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OPENSEQ.org
zwint1 200-377
ID: 1496401374 Query Sequence

 Download Alignment
We filter this alignment to remove positions that have > 50% gaps before running GREMLIN.
Length: 178 (103)
Sequences: 209 (133.7)
Seq/Len: 2.029
Nf(neff/√len): 13.2
Jackhmmer Results: (2016_04)
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: 2.029).

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
80_L86_K1.7450.97
4_Q7_V1.5580.93
29_E42_L1.5400.93
6_L11_H1.5130.92
79_A84_M1.4790.91
90_Q96_E1.4680.90
3_L12_R1.4300.88
71_G86_K1.4120.88
9_M13_G1.4090.87
95_S98_Q1.3630.85
83_V98_Q1.3630.85
91_G101_R1.3550.85
64_L71_G1.3300.83
59_L83_V1.2670.79
96_E103_R1.2430.77
62_T78_V1.2350.76
35_G65_V1.2220.75
5_S8_T1.2160.75
10_T16_Y1.2040.74
47_T54_F1.1920.73
64_L81_E1.1850.72
37_K45_T1.1720.71
94_L104_Y1.1530.69
5_S10_T1.1500.69
45_T61_G1.1490.69
95_S99_S1.1380.67
52_D83_V1.1360.67
91_G94_L1.1310.67
79_A87_Y1.1280.66
4_Q22_S1.1130.65
42_L49_T1.1030.64
17_R23_P1.1010.64
46_I68_A1.0810.62
90_Q94_L1.0770.61
4_Q11_H1.0660.60
28_L41_P1.0600.59
8_T17_R1.0550.59
78_V81_E1.0540.59
80_L105_A1.0540.59
9_M15_Q1.0520.58
72_P82_E1.0480.58
7_V11_H1.0460.58
67_E70_N1.0460.58
7_V17_R1.0450.58
30_I104_Y1.0430.57
25_E80_L1.0430.57
31_L51_K1.0340.57
58_V65_V1.0330.56
91_G96_E1.0320.56
42_L54_F1.0290.56
87_Y104_Y1.0290.56
36_E51_K1.0280.56
11_H15_Q1.0210.55
75_Q80_L1.0190.55
74_R79_A1.0190.55
7_V21_V1.0170.55
5_S22_S1.0130.54
82_E86_K1.0130.54
93_M99_S1.0020.53
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  
2ve7A20.599.10.789Contact Map
3vz9B10.5337990.793Contact Map
2ftxA10.471998.20.842Contact Map
4dzoA20.505640.20.941Contact Map
4bhqA20.325828.70.946Contact Map
3n4sA40.477524.20.948Contact Map
4emcA20.483116.20.952Contact Map
1uv7A20.297811.80.955Contact Map
4um9B10.921310.10.956Contact Map
3o2uA20.66858.90.957Contact 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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