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2msv

ID: 1504790074 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 50% gaps before running GREMLIN.
Length: 166 (130)
Sequences: 2170 (1778.8)
Seq/Len: 16.692
Nf(neff/√len): 156.0

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: 16.692).

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
118_S122_K2.9441.00
83_E116_K2.2221.00
46_R114_N1.9651.00
94_R106_D1.9621.00
99_R106_D1.8401.00
85_N89_E1.8031.00
71_T75_N1.7881.00
46_R118_S1.7481.00
134_M138_P1.7171.00
52_K56_M1.7111.00
23_G47_V1.7051.00
50_L121_W1.5881.00
26_I81_L1.5441.00
30_C33_M1.5201.00
87_E91_F1.4851.00
96_N100_F1.4671.00
86_G89_E1.4301.00
84_A113_V1.3050.99
77_F121_W1.2990.99
16_L20_I1.2980.99
95_S98_C1.2980.99
81_L84_A1.2570.99
54_L94_R1.2510.99
12_I15_N1.2510.99
129_Q132_Q1.2270.98
40_C47_V1.2130.98
20_I24_Q1.1990.98
87_E113_V1.1910.98
40_C88_I1.1850.98
135_P138_P1.1800.98
43_L46_R1.1720.98
84_A117_L1.1640.97
72_T90_K1.1560.97
135_P139_I1.1550.97
10_G13_L1.1520.97
26_I33_M1.1470.97
15_N18_H1.1470.97
30_C44_G1.1460.97
48_L95_S1.1410.97
78_K82_E1.1410.97
130_V133_R1.1240.97
37_K43_L1.1150.96
91_F99_R1.1120.96
80_A120_V1.1110.96
16_L23_G1.0930.96
134_M137_S1.0840.96
53_P126_L1.0760.95
11_G14_E1.0750.95
42_R115_R1.0690.95
25_V85_N1.0620.95
120_V123_E1.0590.95
121_W125_S1.0560.95
82_E86_G1.0520.95
110_F127_L1.0500.94
26_I85_N1.0480.94
136_V139_I1.0430.94
108_I112_D1.0400.94
132_Q136_V1.0330.94
79_A83_E1.0320.94
26_I34_K1.0300.94
24_Q28_K1.0290.94
25_V89_E1.0280.94
130_V139_I1.0270.94
11_G15_N1.0210.93
9_G12_I1.0100.93
79_A82_E1.0070.93
117_L123_E1.0010.92
15_N22_L1.0010.92
33_M37_K1.0010.92
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  
2msvA10.921799.80.2Contact Map
4btfA10.75399.20.475Contact Map
2c9kA10.897674.30.83Contact Map
3eb7A30.903650.10.854Contact Map
1ji6A10.921743.30.86Contact Map
4w8jA10.885531.70.87Contact Map
1ciyA10.8855300.871Contact Map
1dlcA10.909629.10.872Contact Map
4uxvA10.879512.50.892Contact Map
4aurA10.686710.70.896Contact 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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