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2bg9

ID: 1499474408 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 91 (91)
Sequences: 1380 (840.9)
Seq/Len: 15.165
Nf(neff/√len): 88.2

Jackhmmer Results: (2016_04)
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: 15.165).

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
22_V36_S2.3461.00
28_D89_H1.9871.00
38_S41_L1.7481.00
77_S80_I1.7201.00
45_V49_V1.7051.00
25_L35_L1.6231.00
31_E34_T1.5491.00
77_S81_V1.5061.00
32_K83_V1.5031.00
43_L75_V1.4441.00
25_L33_M1.4331.00
30_G34_T1.4271.00
5_V9_I1.3960.99
8_V13_L1.3090.99
15_F43_L1.3020.99
16_S71_T1.3000.99
19_T75_V1.2930.99
31_E38_S1.2530.99
74_F78_S1.2380.98
24_Y34_T1.2330.98
39_V42_S1.2210.98
18_L48_L1.2060.98
13_L18_L1.2010.98
12_C72_M1.1610.97
8_V53_L1.1460.97
3_Y50_I1.1410.97
34_T38_S1.1380.97
15_F19_T1.1340.97
17_F53_L1.1240.97
67_Y71_T1.1170.96
53_L56_S1.1150.96
81_V85_V1.1110.96
32_K74_F1.1010.96
16_S22_V1.0950.96
68_M71_T1.0860.96
17_F21_L1.0860.96
25_L28_D1.0830.96
30_G86_I1.0810.95
22_V38_S1.0740.95
84_V88_T1.0510.94
51_V54_I1.0500.94
39_V48_L1.0480.94
3_Y58_S1.0420.94
75_V85_V1.0410.94
59_S64_I1.0390.94
21_L33_M1.0290.94
66_K69_L1.0280.94
61_V70_F1.0220.93
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  
1oedC1199.90.093Contact Map
4aq5C1199.90.1Contact Map
1oedB1199.90.102Contact Map
1oedA2199.90.106Contact Map
4aq5B1199.90.108Contact Map
1oedE1199.90.11Contact Map
4aq5E1199.90.112Contact Map
4aq5A2199.90.113Contact Map
4pirA50.95699.90.142Contact Map
2bg9C1199.90.158Contact 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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