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T0841

ID: 1404412446 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 253 (231)
Sequences: 9853 (7712.6)
Seq/Len: 42.654
Nf(neff/√len): 507.5

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: 42.654).

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
138_C203_C6.2421.00
45_G53_I3.8001.00
52_W107_L3.5251.00
33_S41_H3.4871.00
31_T141_A3.2291.00
27_N157_V3.2151.00
47_L114_V3.0961.00
43_C59_C3.0211.00
28_S157_V2.9641.00
193_C221_C2.8841.00
58_Q197_Y2.7911.00
30_W124_C2.6761.00
74_L114_V2.6571.00
94_A109_K2.6251.00
60_F106_V2.5901.00
191_G228_A2.5261.00
54_L211_L2.4581.00
46_S211_L2.3301.00
52_W109_K2.2531.00
158_A190_V2.1871.00
32_V45_G2.1411.00
28_S141_A2.1221.00
51_Q113_S2.0871.00
100_P243_V2.0871.00
110_L114_V2.0621.00
20_V23_G2.0581.00
92_P111_E2.0431.00
116_L122_L1.9971.00
103_S236_F1.9911.00
95_K109_K1.9621.00
140_I192_A1.9441.00
51_Q109_K1.9291.00
91_V114_V1.9211.00
32_V74_L1.9181.00
179_S235_V1.8921.00
93_V108_L1.8751.00
105_L236_F1.8711.00
140_I158_A1.8561.00
46_S214_I1.8511.00
46_S123_I1.8491.00
141_A202_A1.8101.00
181_M201_L1.7561.00
123_I211_L1.7461.00
97_V243_V1.7431.00
168_C182_C1.7131.00
138_C162_V1.7041.00
49_K52_W1.6731.00
217_P229_V1.6671.00
237_V241_H1.6641.00
231_T236_F1.6291.00
73_W76_T1.6261.00
55_T60_F1.5951.00
50_E113_S1.5941.00
73_W90_R1.5841.00
123_I202_A1.5551.00
192_A215_I1.5341.00
191_G230_F1.5161.00
164_S167_E1.5081.00
165_N232_R1.4891.00
32_V53_I1.4771.00
148_G223_R1.4761.00
72_V75_G1.4691.00
35_R41_H1.4161.00
94_A111_E1.3970.99
30_W209_W1.3970.99
31_T155_L1.3950.99
91_V111_E1.3930.99
152_D156_N1.3750.99
180_E217_P1.3640.99
232_R235_V1.3560.99
47_L74_L1.3550.99
161_N184_E1.3250.99
26_G77_L1.3210.99
140_I215_I1.3210.99
179_S236_F1.3080.99
140_I160_L1.2920.99
105_L231_T1.2750.99
138_C212_E1.2740.99
203_C212_E1.2580.99
134_P164_S1.2490.99
26_G119_R1.2470.99
201_L230_F1.2340.98
138_C201_L1.2240.98
215_I218_N1.2210.98
28_S139_E1.2180.98
47_L116_L1.2010.98
31_T44_G1.2010.98
74_L120_V1.1990.98
191_G222_A1.1830.98
124_C209_W1.1640.97
34_L72_V1.1610.97
52_W243_V1.1570.97
177_R180_E1.1510.97
139_E159_L1.1500.97
98_C106_V1.1470.97
183_T201_L1.1380.97
30_W202_A1.1230.97
163_I227_P1.1170.96
160_L230_F1.1120.96
53_I72_V1.1010.96
55_T106_V1.0840.96
125_L237_V1.0840.96
137_K159_L1.0730.95
99_G102_G1.0620.95
76_T88_L1.0490.94
47_L53_I1.0490.94
31_T200_P1.0440.94
161_N185_G1.0360.94
58_Q104_Q1.0330.94
126_P237_V1.0170.93
117_N120_V1.0150.93
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: (28Jun14)
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  
4durA20.94471000.073Contact Map
3nxpA10.97231000.099Contact Map
4nzqA10.98021000.102Contact Map
2f83A10.84581000.113Contact Map
2b9lA10.97631000.119Contact Map
4kkdA20.95261000.122Contact Map
4igdA10.93281000.123Contact Map
2asuB10.88931000.123Contact Map
2xxlA20.95261000.135Contact Map
4f4oC40.88541000.137Contact 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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