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T0831 109-352 Tp831 -force run

ID: 1407214705 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 244 (244)
Sequences: 116 (90.8)
Seq/Len: 0.475
Nf(neff/√len): 5.8

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: 0.475).

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
136_F242_V2.1100.89
125_R136_F1.8750.79
125_R131_L1.8380.77
125_R238_L1.8250.76
125_R242_V1.8240.76
231_L242_V1.7700.73
136_F231_L1.7460.72
125_R231_L1.6630.66
183_G229_K1.6620.66
131_L242_V1.5780.61
191_E228_Y1.5260.57
55_V114_N1.5210.56
52_V212_D1.5120.56
79_C86_L1.4940.54
185_W228_Y1.4920.54
119_A126_P1.4840.54
147_E185_W1.4650.52
226_K232_H1.4580.52
125_R185_W1.4420.50
123_H242_V1.4290.49
229_K235_W1.4290.49
35_W227_E1.4020.47
124_L242_V1.3990.47
191_E225_K1.3980.47
124_L229_K1.3630.44
97_Q131_L1.3610.44
93_L188_S1.3610.44
193_S221_F1.3490.43
98_K117_E1.3480.43
104_V237_A1.3230.41
85_L228_Y1.3090.40
111_P131_L1.3020.40
161_I167_E1.3000.40
7_V16_P1.2890.39
161_I168_D1.2820.38
55_V112_S1.2640.37
238_L242_V1.2560.37
119_A124_L1.2540.36
124_L183_G1.2460.36
58_E193_S1.2400.35
162_F167_E1.2400.35
6_E233_E1.2390.35
213_E235_W1.2270.34
225_K243_S1.2140.34
91_E199_S1.2130.34
42_A145_E1.2070.33
34_W191_E1.2050.33
222_E225_K1.2040.33
126_P214_G1.2030.33
214_G225_K1.2020.33
235_W238_L1.1980.33
120_T125_R1.1960.32
87_T202_K1.1930.32
115_V221_F1.1880.32
170_E177_A1.1860.32
78_D84_F1.1840.32
12_Q19_Q1.1810.31
135_V197_I1.1740.31
166_I170_E1.1680.31
7_V14_L1.1610.30
168_D171_G1.1600.30
55_V105_K1.1590.30
123_H136_F1.1590.30
55_V196_A1.1590.30
119_A147_E1.1510.29
38_V55_V1.1500.29
59_I230_L1.1350.28
162_F171_G1.1240.28
82_L131_L1.1230.28
170_E173_V1.1210.28
86_L156_K1.1170.27
173_V177_A1.1160.27
185_W191_E1.1150.27
53_Q196_A1.1130.27
40_H48_D1.1120.27
125_R183_G1.1110.27
147_E151_F1.1110.27
191_E214_G1.1070.27
41_R84_F1.1000.26
7_V55_V1.0990.26
19_Q26_R1.0970.26
26_R39_I1.0920.26
170_E175_D1.0890.26
55_V239_R1.0850.25
66_Q69_K1.0850.25
62_N100_V1.0760.25
121_V242_V1.0750.25
32_S119_A1.0720.25
129_L194_M1.0670.24
158_Q193_S1.0640.24
61_S225_K1.0590.24
167_E173_V1.0590.24
153_N181_T1.0580.24
54_R84_F1.0560.24
119_A123_H1.0550.24
32_S227_E1.0480.23
38_V128_R1.0460.23
172_L176_R1.0450.23
107_L239_R1.0440.23
2_K5_T1.0430.23
60_T90_M1.0430.23
140_D143_F1.0420.23
13_A20_T1.0410.23
11_Q92_E1.0380.23
39_I215_S1.0360.23
116_I119_A1.0360.23
42_A73_S1.0310.22
119_A185_W1.0310.22
125_R226_K1.0310.22
10_A115_V1.0270.22
86_L119_A1.0260.22
167_E177_A1.0240.22
85_L192_R1.0220.22
195_K215_S1.0210.22
52_V85_L1.0190.22
24_L81_G1.0160.22
39_I72_M1.0130.22
105_K144_T1.0110.21
50_E214_G1.0110.21
139_A240_N1.0100.21
143_F149_K1.0060.21
81_G200_F1.0050.21
15_Y146_Y1.0050.21
46_T53_Q1.0030.21
113_R201_A1.0030.21
86_L193_S1.0000.21
120_T214_G1.0000.21
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: (17Jul14)
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  
4lvhA40.057419.40.952Contact Map
2yp5A10.561516.30.953Contact Map
2wr1A30.565616.30.953Contact Map
3ghgC40.516411.30.957Contact Map
1m1jC20.508210.90.957Contact Map
2w83C20.27467.60.96Contact Map
4f23A30.61487.30.96Contact Map
4mc5A30.57796.50.961Contact Map
3ghgA40.43036.20.962Contact Map
2v0oA30.45495.10.963Contact 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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