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ID: 1513356916 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 109 (109)
Sequences: 332 (191)
Seq/Len: 3.046
Nf(neff/√len): 18.3

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: 3.046).

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
3_E7_G2.4681.00
53_T60_V2.4141.00
1_C7_G2.0351.00
2_W17_D1.8650.99
63_Q67_W1.6860.98
17_D83_K1.6670.98
66_V80_A1.6510.98
2_W8_E1.6430.98
32_I46_D1.5680.97
2_W7_G1.5670.97
69_G76_M1.5440.97
57_L67_W1.5400.97
4_N8_E1.5360.96
88_F91_R1.5330.96
57_L63_Q1.5330.96
82_V85_F1.4800.95
70_L85_F1.4630.95
50_F67_W1.3990.93
59_L84_L1.3740.92
10_I16_V1.3130.90
16_V104_K1.3010.89
71_Y109_S1.2430.86
56_V77_A1.2420.86
60_V106_F1.2340.86
6_V78_L1.2280.85
43_C72_F1.2060.84
10_I104_K1.2060.84
79_V87_V1.1980.83
4_N7_G1.1870.83
1_C9_E1.1850.82
71_Y108_A1.1790.82
29_D98_A1.1650.81
33_A37_R1.1620.81
50_F63_Q1.1530.80
13_L17_D1.1520.80
1_C8_E1.1470.80
53_T106_F1.1380.79
69_G74_P1.1330.78
9_E12_K1.0970.75
52_V84_L1.0900.75
73_S92_Y1.0900.75
73_S85_F1.0690.72
29_D55_N1.0640.72
9_E106_F1.0600.72
20_V86_I1.0570.71
70_L84_L1.0540.71
103_K107_R1.0530.71
22_I90_F1.0450.70
2_W9_E1.0360.69
25_G94_V1.0300.68
1_C4_N1.0280.68
38_T85_F1.0210.67
54_S58_D1.0160.67
57_L77_A1.0130.67
12_K48_S1.0130.67
50_F57_L1.0090.66
18_L92_Y1.0050.66
57_L60_V1.0020.65
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  
2mzzA1014.20.931Contact Map
4xxoA2080.939Contact Map
4wisA20.93584.60.945Contact Map
4bkfC20.09172.40.952Contact Map
4k5yA30.96332.30.952Contact Map
3og6A10.23851.70.956Contact Map
1osnA40.31191.70.956Contact Map
1jb0M10.11011.40.958Contact Map
4b19A10.27521.20.96Contact Map
2vq5A20.35781.20.96Contact 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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