Y299_P1.2120.19
59_G379_T1.2100.19
7_V39_V1.2070.19
324_A388_K1.2050.19
168_E188_Y1.1990.19
103_G111_F1.1990.19
259_I266_N1.1990.19
270_T287_F1.1960.19
29_V375_V1.1950.19
168_E171_H1.1950.19
171_H207_Q1.1940.19
206_T237_S1.1840.18
231_E269_Y1.1810.18
139_R371_F1.1780.18
15_V196_I1.1770.18
91_I186_M1.1770.18
140_G203_P1.1750.18
7_V29_V1.1700.18
129_V137_G1.1700.18
137_G287_F1.1670.18
221_L270_T1.1670.18
48_P319_F1.1670.18
157_F272_Y1.1640.18
76_L167_G1.1640.18
140_G371_F1.1610.18
257_M296_Y1.1590.18
137_G202_S1.1560.17
190_S370_F1.1540.17
14_Y257_M1.1540.17
319_F365_L1.1470.17
162_T252_T1.1460.17
139_R355_G1.1410.17
34_N42_Y1.1400.17
229_I297_K1.1390.17
176_A255_F1.1390.17
24_I103_G1.1390.17
131_D134_D1.1370.17
26_Q274_Y1.1360.17
195_R286_S1.1350.17
91_I326_S1.1340.17
221_L298_R1.1270.16
272_Y298_R1.1250.16
240_Q397_L1.1250.16
237_S283_L1.1230.16
45_L99_I1.1220.16
213_P234_N1.1200.16
289_R355_G1.1190.16
48_P128_Y1.1160.16
101_L204_F1.1160.16
385_P388_K1.1150.16
186_M214_D1.1090.16
141_P240_Q1.1070.16
209_P234_N1.1060.16
341_H354_Q1.1030.16
14_Y263_G1.1030.16
87_G285_A1.1030.16
197_L397_L1.1020.16
51_A128_Y1.1020.16
265_G394_W1.1020.16
295_W344_T1.0980.15
135_Y292_T1.0970.15
156_W299_P1.0960.15
149_L365_L1.0950.15
193_E290_P1.0940.15
253_Y292_T1.0860.15
202_S283_L1.0830.15
12_N371_F1.0820.15
197_L242_Y1.0820.15
300_H394_W1.0810.15
136_W150_P1.0800.15
243_L308_P1.0790.15
158_Y254_K1.0790.15
308_P365_L1.0780.15
231_E234_N1.0750.15
43_F119_A1.0750.15
61_S103_G1.0740.15
253_Y355_G1.0730.15
40_S98_R1.0730.15
141_P164_P1.0730.15
30_T76_L1.0720.15
323_W390_P1.0720.15
114_I217_K1.0710.15
319_F326_S1.0690.15
7_V84_V1.0680.15
203_P289_R1.0680.15
66_S125_K1.0670.15
171_H174_Y1.0670.15
289_R371_F1.0660.14
234_N237_S1.0640.14
213_P237_S1.0630.14
64_K71_G1.0630.14
10_S272_Y1.0630.14
274_Y348_Q1.0610.14
200_V284_I1.0610.14
365_L381_F1.0580.14
49_T220_L1.0550.14
108_G113_E1.0550.14
16_T266_N1.0540.14
34_N364_Y1.0500.14
172_S390_P1.0500.14
218_I230_G1.0480.14
139_R203_P1.0460.14
155_E260_R1.0450.14
94_A312_Y1.0420.14
145_L184_F1.0420.14
190_S194_R1.0420.14
172_S218_I1.0410.14
145_L176_A1.0400.14
49_T192_T1.0380.14
280_E295_W1.0380.14
145_L234_N1.0380.14
57_A76_L1.0370.14
12_N202_S1.0370.14
243_L360_D1.0370.14
319_F374_S1.0360.14
91_I389_E1.0350.14
192_T248_K1.0350.14
259_I295_W1.0340.14
188_Y367_M1.0330.14
14_Y310_Q1.0320.13
206_T213_P1.0310.13
99_I134_D1.0280.13
181_E204_F1.0280.13
175_M290_P1.0280.13
344_T370_F1.0280.13
218_I234_N1.0270.13
45_L196_I1.0260.13
44_Y374_S1.0250.13
190_S322_Q1.0240.13
213_P397_L1.0230.13
13_G41_I1.0230.13
89_I134_D1.0220.13
29_V357_N1.0210.13
35_P191_P1.0210.13
203_P239_G1.0200.13
241_S337_A1.0200.13
14_Y368_G1.0180.13
175_M240_Q1.0180.13
132_F349_V1.0150.13
60_H161_I1.0150.13
319_F338_T1.0140.13
177_A397_L1.0140.13
188_Y223_Q1.0140.13
104_V170_M1.0130.13
40_S43_F1.0130.13
193_E305_N1.0130.13
355_G371_F1.0120.13
14_Y121_N1.0100.13
367_M371_F1.0100.13
137_G212_I1.0090.13
218_I231_E1.0080.13
209_P212_I1.0080.13
137_G345_A1.0070.13
76_L191_P1.0050.13
164_P261_P1.0050.13
13_G268_T1.0040.13
205_D361_N1.0040.13
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  
2bgoA10.2791.30.969Contact Map
2vzsA20.022587.60.971Contact Map
4kmqA10.2884.20.972Contact Map
2vzpA20.27578.70.974Contact Map
2w87A20.307573.80.975Contact Map
2y8kA10.2965.10.976Contact Map
2w47A10.29556.70.978Contact Map
2xwxA20.297549.60.979Contact Map
2wz8A10.287546.80.979Contact Map
2w3jA10.30538.40.98Contact 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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