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T0814 60-180

ID: 1404854169 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 121 (118)
Sequences: 228 (200.8)
Seq/Len: 1.932
Nf(neff/√len): 18.5

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: 1.932).

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
23_N27_T4.6081.00
75_S101_E2.9431.00
7_G15_Y2.4371.00
82_V93_F2.2641.00
15_Y92_I2.1200.99
21_H29_S1.8690.98
3_I95_A1.8040.97
33_P41_Q1.7800.97
42_G73_K1.7770.97
20_V81_Q1.5940.94
38_N71_Q1.5140.91
22_C96_C1.4330.88
65_L72_F1.4150.87
36_Y99_V1.4000.86
11_G91_I1.3820.85
92_I106_I1.3780.85
2_E69_D1.3720.85
63_L80_I1.3570.84
47_D62_R1.3470.83
26_W77_N1.3300.82
18_N81_Q1.3170.81
15_Y93_F1.3070.80
41_Q93_F1.3050.80
17_Y67_N1.2600.77
81_Q91_I1.2350.75
56_T61_Y1.2240.74
10_S57_Q1.2200.74
17_Y39_G1.2180.73
19_V72_F1.1730.69
7_G96_C1.1680.69
39_G67_N1.1520.67
8_L101_E1.1400.66
7_G80_I1.1380.66
90_Q104_V1.1350.66
35_E60_N1.1320.65
16_A41_Q1.1310.65
112_G119_N1.1300.65
27_T62_R1.1270.65
32_S73_K1.1130.63
3_I94_T1.1090.63
41_Q72_F1.1090.63
18_N49_A1.0950.62
25_D29_S1.0840.60
43_T104_V1.0790.60
87_T100_V1.0790.60
34_I65_L1.0780.60
14_R24_A1.0740.59
13_T84_N1.0650.58
50_N59_S1.0450.56
36_Y110_V1.0440.56
14_R44_T1.0370.55
60_N110_V1.0330.55
11_G82_V1.0330.55
16_A52_I1.0280.54
64_L91_I1.0250.54
12_Y50_N1.0230.54
29_S97_F1.0180.53
69_D92_I1.0040.52
107_S115_D1.0010.51
113_N119_N1.0000.51
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  
3v9fA40.56228.70.935Contact Map
2hr0A10.950413.60.944Contact Map
3ottA20.652913.20.944Contact Map
3cu7A20.925612.50.945Contact Map
4a2lA60.578511.50.946Contact Map
2pn5A10.909110.50.947Contact Map
3prxB20.85129.30.948Contact Map
2p9rA20.79348.10.949Contact Map
3hrzA10.8437.30.95Contact Map
4acqA40.93396.60.952Contact 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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