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4ku0

ID: 1500381492 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 96 (93)
Sequences: 1933 (1169.9)
Seq/Len: 20.785
Nf(neff/√len): 121.3

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: 20.785).

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
75_Q78_D3.3271.00
37_V40_D2.8151.00
59_T74_V2.7961.00
5_Y8_C2.7671.00
6_D24_T2.5601.00
31_G90_S2.3011.00
68_V73_A2.2011.00
58_V81_S2.1711.00
4_S21_V2.1251.00
29_F67_Y2.1061.00
25_Q69_T2.0801.00
39_G71_K1.9051.00
9_V89_A1.7741.00
27_K69_T1.6551.00
32_G70_G1.6531.00
61_P78_D1.6481.00
25_Q37_V1.6401.00
31_G92_K1.6211.00
23_A40_D1.6201.00
35_V73_A1.5821.00
23_A41_P1.5421.00
30_T35_V1.5231.00
28_V66_V1.4861.00
7_K33_I1.4661.00
9_V20_V1.4541.00
36_L59_T1.4541.00
21_V36_L1.4341.00
38_A72_K1.4251.00
41_P58_V1.3970.99
61_P79_P1.3560.99
79_P85_T1.2530.99
37_V71_K1.2360.98
80_I84_D1.2340.98
38_A62_R1.2100.98
59_T86_V1.2060.98
63_T75_Q1.1940.98
28_V68_V1.1790.98
74_V86_V1.1520.97
76_M89_A1.1010.96
24_T34_A1.0930.96
6_D23_A1.0920.96
22_N46_T1.0850.96
13_H84_D1.0840.96
5_Y90_S1.0650.95
3_L73_A1.0650.95
57_G81_S1.0630.95
28_V35_V1.0570.95
13_H80_I1.0410.94
6_D34_A1.0190.93
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  
4ku0D1199.9-0.022Contact Map
4jivD10.968899.90.057Contact Map
4jiwD40.968899.90.059Contact Map
4zjmA101.90.92Contact Map
4xinA20.572910.931Contact Map
1hxrA20.614610.932Contact Map
2x9aA20.23960.90.934Contact Map
3oepA10.77080.80.937Contact Map
3zqjA60.88540.70.938Contact Map
3u6pA10.31250.70.939Contact 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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