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sec3_Cterm
ID: 1488292795 Query Sequence

 Download Alignment
We filter this alignment to remove positions that have > 50% gaps before running GREMLIN.
Length: 128 (93)
Sequences: 310 (198.4)
Seq/Len: 3.333
Nf(neff/√len): 20.6
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: 3.333).

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
120_N124_Q1.6320.98
117_G122_E1.5240.97
72_S79_E1.4840.96
106_L110_E1.4760.96
60_Q63_F1.4650.96
49_N77_A1.4210.95
97_C110_E1.3930.94
92_D95_L1.3790.94
107_F111_L1.3740.93
41_S90_L1.3680.93
39_S43_L1.3480.93
99_S102_S1.3310.92
91_Q107_F1.3230.92
97_C106_L1.3200.92
43_L119_I1.3180.91
96_G107_F1.2820.90
50_E100_I1.2810.90
64_S67_G1.2800.90
105_N124_Q1.2770.90
75_N89_Q1.2770.90
50_E122_E1.2670.89
40_I86_I1.2600.89
48_W126_S1.2580.89
63_F66_D1.2580.89
101_N111_L1.2370.88
55_K108_S1.2320.87
91_Q101_N1.2270.87
40_I90_L1.1990.85
61_T65_F1.1950.85
53_T59_K1.1940.85
118_V122_E1.1760.84
61_T77_A1.1560.82
68_A72_S1.1540.82
42_R57_V1.1490.82
90_L94_A1.1470.82
60_Q67_G1.1410.81
73_V77_A1.1350.81
79_E86_I1.1180.79
55_K104_I1.1150.79
64_S70_I1.1040.78
104_I111_L1.0870.77
58_L121_I1.0800.76
121_I125_P1.0610.74
110_E122_E1.0500.73
110_E117_G1.0500.73
83_L101_N1.0450.73
117_G120_N1.0410.72
45_T86_I1.0370.72
51_G86_I1.0350.72
114_A119_I1.0340.71
38_Q83_L1.0330.71
48_W112_S1.0270.71
44_S88_S1.0240.70
62_E117_G1.0090.69
64_S126_S1.0090.69
40_I64_S1.0070.69
57_V69_I1.0060.68
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  
1wb9A20.984410.60.929Contact Map
3i00A20.57819.30.931Contact Map
3ghgA40.94538.90.932Contact Map
2no2A10.78918.20.933Contact Map
3t5vC20.39067.70.933Contact Map
3c9iA60.90625.60.938Contact Map
2ykoA30.36725.50.938Contact Map
3ojaB10.84385.10.939Contact Map
4c46A30.43754.50.94Contact Map
1deqA40.8754.20.941Contact 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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