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T0808 200-300

ID: 1404925126 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 101 (101)
Sequences: 109 (85.4)
Seq/Len: 1.079
Nf(neff/√len): 8.5

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: 1.079).

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
76_M90_A2.5631.00
21_S56_S2.5070.99
27_N30_E2.3820.99
16_L59_Q2.2900.99
72_Y92_F1.8500.93
11_T36_K1.6170.85
81_D84_G1.5500.82
21_S31_I1.4590.76
5_M33_D1.4360.74
33_D82_G1.4020.72
5_M15_I1.3820.70
16_L61_Y1.3800.70
53_N56_S1.3550.68
70_N94_A1.3520.68
5_M29_K1.3390.67
49_G53_N1.3250.66
79_R98_K1.2780.61
8_N14_R1.2240.57
78_I85_N1.2010.54
44_K70_N1.1970.54
34_D38_K1.1910.53
98_K101_K1.1700.51
32_P53_N1.1590.50
85_N99_E1.1470.49
31_I56_S1.1360.48
18_S43_G1.1330.48
18_S46_V1.1280.47
21_S50_E1.1250.47
81_D85_N1.1240.47
9_S12_E1.1180.47
19_V95_T1.1160.46
27_N93_Y1.1100.46
29_K33_D1.1070.45
36_K99_E1.1010.45
80_P90_A1.0980.45
8_N11_T1.0910.44
29_K81_D1.0890.44
73_K89_T1.0880.44
94_A97_E1.0820.43
29_K35_Q1.0770.43
29_K34_D1.0740.42
52_G60_S1.0720.42
37_I40_L1.0640.41
17_F52_G1.0500.40
30_E33_D1.0400.39
62_L73_K1.0330.39
73_K93_Y1.0300.38
71_T74_F1.0280.38
33_D96_D1.0270.38
25_T32_P1.0240.38
10_P87_T1.0230.38
58_G69_G1.0150.37
23_F32_P1.0030.36
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  
1yo8A10.722827.30.922Contact Map
2rfwA40.574319.70.927Contact Map
2bhuA10.851511.90.934Contact Map
1ojjA20.55458.90.938Contact Map
3vgfA10.79218.40.938Contact Map
2fhfA10.85157.80.939Contact Map
1eg1A20.55456.60.941Contact Map
4a02A10.37626.50.941Contact Map
2yoyA20.376260.942Contact Map
2fsvC10.33665.60.943Contact 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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