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1xd6

ID: 1452700919 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 112 (110)
Sequences: 1182 (889)
Seq/Len: 10.745
Nf(neff/√len): 84.8

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: 10.745).

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
54_L62_L3.3401.00
22_L35_D3.1401.00
85_L93_V2.9281.00
87_L93_V2.4051.00
57_Q63_V2.0621.00
88_Q94_V2.0241.00
23_F31_L1.9751.00
26_Q32_V1.9581.00
88_Q92_N1.8681.00
29_C52_C1.8621.00
16_L89_R1.7931.00
92_N105_A1.7041.00
26_Q42_A1.6801.00
56_M95_I1.6511.00
97_D101_N1.6381.00
88_Q96_Y1.5741.00
96_Y102_A1.5641.00
26_Q34_Y1.5461.00
4_L8_K1.5231.00
59_D63_V1.5161.00
2_D86_I1.4921.00
57_Q61_N1.4841.00
25_M64_I1.4671.00
40_V91_R1.3530.99
23_F54_L1.3510.99
21_Y40_V1.3000.99
56_M97_D1.3000.99
66_S69_R1.2990.99
105_A108_T1.2690.99
65_Y70_A1.2500.99
88_Q105_A1.2280.98
28_D32_V1.2150.98
61_N65_Y1.1920.98
4_L31_L1.1880.98
32_V42_A1.1810.98
5_N8_K1.1560.97
61_N74_S1.1370.97
92_N108_T1.1160.96
32_V45_T1.1130.96
9_S53_I1.0920.96
18_E89_R1.0920.96
39_A42_A1.0900.96
23_F87_L1.0650.95
32_V43_S1.0590.95
90_D96_Y1.0580.95
4_L85_L1.0560.95
21_Y48_K1.0190.93
23_F33_L1.0030.93
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  
1b2pA20.955499.90.204Contact Map
1xd5A4199.90.211Contact Map
3dzwA20.964399.90.223Contact Map
4tkcA1099.90.229Contact Map
3a0cA40.946499.90.23Contact Map
2dpfA40.973299.90.231Contact Map
3r0eB20.928699.90.257Contact Map
3mezB20.937599.90.267Contact Map
4le7A20.964399.80.292Contact Map
4h3oA20.919699.80.296Contact 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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