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T0808 300-418 -force run

ID: 1404889125 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 119 (117)
Sequences: 89 (78.1)
Seq/Len: 0.761
Nf(neff/√len): 7.2

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: 0.761).

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
6_F68_V2.1780.96
54_T102_C2.1600.96
64_A72_Y1.9430.91
52_R102_C1.8120.87
60_H96_M1.7860.86
43_A107_K1.6960.81
38_F84_L1.6040.76
29_Q87_G1.5920.75
38_F93_S1.5710.74
63_T100_F1.4680.67
15_Y18_P1.4620.66
10_K87_G1.3900.60
14_W66_A1.3790.59
14_W63_T1.3770.59
42_W50_W1.3670.58
18_P53_L1.3660.58
8_R74_G1.3570.58
104_P107_K1.3310.55
94_V103_K1.3130.54
30_G71_D1.3050.53
12_N19_H1.2940.52
54_T106_G1.2850.51
35_E78_K1.2440.48
9_P89_F1.2310.47
19_H113_W1.2050.45
63_T89_F1.2040.44
27_P84_L1.2040.44
18_P36_V1.1950.44
103_K108_E1.1930.44
112_D115_A1.1630.41
30_G89_F1.1550.40
13_T17_R1.1460.40
38_F45_S1.1440.39
42_W109_P1.1420.39
9_P71_D1.1270.38
42_W54_T1.1190.37
60_H73_Q1.1130.37
71_D89_F1.1120.37
3_I9_P1.1020.36
86_M90_F1.1020.36
45_S51_S1.0920.35
28_E100_F1.0910.35
55_D101_Y1.0900.35
44_R108_E1.0780.34
8_R90_F1.0740.34
3_I41_Q1.0740.34
19_H110_E1.0640.33
34_R82_F1.0610.33
15_Y62_A1.0500.32
33_S85_K1.0490.32
2_L57_T1.0430.32
9_P30_G1.0370.31
57_T65_S1.0330.31
107_K112_D1.0320.31
30_G69_R1.0300.31
83_Y96_M1.0290.30
105_T115_A1.0200.30
8_R86_M1.0110.29
74_G86_M1.0050.29
22_L74_G1.0010.28
41_Q56_A1.0010.28
50_W54_T1.0000.28
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  
2llzA10.705931.20.933Contact Map
3owtC10.09246.80.951Contact Map
3tg7A10.69755.50.953Contact Map
4h62V10.067250.954Contact Map
2fq3A10.26894.80.954Contact Map
2ww6A30.21014.70.954Contact Map
2vovA10.462240.956Contact Map
3v7dA20.31093.50.957Contact Map
2iqtA10.33613.40.957Contact Map
2p1mA10.35293.10.958Contact 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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