OPENSEQ.org
Welcome: casp11@openseq.org My Submissions
T0834 -force run

ID: 1403893667 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 219 (218)
Sequences: 61 (52.3)
Seq/Len: 0.280
Nf(neff/√len): 3.5

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: 0.280).

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
48_E196_S1.7790.58
102_H210_N1.7350.55
37_L89_S1.6790.51
58_Y123_L1.6350.49
138_G175_I1.6300.48
32_F118_A1.6020.46
37_L168_L1.5950.46
13_L191_A1.5830.45
55_Q70_L1.5730.45
185_L211_I1.5370.42
136_A211_I1.5210.41
114_E157_S1.5190.41
32_F164_S1.5180.41
101_I128_H1.4050.34
14_F127_M1.3960.33
3_L111_R1.3890.33
90_L102_H1.3860.33
128_H131_E1.3860.33
160_S164_S1.3610.31
134_N146_N1.3460.31
80_F184_W1.3390.30
2_S37_L1.3380.30
58_Y209_G1.3170.29
14_F19_A1.3070.28
25_I207_Q1.2970.28
113_A118_A1.2960.28
30_T37_L1.2870.27
31_D193_L1.2740.27
130_Q149_E1.2720.27
2_S73_L1.2610.26
2_S56_L1.2590.26
84_L163_G1.2560.26
155_L184_W1.2420.25
17_N62_Q1.2420.25
83_S109_A1.2370.25
77_P104_G1.2350.25
90_L109_A1.2220.24
151_A197_L1.2200.24
61_A211_I1.2150.24
74_I116_Y1.2140.24
17_N59_K1.2140.24
39_P117_P1.2130.24
60_L174_D1.2120.24
90_L108_Y1.1980.23
110_F138_G1.1940.23
122_N157_S1.1940.23
91_S207_Q1.1930.23
116_Y126_Y1.1910.23
136_A185_L1.1850.22
11_V47_S1.1610.21
215_V218_H1.1570.21
156_V168_L1.1540.21
133_P201_D1.1530.21
135_A139_T1.1420.20
19_A127_M1.1360.20
29_Q152_I1.1260.20
188_A211_I1.1250.20
114_E202_N1.1140.19
140_L155_L1.1120.19
18_S54_I1.1120.19
110_F173_G1.1100.19
9_L59_K1.1050.19
88_S167_D1.1030.19
28_I122_N1.1020.19
51_L81_T1.1020.19
173_G177_Y1.0990.19
91_S160_S1.0980.19
80_F155_L1.0960.19
188_A198_L1.0910.18
5_E216_E1.0900.18
72_P123_L1.0900.18
61_A108_Y1.0860.18
136_A166_S1.0850.18
98_S176_Y1.0800.18
196_S199_S1.0760.18
166_S189_N1.0720.18
20_T91_S1.0700.18
207_Q218_H1.0700.18
33_P106_G1.0700.18
148_G175_I1.0680.17
56_L87_G1.0670.17
22_S216_E1.0650.17
72_P141_L1.0630.17
2_S129_I1.0630.17
99_G163_G1.0540.17
136_A168_L1.0540.17
72_P131_E1.0500.17
35_R163_G1.0490.17
13_L194_S1.0450.17
20_T61_A1.0420.16
65_T139_T1.0410.16
168_L184_W1.0380.16
51_L77_P1.0370.16
16_Y166_S1.0360.16
174_D205_F1.0350.16
74_I218_H1.0320.16
133_P198_L1.0320.16
177_Y203_T1.0310.16
18_S61_A1.0300.16
140_L193_L1.0300.16
154_A194_S1.0290.16
160_S188_A1.0290.16
12_S201_D1.0280.16
17_N84_L1.0250.16
116_Y178_L1.0240.16
168_L200_A1.0240.16
10_F123_L1.0210.16
31_D107_T1.0200.16
67_K70_L1.0170.16
59_K146_N1.0160.16
83_S107_T1.0150.16
151_A178_L1.0130.15
4_P51_L1.0100.15
156_V188_A1.0050.15
90_L210_N1.0050.15
65_T207_Q1.0030.15
41_S155_L1.0030.15
136_A150_D1.0010.15
67_K100_L1.0010.15
74_I172_K1.0000.15
16_Y27_S1.0000.15
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: (06Aug15)
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  
4r7qA10.9681000.046Contact Map
2eboA30.2749.50.973Contact Map
1s3cA10.5898.30.973Contact Map
3rdwA20.4847.10.974Contact Map
3hshA60.25576.60.975Contact Map
3fz4A10.49326.60.975Contact Map
3n3fA20.24666.40.975Contact Map
2izyA80.21925.20.976Contact Map
3gkxA20.49774.90.976Contact Map
4n21A60.35624.60.976Contact 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.

Page generated in 0.0206 seconds.