OPENSEQ.org
BPTI

ID: 1517905325 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 58 (56)
Sequences: 4535 (3441.7)
Seq/Len: 80.982
Nf(neff/√len): 459.9

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: 80.982).

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
14_C38_C3.8801.00
9_P22_F3.1531.00
48_A52_M3.0961.00
24_N31_Q2.7391.00
20_R44_N2.4921.00
17_R34_V2.4491.00
27_A31_Q2.4371.00
20_R46_K1.9201.00
4_F54_T1.8681.00
47_S50_D1.8361.00
13_P39_R1.8311.00
21_Y48_A1.8211.00
19_I32_T1.8191.00
51_C55_C1.7251.00
52_M56_G1.6361.00
22_F31_Q1.5581.00
7_E42_R1.5371.00
6_L25_A1.5121.00
19_I34_V1.4751.00
49_E53_R1.2260.98
46_K50_D1.2220.98
28_G56_G1.1510.97
41_K44_N1.0850.96
7_E45_F1.0490.94
17_R36_G1.0200.93
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  
2ddiA1199.1-0.188Contact Map
1yc0I1199.1-0.176Contact Map
4bqdA2199.1-0.176Contact Map
1co7I10.706999.1-0.175Contact Map
3aubA2199.1-0.173Contact Map
1g6xA1199.1-0.173Contact Map
1y62A60.965599.1-0.171Contact Map
3augA2199-0.168Contact Map
1bf0A1199-0.166Contact Map
1jc6A1199-0.162Contact 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.

Page generated in 0.0477 seconds.