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OPENSEQ.org
ProTa
ID: 1454407116 Query Sequence

 Download Alignment
We filter this alignment to remove positions that have > 50% gaps before running GREMLIN.
Length: 111 (110)
Sequences: 114 (80.7)
Seq/Len: 1.036
Nf(neff/√len): 7.7
HHblits Results: (2015_06)
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: 1.036).

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
76_D80_D2.1270.97
43_E48_E2.0290.96
103_K107_T1.9040.94
103_K106_K1.8980.94
7_D12_I1.8590.93
62_E75_E1.6810.87
86_A91_A1.6780.87
25_E28_E1.6690.87
66_E70_G1.6540.86
92_A103_K1.6480.86
9_S14_T1.6220.85
93_E96_E1.5860.83
68_E71_D1.3980.70
94_D100_V1.3830.69
6_V11_E1.3310.65
29_N36_N1.3230.64
23_V27_A1.3140.63
8_T12_I1.3050.63
54_D59_E1.3010.62
69_E79_E1.2980.62
54_D60_G1.2920.61
46_E50_D1.2910.61
102_T105_Q1.2530.58
63_E67_E1.2520.58
7_D15_K1.2440.57
104_K110_D1.2390.57
83_A88_G1.2080.54
94_D104_K1.2030.53
61_G101_D1.1870.52
96_E109_E1.1850.52
99_D106_K1.1800.51
65_E70_G1.1770.51
51_N78_D1.1360.47
83_A86_A1.1090.45
56_E59_E1.0950.43
1_M6_V1.0940.43
69_E73_E1.0860.42
92_A105_Q1.0840.42
102_T110_D1.0810.42
94_D110_D1.0690.41
30_G36_N1.0690.41
58_E63_E1.0660.41
92_A104_K1.0640.40
72_G79_E1.0620.40
4_A18_K1.0580.40
19_E39_A1.0570.40
6_V15_K1.0500.39
14_T58_E1.0490.39
24_V28_E1.0460.39
57_E63_E1.0450.39
9_S13_T1.0400.38
91_A107_T1.0350.38
59_E63_E1.0240.37
55_E96_E1.0220.37
62_E76_D1.0170.36
55_E62_E1.0170.36
34_P38_N1.0070.35
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  
2l9iA10.252398.30.694Contact Map
4u7aA1070.40.866Contact Map
4fp9B40.243212.50.913Contact Map
4kblA201.10.949Contact Map
4gyiA10.27031.10.949Contact Map
4mitE40.11710.90.952Contact Map
3btpA100.90.952Contact Map
1ujsA10.27030.80.953Contact Map
4rmfA10.18920.70.956Contact Map
1qzpA10.21620.70.956Contact 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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