OPENSEQ.org
Welcome: casp11@openseq.org My Submissions
T0836 -force run

ID: 1405445302 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 204 (200)
Sequences: 73 (54.6)
Seq/Len: 0.365
Nf(neff/√len): 3.9

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: 0.365).

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
60_F87_A2.5910.95
99_W143_T2.0990.83
176_K180_L1.9150.74
59_Y64_Q1.8920.73
142_A169_D1.7250.63
87_A156_N1.7010.61
136_G140_W1.6590.58
5_L11_T1.6490.57
106_A139_M1.6460.57
167_D170_A1.6330.56
60_F156_N1.6110.55
22_I195_T1.5890.53
65_I160_A1.5780.52
24_I31_H1.4850.46
146_F151_V1.4740.45
71_I78_A1.4640.44
7_N11_T1.4530.44
158_K164_V1.4480.43
4_L11_T1.4450.43
16_F190_I1.4160.41
112_L117_T1.4080.41
58_Y172_A1.3630.38
45_L101_M1.3480.37
60_F88_L1.3480.37
152_F181_V1.3440.36
65_I77_P1.3240.35
61_N64_Q1.3230.35
69_P75_L1.3210.35
24_I142_A1.3110.34
99_W103_V1.3080.34
14_V18_L1.3080.34
59_Y62_F1.3020.34
87_A177_T1.2970.33
104_L108_N1.2920.33
147_F152_F1.2820.32
18_L21_V1.2630.31
160_A179_M1.2500.30
57_L153_I1.2460.30
100_V117_T1.2300.29
57_L192_M1.2260.29
99_W146_F1.2240.29
65_I179_M1.2210.29
84_A161_L1.2180.28
153_I178_A1.2130.28
89_F99_W1.2110.28
178_A192_M1.1980.27
65_I181_V1.1940.27
93_W96_L1.1900.27
67_V194_A1.1840.27
173_K177_T1.1810.26
49_F101_M1.1790.26
160_A181_V1.1710.26
149_V153_I1.1690.26
115_A136_G1.1670.26
137_T195_T1.1590.25
159_I174_A1.1570.25
88_L153_I1.1520.25
96_L146_F1.1520.25
60_F177_T1.1400.24
112_L164_V1.1270.24
3_G10_N1.1240.23
13_I165_E1.1210.23
16_F90_W1.1160.23
50_G193_L1.1150.23
49_F58_Y1.1030.22
60_F178_A1.1020.22
64_Q84_A1.0990.22
150_W161_L1.0980.22
77_P160_A1.0940.22
57_L87_A1.0930.22
3_G12_I1.0900.22
61_N192_M1.0840.21
21_V167_D1.0840.21
85_P153_I1.0830.21
95_A98_T1.0800.21
18_L90_W1.0790.21
57_L178_A1.0760.21
89_F94_A1.0750.21
21_V170_A1.0740.21
17_V20_L1.0730.21
9_R105_L1.0710.21
147_F151_V1.0690.21
52_L73_A1.0680.21
153_I192_M1.0660.21
29_S32_G1.0630.20
85_P149_V1.0620.20
57_L149_V1.0540.20
13_I21_V1.0540.20
29_S130_M1.0530.20
159_I166_A1.0490.20
62_F135_I1.0490.20
103_V146_F1.0450.20
72_P139_M1.0440.20
115_A140_W1.0430.20
159_I170_A1.0240.19
50_G149_V1.0240.19
149_V178_A1.0230.19
119_G131_G1.0200.18
25_G28_H1.0190.18
50_G98_T1.0140.18
17_V26_Y1.0130.18
57_L88_L1.0060.18
57_L61_N1.0050.18
59_Y84_A1.0040.18
26_Y31_H1.0040.18
98_T149_V1.0040.18
14_V186_T1.0000.18
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  
3qe7A10.26962.80.977Contact Map
1fftC20.49022.60.977Contact Map
3hd7A20.1522.50.977Contact Map
1zxgA10.1521.40.98Contact Map
1n7lA10.12251.30.981Contact Map
3k8gA20.30391.30.981Contact Map
1m56C20.49021.30.981Contact Map
1v54C20.49021.30.981Contact Map
3zs9C20.13241.10.981Contact Map
3j01B10.56861.10.982Contact 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 0.0371 seconds.