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parp1- try2

ID: 1517844945 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 106 (96)
Sequences: 227 (159.2)
Seq/Len: 2.365
Nf(neff/√len): 16.2

HHblits Results: (2016_02)
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: 2.365).

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
26_I31_G3.1481.00
4_L29_L2.0660.99
23_K27_E1.9080.99
11_T44_I1.7370.98
11_T26_I1.6920.97
49_E56_K1.5640.95
15_L22_V1.5600.95
94_P99_V1.5050.93
33_L79_S1.5000.93
96_G99_V1.4760.93
4_L76_V1.4550.92
59_E62_E1.4420.91
3_P29_L1.4000.90
48_K51_E1.3460.87
85_E88_L1.3390.87
11_T33_L1.3220.86
94_P98_E1.3150.85
94_P97_A1.2690.83
53_M61_K1.2650.82
39_K64_N1.2500.81
50_V57_M1.2350.80
14_K24_A1.2160.79
14_K67_V1.2150.79
9_I42_L1.2130.78
42_L72_F1.1990.77
15_L30_G1.1840.76
93_S99_V1.1820.76
4_L13_G1.1770.75
85_E89_A1.1700.75
15_L18_N1.1580.74
37_A74_Q1.1470.73
93_S98_E1.1280.71
31_G34_T1.1220.70
28_K35_G1.1210.70
77_S80_T1.1130.70
19_K56_K1.1050.69
84_Q89_A1.1010.68
68_V72_F1.0930.67
10_L33_L1.0780.66
17_R31_G1.0750.66
83_L87_F1.0650.65
69_S80_T1.0420.62
67_V70_E1.0400.62
93_S97_A1.0310.61
37_A43_C1.0250.60
93_S96_G1.0170.59
31_G70_E1.0170.59
24_A74_Q1.0060.58
5_S37_A1.0050.58
68_V73_L1.0040.58
45_S67_V1.0020.58
95_W98_E1.0010.57
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  
2cokA1199.80.34Contact Map
1l7bA10.801999.60.459Contact Map
2k6gA10.735899.50.469Contact Map
2ebuA10.858599.50.473Contact Map
4q66A40.735899.50.473Contact Map
4yg8A10.971799.50.476Contact Map
1dgsA2099.50.485Contact Map
2owoA1099.50.49Contact Map
3ef1A10.811399.40.498Contact Map
3pd7A20.877499.40.5Contact 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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