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pfxn_loop

ID: 1506697949 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 105 (103)
Sequences: 976 (647.2)
Seq/Len: 9.476
Nf(neff/√len): 63.8

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: 9.476).

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
57_Q70_D3.2641.00
83_D91_A2.8571.00
2_N5_E2.6371.00
3_D56_H2.1471.00
7_I11_D2.0531.00
69_Y81_S1.7731.00
6_F53_Q1.7311.00
90_S94_F1.6971.00
38_T46_K1.6841.00
62_T92_A1.6831.00
37_L41_F1.5071.00
7_I51_R1.4291.00
67_H78_D1.4000.99
60_L85_F1.3940.99
62_T65_N1.3910.99
75_K84_E1.3850.99
1_M5_E1.3830.99
32_Q78_D1.3790.99
31_D53_Q1.3420.99
69_Y88_F1.3220.99
18_E22_E1.3220.99
52_Q55_L1.3200.99
77_I82_G1.3150.99
55_L68_H1.2980.99
3_D53_Q1.2820.99
70_D79_D1.2800.99
61_A66_G1.2560.98
84_E87_T1.2520.98
91_A95_K1.2430.98
69_Y83_D1.2310.98
37_L80_R1.2230.98
42_E45_T1.2160.98
93_I97_S1.1940.98
94_F102_D1.1940.98
34_G51_R1.1890.98
71_Y74_G1.1740.97
9_L71_Y1.1670.97
67_H88_F1.1220.96
90_S103_F1.1190.96
13_L89_L1.1110.96
67_H81_S1.1000.96
13_L58_V1.0970.95
36_L46_K1.0920.95
47_L63_L1.0830.95
10_A14_Y1.0680.95
45_T63_L1.0660.94
94_F101_V1.0650.94
88_F92_A1.0560.94
21_I93_I1.0530.94
52_Q66_G1.0440.94
47_L92_A1.0420.94
45_T66_G1.0390.93
63_L66_G1.0300.93
5_E27_D1.0220.93
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  
4hs5A21100-0.002Contact Map
1ew4A10.99051000.002Contact Map
4jpdA111000.007Contact Map
3t3lA111000.013Contact Map
3oeqA10.94291000.065Contact Map
4da2A20.923837.20.899Contact Map
2fkbA30.904810.20.922Contact Map
3k6qA40.84768.10.926Contact Map
4jzuA20.77147.50.927Contact Map
4ydzA407.20.927Contact 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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