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T0852 1-260

ID: 1405102180 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 260 (234)
Sequences: 4729 (3402.8)
Seq/Len: 20.209
Nf(neff/√len): 222.4

HHblits Results: (2013_03)
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: 20.209).

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
149_M160_I4.4821.00
162_S165_P2.8881.00
124_Q129_I2.7051.00
53_L85_V2.6221.00
202_Y206_I2.5461.00
209_E213_R2.5361.00
39_I85_V2.5231.00
83_I129_I2.4821.00
124_Q133_K2.4661.00
206_I227_D2.4591.00
27_S34_K2.4521.00
51_Y83_I2.4381.00
211_A215_A2.3801.00
54_I136_I2.2571.00
113_E117_A2.1811.00
54_I82_C2.1651.00
45_Y51_Y2.1281.00
25_T34_K2.1141.00
41_K83_I2.1121.00
145_A160_I2.0881.00
45_Y128_P2.0801.00
122_Y126_K2.0651.00
209_E223_Y1.9901.00
112_F152_E1.9371.00
44_K81_K1.8811.00
195_D229_K1.8431.00
28_S118_E1.8341.00
160_I189_Y1.7861.00
55_V124_Q1.7701.00
210_R214_S1.7491.00
134_G159_M1.7491.00
27_S32_N1.7311.00
161_V244_A1.7301.00
24_E37_I1.6951.00
123_I129_I1.6601.00
56_V136_I1.6321.00
226_V243_Q1.6271.00
112_F148_Y1.5971.00
120_V157_F1.5711.00
26_F114_F1.5461.00
114_F119_L1.5321.00
190_Y226_V1.5201.00
146_N162_S1.5141.00
167_A208_F1.5121.00
135_V148_Y1.4761.00
55_V120_V1.4571.00
23_S36_K1.4561.00
53_L129_I1.4521.00
55_V85_V1.4481.00
56_V86_G1.4311.00
146_N189_Y1.4301.00
130_A133_K1.4171.00
191_M209_E1.4081.00
39_I83_I1.3730.99
163_L244_A1.3560.99
165_P205_A1.3500.99
195_D230_G1.3330.99
85_V123_I1.3190.99
162_S191_M1.3090.99
57_L144_L1.3090.99
55_V123_I1.3080.99
146_N165_P1.2950.99
135_V160_I1.2910.99
136_I163_L1.2750.99
25_T36_K1.2640.99
147_Y151_A1.2520.99
195_D227_D1.2500.99
164_N197_E1.2500.99
159_M188_F1.2390.98
116_S152_E1.2310.98
152_E155_P1.2220.98
28_S31_L1.2160.98
37_I119_L1.2150.98
228_F240_G1.2130.98
139_E233_V1.2110.98
49_Q81_K1.2060.98
213_R223_Y1.1960.98
211_A214_S1.1780.98
22_I41_K1.1770.98
146_N167_A1.1640.97
40_Y71_R1.1480.97
112_F151_A1.1470.97
57_L111_F1.1430.97
53_L83_I1.1410.97
55_V133_K1.1370.97
116_S156_T1.1120.96
46_T49_Q1.1060.96
231_S237_K1.1040.96
63_M86_G1.0910.96
192_A240_G1.0860.96
191_M208_F1.0850.96
120_V133_K1.0810.95
24_E122_Y1.0810.95
209_E225_F1.0780.95
241_I245_L1.0710.95
202_Y227_D1.0640.95
212_M223_Y1.0630.95
177_H180_A1.0570.95
242_A246_D1.0540.95
203_D207_Q1.0430.94
114_F118_E1.0370.94
143_F147_Y1.0330.94
138_S164_N1.0280.94
117_A121_P1.0270.94
26_F37_I1.0250.93
207_Q210_R1.0220.93
42_P83_I1.0170.93
196_V230_G1.0130.93
57_L87_V1.0090.93
206_I225_F1.0040.93
133_K158_N1.0030.93
41_K51_Y1.0010.92
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: (05Jul14)
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  
3gffA20.90381000.453Contact Map
3c8dA40.91541000.531Contact Map
2gzsA10.88081000.531Contact Map
4folA40.91000.541Contact Map
1jjfA10.87311000.544Contact Map
2qm0A20.926999.90.55Contact Map
3ls2A40.907799.90.556Contact Map
4h18A40.861599.90.573Contact Map
4b6gA20.919299.90.578Contact Map
3i6yA20.923199.90.583Contact 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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