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3ze3

ID: 1501760511 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 50% gaps before running GREMLIN.
Length: 116 (114)
Sequences: 693 (692)
Seq/Len: 6.079
Nf(neff/√len): 64.8

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: 6.079).

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
74_V85_S4.1771.00
14_K86_G3.1351.00
19_A65_L2.7381.00
20_W30_G2.5741.00
63_V66_L2.4791.00
76_R85_S2.4691.00
60_V96_V2.0171.00
68_S91_L1.8311.00
58_M102_D1.8011.00
73_V88_A1.7691.00
40_A50_R1.7551.00
16_L94_A1.7421.00
33_V57_V1.6991.00
62_I99_A1.6291.00
46_D49_T1.5830.99
5_I28_Q1.5480.99
17_R21_I1.5190.99
107_W111_L1.4520.99
63_V99_A1.4380.99
84_L88_A1.4240.99
40_A53_L1.3750.98
8_A25_A1.3720.98
25_A29_E1.3670.98
73_V77_I1.3540.98
25_A28_Q1.3470.98
12_S93_S1.3370.97
63_V95_A1.3220.97
65_L91_L1.2960.97
45_V110_L1.2760.96
65_L94_A1.2760.96
29_E96_V1.2700.96
72_A87_R1.2680.96
75_D89_K1.2640.96
68_S72_A1.2530.96
3_T7_K1.2420.96
30_G61_M1.2390.96
8_A12_S1.2150.95
68_S87_R1.2010.95
26_F29_E1.1960.94
44_D50_R1.1890.94
18_A87_R1.1640.93
108_A112_W1.1570.93
72_A91_L1.1570.93
7_K10_G1.1470.93
88_A92_G1.1410.92
19_A26_F1.1260.92
77_I85_S1.1070.91
26_F61_M1.1050.91
108_A111_L1.0630.88
18_A91_L1.0590.88
29_E100_I1.0580.88
74_V88_A1.0500.87
78_G85_S1.0480.87
19_A91_L1.0400.87
38_V42_W1.0400.87
45_V50_R1.0370.87
45_V53_L1.0320.86
5_I9_A1.0270.86
49_T110_L1.0120.85
69_A88_A1.0100.85
73_V85_S1.0080.84
65_L98_I1.0050.84
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  
3ze3A61100-0Contact Map
1rh5B10.37936.50.932Contact Map
4w25210.41385.20.935Contact Map
4b03D30.56033.90.939Contact Map
3b8cA20.9313.90.939Contact Map
4od4A60.784530.942Contact Map
4k1cA20.89662.90.942Contact Map
1pi7A10.163820.947Contact Map
3nd0A20.23281.90.948Contact Map
4cctD30.55171.80.948Contact 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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