OPENSEQ.org
knl_2

ID: 1517068510 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 50% gaps before running GREMLIN.
Length: 142 (137)
Sequences: 302 (202.5)
Seq/Len: 2.204
Nf(neff/√len): 17.3

Jackhmmer Results: (2016_04)
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: 2.204).

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 > 50% 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
126_W129_W1.9950.99
22_D25_K1.8390.98
82_T137_L1.7300.97
65_E68_R1.6740.96
12_V54_P1.5540.94
122_A125_E1.4740.92
14_F89_P1.4020.89
67_W110_Q1.4010.89
52_D77_F1.3750.87
54_P92_L1.3410.85
88_H133_Q1.3390.85
82_T93_L1.3300.85
120_L130_R1.3220.84
12_V39_I1.3110.84
70_I93_L1.3080.84
62_R111_L1.2810.82
108_K112_Q1.2770.81
117_Y128_E1.2610.80
18_K122_A1.2520.80
16_D42_I1.2510.80
110_Q122_A1.2490.79
3_L6_F1.2360.78
66_L111_L1.2280.78
115_K127_Y1.2280.78
29_F82_T1.2270.78
2_T85_D1.2240.77
41_R44_N1.2190.77
96_Y134_L1.2150.77
19_L25_K1.2010.76
63_C123_A1.1920.75
7_I21_D1.1910.75
44_N130_R1.1870.74
105_Q128_E1.1770.74
65_E80_F1.1550.72
65_E129_W1.1550.72
10_V22_D1.1480.71
56_L63_C1.1360.70
4_R26_K1.1300.69
13_G42_I1.1240.69
26_K103_M1.1230.68
56_L122_A1.1230.68
68_R137_L1.1170.68
15_L115_K1.1150.68
86_R109_D1.1140.68
132_K136_G1.1140.68
23_L112_Q1.1130.67
14_F58_V1.1130.67
84_I105_Q1.1070.67
95_E107_M1.1060.67
71_N137_L1.1000.66
23_L123_A1.0960.66
42_I47_S1.0870.65
11_G14_F1.0850.65
61_F129_W1.0850.65
111_L130_R1.0770.64
14_F95_E1.0730.63
63_C88_H1.0710.63
83_Q137_L1.0660.63
39_I100_S1.0590.62
12_V71_N1.0580.62
7_I121_E1.0470.60
84_I104_K1.0420.60
10_V99_S1.0400.60
87_S130_R1.0370.59
42_I45_V1.0320.59
35_N103_M1.0300.59
27_V101_E1.0290.58
56_L79_D1.0280.58
64_K136_G1.0250.58
108_K122_A1.0210.58
82_T102_K1.0180.57
9_E97_F1.0140.57
31_L98_S1.0130.57
58_V66_L1.0080.56
62_R118_S1.0040.56
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  
2ve7C20.7887270.917Contact Map
1o5hA20.8592160.925Contact Map
3fhnA40.887310.60.931Contact Map
1tt9A40.88739.20.933Contact Map
4eveA10.73246.60.937Contact Map
4j2cA20.66260.938Contact Map
1gl2D10.387360.938Contact Map
4a1nA10.56345.20.94Contact Map
2b3tB10.40855.10.94Contact Map
1fyhA20.54234.60.942Contact 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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