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4nn2

ID: 1500382120 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 124 (123)
Sequences: 261 (189.2)
Seq/Len: 2.122
Nf(neff/√len): 17.1

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: 2.122).

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
119_C122_H2.8221.00
57_D60_T2.2431.00
64_E67_R2.0890.99
32_H35_C2.0110.99
68_G82_T1.9990.99
5_C8_C1.7550.97
118_Y122_H1.7220.97
71_M84_G1.6870.96
76_C90_C1.6240.95
40_S56_F1.5610.94
90_C98_C1.5480.93
5_C32_H1.5160.92
76_C81_A1.4870.91
99_G106_Y1.4760.91
18_R99_G1.4470.90
5_C35_C1.4450.90
14_E17_A1.4160.89
81_A90_C1.4120.88
37_L56_F1.3910.87
120_K123_S1.3830.87
75_L104_A1.3800.87
52_E57_D1.3640.86
52_E61_V1.3620.86
62_L78_Q1.3180.83
56_F64_E1.2770.81
44_Q56_F1.2550.79
76_C95_H1.2530.79
90_C95_H1.2520.79
57_D61_V1.2300.77
46_T57_D1.2190.76
94_Y102_D1.2120.75
40_S67_R1.2100.75
33_Y37_L1.2060.75
46_T52_E1.2050.75
81_A85_C1.2030.75
99_G102_D1.1800.73
83_I94_Y1.1740.72
85_C98_C1.1680.72
7_F36_M1.1610.71
65_I68_G1.1490.70
96_Y121_N1.1390.69
119_C124_G1.1250.67
95_H98_C1.1240.67
39_S63_Q1.1220.67
111_S117_L1.1170.67
10_V101_Q1.1140.66
81_A95_H1.1020.65
20_K99_G1.0860.63
6_G65_I1.0760.62
40_S84_G1.0630.61
73_C76_C1.0590.61
31_A35_C1.0590.61
65_I96_Y1.0460.59
67_R71_M1.0450.59
104_A115_Y1.0440.59
47_T61_V1.0440.59
29_A56_F1.0410.59
50_R61_V1.0400.59
73_C90_C1.0360.58
64_E71_M1.0360.58
45_L60_T1.0340.58
44_Q60_T1.0330.58
82_T106_Y1.0330.58
40_S64_E1.0310.58
76_C98_C1.0190.56
64_E84_G1.0130.56
32_H36_M1.0110.55
51_A55_D1.0080.55
9_H15_N1.0080.55
10_V82_T1.0080.55
38_F82_T1.0050.55
41_G67_R1.0010.54
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  
4nn2A20.99191000.417Contact Map
2lq6A10.508199.30.699Contact Map
4lk9A10.814593.60.878Contact Map
3v43A10.822691.10.887Contact Map
2kwjA10.8065880.894Contact Map
4gneA10.4194820.902Contact Map
4cosA10.37980.20.903Contact Map
1wewA10.540379.30.904Contact Map
2ro1A10.387178.10.905Contact Map
2ri7A10.3871780.905Contact 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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