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T0824

ID: 1403117553 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 110 (107)
Sequences: 126 (106)
Seq/Len: 1.178
Nf(neff/√len): 10.2

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: 1.178).

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
24_D78_R5.1791.00
92_V107_F2.5591.00
59_D86_R1.7790.93
63_W107_F1.7500.92
67_M96_L1.6910.90
11_P34_C1.4550.78
34_C68_C1.4220.76
48_S103_T1.3990.74
34_C65_M1.3630.71
10_F68_C1.3440.70
34_C63_W1.3320.69
43_K58_F1.3220.68
8_L20_A1.2800.64
18_T88_A1.2630.63
37_E40_G1.2610.63
12_A23_S1.2560.62
40_G99_Y1.2430.61
17_E21_H1.2370.60
60_R79_Y1.2360.60
21_H84_D1.2250.59
31_A63_W1.2210.59
19_G25_A1.2180.59
68_C105_I1.2130.58
58_F79_Y1.2090.58
77_V93_G1.2080.58
16_P29_G1.1970.57
32_D106_L1.1880.56
25_A29_G1.1740.54
53_P79_Y1.1690.54
18_T65_M1.1630.53
44_R93_G1.1600.53
11_P68_C1.1460.52
91_W96_L1.1400.51
34_C91_W1.1400.51
84_D88_A1.1270.50
37_E44_R1.1190.49
18_T26_I1.1140.49
24_D69_E1.0820.46
41_A74_G1.0740.45
21_H76_S1.0720.45
3_R8_L1.0700.44
41_A101_D1.0690.44
60_R65_M1.0630.44
10_F91_W1.0580.43
80_V105_I1.0570.43
7_V42_D1.0550.43
28_A78_R1.0480.42
11_P91_W1.0460.42
24_D27_K1.0410.42
12_A52_I1.0380.41
20_A28_A1.0310.41
42_D46_Q1.0200.40
63_W96_L1.0190.40
51_G60_R1.0170.39
3_R6_D1.0160.39
10_F34_C1.0160.39
92_V99_Y1.0150.39
68_C91_W1.0100.39
20_A78_R1.0060.38
8_L81_S1.0010.38
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: (14Jun14)
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  
3j3bT10.390923.20.933Contact Map
4a17P10.390922.40.934Contact Map
3u5eT10.390922.30.934Contact Map
3iz5U10.421.40.935Contact Map
3zf7U10.390920.80.935Contact Map
1vq8Q10.390918.40.937Contact Map
2zqeA10.727313.40.94Contact Map
3qd7X10.7455120.942Contact Map
3j21R10.390911.10.943Contact Map
3cvzA40.745510.10.943Contact 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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